Patent Application
20230313129
The invention relates generally to engineered tRNAs, engineered aminoacyl-tRNA synthetases, unnatural amino acids, and cells comprising the same, and their use in the incorporation of unnatural amino acids into proteins.
In nature, proteins are produced in cells via processes known as transcription and translation. During transcription, a gene comprising a series of codons that collectively encode a protein of interest is transcribed into messenger RNA (mRNA). During translation, a ribosome, attaches to and moves along the mRNA and incorporates specific amino acids into a polypeptide chain being synthesized (translated) from the mRNA at positions corresponding to the codons to produce the protein. During translation, specific, naturally occurring amino acids coupled to transfer RNAs (tRNAs) enter the ribosome. The tRNAs, which contain an anti-codon sequence, hybridize to their respective codon sequences in mRNA and transfer the amino acid they are carrying into the nascent protein chain at the appropriate position as the protein is synthesized.
Over the last few decades, significant efforts have been made to produce homogenous preparations of site-specifically modified proteins, e.g., mammalian proteins, on a commercial scale for use in a variety of applications including, for example, therapeutics and diagnostics. Furthermore, efforts have been made to produce these modified mammalian proteins in eukaryotic cells (e.g., mammalian cells) because the proteins may be more readily produced in a properly folded and fully active form and/or post-translationally modified in a manner similar to the native protein naturally produced in a mammalian cell.
One approach for producing proteins that contain site-specific modifications involves the site-specific incorporation of one or more unnatural amino acids (UAAs) into a protein of interest. The ability to site-specifically incorporate UAAs into proteins in vivo has become a powerful tool to augment protein function or introduce new chemical functionalities not found in nature. The core elements required for this technology include: an engineered tRNA, an engineered aminoacyl-tRNA synthetase (aaRS) that charges the tRNA with a UAA, and a unique codon, e.g., a stop codon, directing the incorporation of the UAA into the protein as it is being synthesized.
Central to this approach is the use of an engineered tRNA/aaRS pair in which the aaRS charges the tRNA with the UAA of interest without cross-reacting with the tRNAs and amino acids normally present in the expression host cell. This has been accomplished by using an engineered tRNA/aaRS pair derived from an organism in different domain of life as the expression host cell so as to maximize the orthogonality between the engineered tRNA/aaRS pair (e.g., an engineered bacterial tRNA/aaRS pair) and the tRNA/aaRS pairs naturally found in the expression host cell (e.g., mammalian cell). The engineered tRNA, which is charged with the UAA via the aaRS, binds or hybridizes to the unique codon, such as a premature stop codon (UAG, UGA, UAA) present in the mRNA encoding the protein to be expressed. See, for example,
Although transient transfection techniques have been used to introduce engineered tRNA/aaRS pairs into expression host cells, the inability to express the proteins reproducibly, for extended periods of time, and with high titers has made this approach unsuitable for the reliable manufacture of commercial scale protein-based products. Despite the efforts made to date, there remains a need for mammalian cell-based expression platforms that address the limitations of transient delivery of the required genetic components, to produce expression systems optimized to express proteins of interest at high titers for extended periods of time.
The present disclosure relates, in general, to the field where orthogonal tRNA/aminoacyl-tRNA synthetase pairs are used for the incorporation of UAAs into a protein of interest as it is being synthesized. The disclosure relates to the optimization of tRNAs, aminoacyl-tRNA synthetases, and/or unnatural amino acids for use in the incorporation of unnatural amino acids into proteins, and to the construction and optimization of expression platforms (cell lines) via genome or molecular biology engineering for commercial scale production of proteins with unnatural amino acids.
In one aspect, the invention provides a eukaryotic (e.g., mammalian) cell line capable of expressing a target protein containing at least one unnatural amino acid from a gene containing a premature stop codon at a position corresponding to the position for incorporation of the unnatural amino acid. The cell line comprises a genome having stably integrated therein (i) a nucleic acid sequence encoding a prokaryotic leucyl-tRNA synthetase mutein capable of charging a tRNA (e.g., a cognate tRNA) with an unnatural amino acid and (ii) a nucleic acid sequence encoding a prokaryotic suppressor leucyl-tRNA capable of being charged with the unnatural amino acid.
In another aspect, the invention provides a eukaryotic (e.g., mammalian) cell line capable of expressing a target protein containing at least one unnatural amino acid from a gene containing a premature stop codon at a position corresponding to the position for incorporation of the unnatural amino acid. The cell line comprises a genome having stably integrated therein (i) a nucleic acid sequence encoding a prokaryotic tryptophanyl-tRNA synthetase mutein capable of charging a tRNA (e.g., a cognate tRNA) with an unnatural amino acid and (ii) a nucleic acid sequence encoding a prokaryotic suppressor tryptophanyl-tRNA capable of being charged with the unnatural amino acid.
In certain embodiments of any of the foregoing cell lines, the cell line is capable of expressing the target protein (e.g., continuously) for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150, or 180 days. In certain embodiments, the cell line is capable of expressing the target protein (e.g., continuously) for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150, or 180 days after an initial expression of the target protein. In certain embodiments, the cell line is capable of expressing the target protein at a level of expression that is at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or about 100% of the level of expression of the template protein expressed in a corresponding cell line from the gene lacking a premature stop codon. For example, the cell line is capable of expressing the target protein (e.g., continuously) at the level of expression for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150, or 180 days.
In certain embodiments of any of the foregoing, the cell line comprises from about 50 to about 500, from about 75 to about 500, from about 100 to about 500, from about 125 to about 500, from about 150 to about 500, from about 175 to about 500, from about 200 to about 500, from about 225 to about 500, from about 250 to about 500, from about 1 to about 450, from about 75 to about 450, from about 100 to about 450, from about 125 to about 450, from about 150 to about 450, from about 175 to about 450, from about 200 to about 450, from about 225 to about 450, from about 250 to about 450, from about 1 to about 400, from about 75 to about 400, from about 100 to about 400, from about 125 to about 400, from about 150 to about 400, from about 175 to about 400, from about 200 to about 400, from about 225 to about 400, from about 250 to about 400, from about 1 to about 350, from about 75 to about 350, from about 100 to about 350, from about 125 to about 350, from about 150 to about 350, from about 175 to about 350, from about 200 to about 350, from about 225 to about 350, or from about 250 to about 350 copies of the nucleic acid encoding the engineered suppressor tRNA. In certain embodiments the cell line comprises greater than 500 copies of the nucleic acid encoding the engineered suppressor tRNA.
In certain embodiments of any of the foregoing cell lines, the cell line comprises from about 1 to about 50, from about 5 to about 50, from about 10 to about 50, from about 15 to about 50, from about 20 to about 50, from about 25 to about 50, from about 30 to about 50, from about 35 to about 50, from about 40 to about 50, from about 1 to about 40, from about 5 to about 40, from about 10 to about 40, from about 15 to about 40, from about 20 to about 40, from about 25 to about 40, from about 30 to about 40, from about 35 to about 40, from about 1 to about 30, from about 5 to about 30, from about 10 to about 30, from about 15 to about 30, from about 20 to about 30, from about 25 to about 30, from about 1 to about 20, from about 5 to about 20, from about 10 to about 20, or from about 15 to about 20 copies of the nucleic acid encoding the engineered synthetase.
In certain embodiments of any of the foregoing cell lines, the prokaryotic suppressor tRNA is an analog or derivative of a bacterial tRNA (e.g., an E. coli tRNA). For example, the suppressor leucyl-tRNA may comprise a nucleic acid sequence selected from any one of SEQ ID NOs: 16-42 or 67, or the suppressor tryptophanyl-tRNA may comprise a nucleic acid selected from any one of SEQ ID NOs: 49-53.
In certain embodiments of any of the foregoing cell lines, the tRNA synthetase mutein is an analog or derivative of a bacterial tRNA synthetase (e.g., an E. coli tRNA synthetase). For example, the leucyl-tRNA synthetase mutein may comprise the amino acid sequence of SEQ ID NO: 1 and at least one mutation at a position corresponding to Gln2, Glu20, Met40, Leu41, Thr252, Tyr499, Tyr527, or His537 of SEQ ID NO: 1. In certain embodiments, the mutation is a substitution with a natural amino acid other than the amino acid found in its wild-type counterpart. In certain embodiments, the tRNA synthetase mutein comprises the amino acid sequence of SEQ ID NO: 14, wherein X2 is Q or E, X20 is E, K, V or M, X40 is M, I, or V, X41 is L, S, V, or A, X252 is T, A, or R, X499 is Y, A, I, H, or S, X527 is Y, G, A, I, L, or V, and X537 is H or G, and the tRNA synthetase mutein comprises at least one mutation relative to SEQ ID NO: 1.
In certain embodiments of any of the foregoing cell lines, the leucyl-tRNA synthetase mutein comprises (i) at least one substitution (e.g., a substitution with a hydrophobic amino acid) at a position corresponding to His537 of SEQ ID NO: 1, (ii) at least one amino acid substitution selected from E20V, E20M, L41V, L41 A, Y499H, Y499A, Y527I, Y527V, Y527G, and any combination thereof, (iii) at least one amino acid substitution selected from E20K and L41 S and any combination thereof and at least one amino acid substitution selected from M40I, T252A, Y499I, and Y527A, and any combination thereof, or (iv) a combination of two or more of (i), (ii) and (iii), for example, (i) and (ii), (i) and (iii), (ii) and (iii) and (i), (ii) and (iii).
In certain embodiments, the tRNA synthetase mutein in the cell line may comprise E20K, M40I, L41 S, T252A, Y499I, Y527A, or H537G, or any combination thereof (e.g., the tRNA synthetase mutein may comprise E20K, M40I, L41S, T252A, Y499I, Y527A, and H537G).
In certain embodiments of any of the foregoing cell lines, the leucyl-tRNA synthetase mutein comprises a substitution at position 20 with an amino acid other than a Glu or Lys, e.g., a substitution with a hydrophobic amino acid (e.g., Leu, Val, or Met). For example, the tRNA synthetase mutein may comprise: E20M, M40I, L41S, T252A, Y499I, Y527A, and H537G; or E20V, M40I, L41S, T252A, Y499I, Y527A, and H537G.
In certain embodiments of any of the foregoing cell lines, the leucyl-tRNA synthetase mutein comprises a substitution at position 41 with an amino acid other than a Leu or Ser, e.g., a substitution with a hydrophobic amino acid other than Leu (e.g., Gly, Ala, Val, or Met). For example, the tRNA synthetase mutein may comprise: E20K, M40I, L41V, T252A, Y499I, Y527A, and H537G; or E20K, M40I, L41A, T252A, Y499I, Y527A, and H537G. In certain embodiments, the tRNA synthetase mutein comprises L41V.
In certain embodiments of any of the foregoing cell lines, the leucyl-tRNA synthetase mutein comprises a substitution at position 499 with an amino acid other than a Tyr, Ile or Ser, e.g., a substitution with a small hydrophobic amino acid (e.g., Gly, Ala, or Val). For example, the tRNA synthetase mutein may comprise E20K, M40I, L41S, T252A, Y499A, Y527A, and H537G. In certain embodiments, the tRNA synthetase mutein comprises a substitution at position 499 with a positively charged amino acid (e.g., Lys, Arg, or His). For example, the tRNA synthetase mutein may comprise E20K, M40I, L41S, T252A, Y499H, Y527A, and H537G.
In certain embodiments of any of the foregoing cell lines, the leucyl-tRNA synthetase mutein comprises a substitution at position 527 with a hydrophobic amino acid other than Ala or Leu (e.g., Gly, Ile, Met, or Val). For example, the tRNA synthetase mutein may comprise. E20K, M40I, L41S, T252A, Y499I, Y527I, and H537G; E20K, M40L, L41S, T252A, Y499I, Y527V and H537G; or E20K, M40I, L41S, T252A, Y499I, Y527G and H537G.
In certain embodiments of any of the foregoing cell lines, the leucyl-tRNA synthetase mutein comprises the amino acid sequence of any one of SEQ ID NOs: 2-13, or the tryptophanyl tRNA synthetase mutein comprises the amino acid sequence of any one of SEQ ID NOs: 44-47.
In another aspect, the invention provides a method of expressing a protein containing an unnatural amino acid. The method comprises culturing or growing any of the foregoing cell lines under conditions that permit incorporation of the unnatural amino acid into the protein being expressed in the cell. In certain embodiments, the protein is expressed (e.g., continuously) for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150, or 180 days. In certain embodiments, the protein is expressed (e.g., continuously) for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150, or 180 days after an initial expression of the protein. In certain embodiments, the protein is expressed at a level that is at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or about 100% of the level of expression of the template protein expressed in a corresponding cell line from the gene lacking a premature stop codon, for example, the cell line is capable of expressing the target protein (e.g., continuously) at the level of expression for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150, or 180 days.
In another aspect, the invention provides a prokaryotic leucyl tRNA synthetase mutein capable of charging a tRNA with an unnatural amino acid for incorporation into a protein. The tRNA synthetase mutein comprises the amino acid sequence of SEQ ID NO: 1 and (i) at least one substitution (e.g., a substitution with a hydrophobic amino acid) at a position corresponding to His537, (ii) at least one amino acid substitution selected from E20V, E20M, L41V, L41A, Y499H, Y499A, Y527L, Y527V, Y527G, and any combination thereof, (iii) at least one amino acid substitution selected from E20K and L41S and any combination thereof and at least one amino acid substitution selected from M40I, T252A, Y499I, and Y527A, and any combination thereof, or (iv) a combination of two or more of (i), (ii) and (iii), for example, (i) and (ii), (i) and (iii), (ii) and (iii) and (i), (ii) and (iii).
For example, the tRNA synthetase mutein may comprise E20K, M40I, L41S, T252A, Y499I, Y527A, or H537G, or any combination thereof (e.g., the tRNA synthetase mutein may comprise E20K, M40I, L41S, T252A, Y499I, Y527A, and H537G).
In certain embodiments, the leucyl-tRNA synthetase mutein comprises a substitution at position 20 with an amino acid other than a Glu or Lys, e.g., a substitution with a hydrophobic amino acid (e.g., Leu, Val, or Met). For example, the tRNA synthetase mutein may comprise: E20M, M40I, L41S, T252A, Y499I, Y527A, and H537G; or E20V, M40I, L41S, T252A, Y499I, Y527A, and H537G.
In certain embodiments, the leucyl-tRNA synthetase mutein comprises a substitution at position 41 with an amino acid other than a Leu or Ser, e.g., a substitution with a hydrophobic amino acid other than Leu (e.g., Gly, Ala, Val, or Met). For example, the tRNA synthetase mutein may comprise: E20K, M40I, L41V, T252A, Y499I, Y527A, and H537G; or E20K, M40I, L41A, T252A, Y499I, Y527A, and H537G.
In certain embodiments, the leucyl-tRNA synthetase mutein comprises a substitution at position 499 with an amino acid other than a Tyr, Ile or Ser, e.g., a substitution with a small hydrophobic amino acid (e.g., Gly, Ala, or Val). For example, the tRNA synthetase mutein may comprise E20K, M40I, L41S, T252A, Y499A, Y527A, and H537G. In certain embodiments, the tRNA synthetase mutein comprises a substitution at position 499 with a positively charged amino acid (e.g., Lys, Arg, or His). For example, the tRNA synthetase mutein may comprise E20K, M40I, L41S, T252A, Y499H, Y527A, and H537G.
In certain embodiments, the tRNA synthetase mutein comprises a substitution at position 527 with a hydrophobic amino acid other than Ala or Leu (e.g., Ile or Val). For example, the tRNA synthetase mutein may comprise: E20K, M40I, L41S, T252A, Y499I, Y527I, and H537G; E20K, M40I, L41S, T252A, Y499I, Y527V and H537G; or E20K, M40I, L41S, T252A, Y499I, Y527G and H537G.
In certain embodiments, the leucyl-tRNA synthetase mutein comprises the amino acid sequence of any one of SEQ ID NOs: 2-13.
In another aspect, the invention provides a nucleic acid encoding any of the foregoing tRNA synthetase muteins.
In another aspect, the invention provides a transfer vector comprising any of the foregoing nucleic acids. In certain embodiments, the transfer vector is capable of introducing the nucleic acid into a cell. In certain embodiments, the transfer vector (or a nucleic acid from the transfer vector) can stably into the genome of the cell. In certain embodiments, the transfer vector (or a nucleic acid from the transfer vector) can be stably maintained in the cell without integration into the genome of the cell.
In another aspect, the invention provides an engineered cell comprising any of the foregoing tRNA synthetase muteins.
In another aspect, the invention provides an engineered cell comprising any of the foregoing nucleic acids, for example, where the nucleic acid is stably integrated into the genome of the cell and/or the nucleic acid is capable of being expressed in the cell to produce a corresponding tRNA synthetase mutein.
In another aspect, the invention provides an engineered cell comprising any of the foregoing transfer vectors. In certain embodiments, the transfer vector (or a nucleic acid from the transfer vector) is stably integrated into the genome of the cell. In certain embodiments, the transfer vector (or a nucleic acid from the transfer vector) is not integrated into the genome of the cell, but is stably maintained in the cell.
In certain embodiments of any of the foregoing engineered cells, the cell further comprises a suppressor leucyl-tRNA capable of incorporating an unnatural amino acid into a protein undergoing expression in the cell. For example, the suppressor leucyl-tRNA may be selected from any one of SEQ ID NOs: 16-42 or 67.
In certain embodiments, a nucleic acid encoding the suppressor leucyl-tRNA is stably integrated into the genome of the cell, and, for example, the nucleic acid is capable of being expressed in the cell to produce a corresponding suppressor tRNA.
In certain embodiments of any of the foregoing engineered cells, the unnatural amino acid is a leucine analog, for example, a leucine analog selected from a linear alkyl halide and a linear aliphatic chain comprising an alkyne, azide, cyclopropene, alkene, ketone, aldehyde, diazirine, or tetrazine functional group.
In certain embodiments of any of the foregoing engineered cells, the protein is expressed from a nucleic acid sequence comprising a premature stop codon, for example, the tRNA synthetase mutein is capable of charging a suppressor leucyl tRNA with an unnatural amino acid which is incorporated into the protein at a position corresponding to the premature stop codon. In certain embodiments, the suppressor tRNA comprises an anticodon sequence that hybridizes to the premature stop codon and permits the unnatural amino to be incorporated into the protein at the position corresponding to the premature stop codon.
In certain embodiments of any of the foregoing engineered cells, the protein to be expressed in the cell is an antibody (or a fragment thereof), bispecific antibody, nanobody, affibody, viral protein, chemokine, antigen, blood coagulation factor, hormone, growth factor, enzyme, or any other polypeptide or protein.
In certain embodiments of any of the foregoing engineered cells, the nucleic acid sequence encoding the tRNA synthetase mutein has a copy number in the range from about 1 to about 50, from about 5 to about 50, from about 10 to about 50, from about 15 to about 50, from about 20 to about 50, from about 25 to about 50, from about 30 to about 50, from about 35 to about 50, from about 40 to about 50, from about 1 to about 40, from about 5 to about 40, from about 10 to about 40, from about 15 to about 40, from about 20 to about 40, from about 25 to about 40, from about 30 to about 40, from about 35 to about 40, from about 1 to about 30, from about 5 to about 30, from about 10 to about 30, from about 15 to about 30, from about 20 to about 30, from about 25 to about 30, from about 1 to about 20, from about 5 to about 20, from about 10 to about 20, or from about 15 to about 20 copies.
In certain embodiments of any of the foregoing engineered cells, the nucleic acid sequences encoding the suppressor leucyl tRNA has a copy number in the range from about 50 to about 500, from about 75 to about 500, from about 100 to about 500, from about 125 to about 500, from about 150 to about 500, from about 175 to about 500, from about 200 to about 500, from about 225 to about 500, from about 250 to about 500, from about 1 to about 450, from about 75 to about 450, from about 100 to about 450, from about 125 to about 450, from about 150 to about 450, from about 175 to about 450, from about 200 to about 450, from about 225 to about 450, from about 250 to about 450, from about 1 to about 400, from about 75 to about 400, from about 100 to about 400, from about 125 to about 400, from about 150 to about 400, from about 175 to about 400, from about 200 to about 400, from about 225 to about 400, from about 250 to about 400, from about 1 to about 350, from about 75 to about 350, from about 100 to about 350, from about 125 to about 350, from about 150 to about 350, from about 175 to about 350, from about 200 to about 350, from about 225 to about 350, or from about 250 to about 350 copies. In certain embodiments the cell line comprises greater than 500 copies of the nucleic acid encoding the engineered, suppressor tRNA.
In certain embodiments of any of the foregoing engineered cells, the suppressor leucyl-tRNA and tRNA synthetase mutein are present in a ratio selected from 2:1, 4:1, 8:1, 12:1, 16:1, 24:1, 36:1, 48:1, and 64:1.
In certain embodiments of any of the foregoing engineered cells, the cell is a prokaryotic cell (e.g., a bacterial cell) or a eukaryotic cell (e.g., a mammalian cell).
These and other aspects and features of the invention are described in the following detailed description and claims.
The invention can be more completely understood with reference to the following drawings.
The present disclosure relates, in general, to the field where orthogonal tRNA/aminoacyl-tRNA synthetase pairs are used for the incorporation of unnatural amino acids into a protein of interest. The disclosure relates to the optimization of engineered orthogonal tRNAs, engineered aminoacyl-tRNA synthetases, and/or unnatural amino acids for use in the incorporation of unnatural amino acids into proteins and to the construction and optimization of expression platforms (cell lines) via genome or molecular biology engineering for commercial scale production of proteins with unnatural amino acids.
As used herein, the term “orthogonal” refers to a molecule (e.g., an orthogonal tRNA or an orthogonal aminoacyl-tRNA synthetase) that is used with reduced efficiency by an expression system of interest (e.g., an endogenous cellular translation system). For example, an orthogonal tRNA in a translation system of interest is aminoacylated by any endogenous aminoacyl-tRNA synthetase of the translation system of interest with reduced or even zero efficiency, when compared to aminoacylation of an endogenous tRNA by an endogenous aminoacyl-tRNA synthetase. In another example, an orthogonal aminoacyl-tRNA synthetase aminoacylates any endogenous tRNA in the translation system of interest with reduced or even zero efficiency, as compared to aminoacylation of an endogenous tRNA by an endogenous aminoacyl-tRNA synthetase.
Various features and aspects of the invention are discussed in more detail below.
The invention relates to engineered aminoacyl-tRNA synthetases (or aaRSs) capable of charging a tRNA with an unnatural amino acid for incorporation into a protein. As used herein, the term “aminoacyl-tRNA synthetase” refers to any enzyme, or a functional fragment thereof, that charges, or is capable of charging, a tRNA with an amino acid (e.g., an unnatural amino acid) for incorporation into a protein. As used herein, the term “functional fragment” of an aminoacyl-tRNA synthetase refers to fragment of a full-length aminoacyl-tRNA synthetase that retains, for example, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or 100% of the enzymatic activity of the corresponding full-length tRNA synthetase (e.g., a naturally occurring tRNA synthetase). Aminoacyl-tRNA synthetase enzymatic activity may be assayed by any method known in the art. For example, in vitro aminoacylation assays are described in Hoben et al. (1985) M
The term aminoacyl-tRNA synthetase includes variants (i.e., muteins) having one or more mutations (e.g., amino acid substitutions, deletions, or insertions) relative to a wild-type aminoacyl-tRNA synthetase sequence. In certain embodiments, an aminoacyl-tRNA synthetase mutein may comprise, consist, or consist essentially of, a single mutation (e.g., a mutation contemplated herein), or a combination of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more than 15 mutations (e.g., mutations contemplated herein). It is contemplated that an aminoacyl-tRNA synthetase mutein may comprise, consist, or consist essentially 1-15, 1-10, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-15, 2-10, 2-7, 2-6, 2-5, 2-4, 2-3, 3-15, 3-10, 3-7, 3-6, 3-5, or 4-10, 4-7, 4-6, 4-5, 5-10, 5-7, 5-6, 6-10, 6-7, 7-10, 7-8, or 8-10 mutations (e.g., mutations contemplated herein).
An aminoacyl-tRNA synthetase mutein may comprise a conservative substitution relative to a wild-type sequence or a sequence disclosed herein. As used herein, the term “conservative substitution” refers to a substitution with a structurally similar amino acid. For example, conservative substitutions may include those within the following groups: Ser and Cys; Leu, Ile, and Val; Glu and Asp; Lys and Arg; Phe, Tyr, and Trp; and Gln, Asn, Glu, Asp, and His. Conservative substitutions may also be defined by the BLAST (Basic Local Alignment Search Tool) algorithm, the BLOSUM substitution matrix (e.g., BLOSUM 62 matrix), or the PAM substitution:p matrix (e.g., the PAM 250 matrix).
In certain embodiments, the substrate specificity of the aminoacyl-tRNA synthetase mutein is altered relative to a corresponding (or template) wild-type aminoacyl-tRNA synthetase such that only a desired unnatural amino acid, but not any of the common 20 amino acids, is charged to the substrate tRNA.
An aminoacyl-tRNA synthetase may be derived from a bacterial source, e.g., Escherichia coli, Thermus thermophilus, or Bacillus stearothermophilus. An aminoacyl-tRNA synthetase may also be derived from an archaeal source, e.g., from the Methanosarcinacaea or Desulftobacterium families, any of the M. barkeri (Mb), M. alvus (Ma), M. mazei (Mm) or D. hafnisense (Dh) families, Methanobacterium thermoautotrophicum, Haloferax volcanii, Halobacterium species NRC-1, or Archaeoglobus fulgidus. In other embodiments, eukaryotic sources can also be used, for example, plants, algae, protists, fungi, yeasts, or animals (e.g., mammals, insects, arthropods, etc.). As used herein, the terms “derivative” or “derived from” refer to a component that is isolated from or made using information from a specified molecule or organism. As used herein, the term “analog” refers to a component (e.g., a tRNA, tRNA synthetase, or unnatural amino acid) that is derived from or analogous with (in terms of structure and/or function) a reference component (e.g., a wild-type tRNA, a wild-type tRNA synthetase, or a natural amino acid). In certain embodiments, derivatives or analogs have at least 40%, 50%, 60%, 70%, 80%, 90%, 100% or more of a given activity as a reference or originator component (e.g., wild-type component).
It is contemplated that the aminoacyl-tRNA synthetase may aminoacylate a substrate tRNA in vitro or in vivo, and can be provided to a translation system (e.g., an in vitro translation system or a cell) as a polypeptide or protein, or as a polynucleotide that encodes the aminoacyl-tRNA synthetase.
In certain embodiments, the aminoacyl-tRNA synthetase is derived from an E. coli leucyl-tRNA synthetase and, for example, the aminoacyl-tRNA synthetase preferentially aminoacylates an E. coli leucyl tRNA (or a variant thereof) with a leucine analog over the naturally-occurring leucine amino acid.
For example, the aminoacyl-tRNA synthetase may comprise SEQ ID NO: 1, or an amino acid sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 1. In certain embodiments, the aminoacyl-tRNA synthetase comprises SEQ ID NO: 1, or a functional fragment or variant thereof, and with one, two, three, four, five or more of the following mutations: (i) a substitution of a glutamine residue at a position corresponding to position 2 of SEQ ID NO: 1, e.g., a substitution by glutamic acid (Q2E); (ii) a substitution of a glutamic acid residue at a position corresponding to position 20 of SEQ ID NO: 1, e.g., a substitution by lysine (E20K), methionine (E20M), or valine (E20V); (iii) a substitution of a methionine residue at a position corresponding to position 40 of SEQ ID NO: 1, e.g., a substitution by isoleucine (M40I) or valine (M40V); (iv) a substitution of a leucine residue at a position corresponding to position 41 of SEQ ID NO: 1, e.g., a substitution by serine (L41S), valine (L41V), or alanine (L41A); (v) a substitution of a threonine residue at a position corresponding to position 252 of SEQ ID NO: 1, e.g., a substitution by alanine (T252A) or arginine (T252R); (vi) a substitution of a tyrosine residue at a position corresponding to position 499 of SEQ ID NO: 1, e.g., a substitution by isoleucine (Y499I), serine (Y499S), alanine (Y499A), or histidine (Y499H); (vii) a substitution of a tyrosine residue at a position corresponding to position 527 of SEQ ID NO: 1, e.g., a substitution by alanine (Y527A), leucine (Y527L), isoleucine (Y527I), valine (Y527V), or glycine (Y527G); or (viii) a substitution of a histidine residue at a position corresponding to position 537 of SEQ ID NO: 1, e.g., a substitution by glycine (H537G), or any combination of the foregoing.
In certain embodiments, the aminoacyl-tRNA synthetase comprises (i) at least one substitution (e.g., a substitution with a hydrophobic amino acid) at a position corresponding to His537 of SEQ ID NO: 1, (ii) at least one amino acid substitution selected from E20V, E20M, L41V, L41 A, Y499H, Y499A, Y527I, Y527V, Y527G, and any combination thereof, (iii) at least one amino acid substitution selected from E20K and L41S and any combination thereof and at least one amino acid substitution selected from M40I, T252A, Y499I, and Y527A, and any combination thereof, or (iv) a combination of two or more of (i), (ii) and (iii), for example, (i) and (ii), (i) and (iii), (ii) and (iii) and (i), (ii) and (iii).
In certain embodiments, the aminoacyl-tRNA synthetase comprises a substitution of a glutamic acid residue at a position corresponding to position 20 of SEQ ID NO: 1, e.g., a substitution with an amino acid other than a Glu or Lys, e.g., a substitution with a hydrophobic amino acid (e.g., Leu, Val, or Met). In certain embodiments, the aminoacyl-tRNA synthetase comprises a substitution of a leucine residue at a position corresponding to position 41 of SEQ ID NO: 1, e.g., a substitution with an amino acid other than a Leu or Ser, e.g., a substitution with a hydrophobic amino acid other than Leu (e.g., Gly, Ala, Val, or Met). In certain embodiments, the aminoacyl-tRNA synthetase comprises a substitution of a tyrosine residue at a position corresponding to position 499 of SEQ ID NO: 1, e.g., a substitution with a small hydrophobic amino acid (e.g., Gly, Ala, or Val) or a substitution with a positively charged amino acid (e.g., Lys, Arg, or His). In certain embodiments, the aminoacyl-tRNA synthetase comprises a substitution of a tyrosine residue at a position corresponding to position 527 of SEQ ID NO: 1, e.g., a substitution with a hydrophobic amino acid other than Ala or Leu (e.g., Gly, Ile, Met, or Val). In certain embodiments, the tRNA synthetase mutein comprises L41V.
In certain embodiments, the aminoacyl-tRNA synthetase comprises a combination of mutations selected from: (i) Q2E, E20K, M40I, L41S, T252A, Y499I, Y527A, and H537G; (ii) Q2E, E20K, M40V, L41S, T252R, Y499S, Y527L, and H537G; (iii) Q2E, M40I, T252A, Y499I, Y527A, and H537G; (iv) Q2E, E20M, M40I, L41S, T252A, Y499I, Y527A, and H537G: (v) Q2E, E20V, M40I, L41S, T252A, Y499I, Y527A, and H537G; (vi) Q2E, E20K, M40I, L41V, T252A, Y499I, Y527A, and H537G; (vii) Q2E, E20K, M40I, L41A, T252A, Y499I, Y527A, and H537G; (viii) Q2E, E20K, M40I, L41S, T252A, Y499A, Y527A, and H537G; (ix) Q2E, E20K, M40I, L41S, T252A, Y499H, Y527A, and H537G; (x) Q2E, E20K, M40I, L41 S, T252A, Y499I, Y527I, and H537G; (xi) Q2E, E20K, M40I, L41S, T252A, Y499I, Y527V, and H537G; (xii) Q2E, E20K, M40I, L41 S, T252A, Y499I, Y527G, and H537G; (xiii) E20K, M40I, L41S, T252A, Y499I, Y527A, and H537G; (xiv) E20M, M40I, L41S, T252A, Y499I, Y527A, and H537G; (xv) E20V, M40I, L41S, T252A, Y499I, Y527A, and H537G; (xvi) E20K, M40I, L41V, T252A, Y499I, Y527A, and H537G; (vii) E20K, M40I, L41A, T252A, Y499I, Y527A, and H537G; (xviii) E20K, M40I, L41S, T252A, Y499A, Y527A, and H537G; (xix) E20K, M40I, L41S, T252A, Y499H, Y527A, and H537G; (xx) E20K, M40, L41S, T252A, Y499I, Y527I, and H537G: (xxi) E20K, M40I, L41 S, T252A, Y499I, Y527V, and H537G; and (xxii) E20K, M40I, L41S, T252A, Y499I, Y527G, and H537G.
In certain embodiments, the aminoacyl-tRNA synthetase comprises the amino acid sequence of any one of SEQ ID NOs: 2-13, or an amino acid sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one of SEQ ID NOs: 2-13.
In certain embodiments, the tRNA synthetase mutein comprises the amino acid sequence of SEQ ID NO: 14, wherein X2 is Q or E, X20 is E, K, V or M, X40 is M, 1, or V, X41 is L, S, V, or A, X252 is T, A, or R, X499 is Y, A, I, H, or S, X527 is Y, A, I, L, or V, and X537 is H or G, and the tRNA synthetase mutein comprises at least one mutation (for example, 2, 3, 4, 5, 6, 7, 8, 9, or more mutations) relative to SEQ ID NO: 1. In certain embodiments, the tRNA synthetase mutein comprises the amino acid sequence of SEQ ID NO: 15, wherein X20 is K, V or M, X41 is S, V, or A, X499 is A, I, or H, and X527 is A, I, or V, and the tRNA synthetase mutein comprises at least one mutation relative to SEQ ID NO: 1.
In certain embodiments, the aminoacyl-tRNA synthetase is derived from an E. coli tryptophanyl-tRNA synthetase and, for example, the aminoacyl-tRNA synthetase preferentially aminoacylates an E. coli tryptophanyl tRNA (or a variant thereof) with a tryptophan analog over the naturally-occurring tryptophan amino acid.
For example, the aminoacyl-tRNA synthetase may comprise SEQ ID NO: 43, or an amino acid sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 43. In certain embodiments, the aminoacyl-tRNA synthetase comprises SEQ ID NO: 43, or a functional fragment or variant thereof, but with one or more of the following mutations: (i) a substitution of a serine residue at a position corresponding to position 8 of SEQ ID NO: 43, e.g., a substitution by alanine (S8A); (ii) a substitution of a valine residue at a position corresponding to position 144 of SEQ ID NO: 43, e.g., a substitution by serine (V144S), glycine (V144G) or alanine (V144A); (iii) a substitution of a valine residue at a position corresponding to position 146 of SEQ ID NO: 43, e.g., a substitution by alanine (V146A), isoleucine (V146I), or cysteine (V146C). In certain embodiments, the aminoacyl-tRNA synthetase comprises a combination of mutations selected from: (i) S8A, V144S, and V146A, (ii) S8A, V144G, and V146I, (iii) S8A, V144A, and V146A, and (iv) S8A, V144G, and V146C.
In certain embodiments, the aminoacyl-tRNA synthetase comprises the amino acid sequence of any one of SEQ ID NOs: 44-47, or an amino acid sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99/a sequence identity to any one of SEQ ID NOs: 44-47.
Sequence identity may be determined in various ways that are within the skill of a person skilled in the art, e.g., using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. BLAST (Basic Local Alignment Search Tool) analysis using the algorithm employed by the programs blastp, blastn, blastx, tblastn and tblastx (Karlin et al., (1990) P
Methods for producing proteins, e.g., aminoacyl-tRNA synthetases, are known in the art. For example, DNA molecules encoding a protein of interest can be synthesized chemically or by recombinant DNA methodologies. The resulting DNA molecules encoding the protein interest can be ligated to other appropriate nucleotide sequences, including, for example, expression control sequences, to produce conventional gene expression constructs (i.e., expression vectors) encoding the desired protein. Production of defined gene constructs is within routine skill in the art.
Nucleic acids encoding desired proteins (e.g., aminoacyl-tRNA synthetases) can be incorporated (ligated) into expression vectors, which can be introduced into host cells through conventional transfection or transformation techniques. Exemplary host cells are E. coli cells, Chinese hamster ovary (CHO) cells, human embryonic kidney 293 (HEK 293) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), and myeloma cells. Transformed host cells can be grown under conditions that permit the host cells to express the desired protein.
Specific expression and purification conditions will vary depending upon the expression system employed. For example, if a gene is to be expressed in E. coli, it is first cloned into an expression vector by positioning the engineered gene downstream from a suitable bacterial promoter, e.g., Trp or Tac, and a prokaryotic signal sequence. The expressed protein may be secreted. The expressed protein may accumulate in refractile or inclusion bodies, which can be harvested after disruption of the cells by French press or sonication. The refractile bodies then are solubilized, and the protein may be refolded and/or cleaved by methods known in the art.
If the engineered gene is to be expressed in eukaryotic host cells, e.g., CHO cells, it is first inserted into an expression vector containing a suitable eukaryotic promoter, a secretion signal, a poly A sequence, and a stop codon. Optionally, the vector or gene construct may contain enhancers and introns. The gene construct can be introduced into eukaryotic host cells using conventional techniques.
A protein of interest (e.g., an aminoacyl-tRNA synthetase) can be produced by growing (culturing) a host cell transfected with an expression vector encoding such a protein under conditions that permit expression of the protein. Following expression, the protein can be harvested and purified or isolated using techniques known in the art, e.g., affinity tags such as glutathione-S-transferase (GST) or histidine tags.
Additional methods for producing aminoacyl-tRNA synthetases, and for altering the substrate specificity of the synthetase can be found in U.S. Patent Application Publication Nos. 2003/0108885 and 2005/0009049, Hamano-Takaku et al. (2000) J
The invention also encompasses nucleic acids encoding aminoacyl-tRNA synthetases disclosed herein. For example, nucleotide sequences encoding leucyl-tRNA synthetase muteins disclosed herein are depicted in SEQ ID NOs: 55-66. Accordingly, the invention provides a nucleic acid comprising the nucleotide sequence of any one of SEQ ID NOs: 55-66, or a nucleotide sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one of SEQ ID NOs: 55-66. The invention also provides a nucleic acid comprising a nucleotide sequence encoding the amino acid sequence encoded by any one of SEQ ID NOs: 55-66, or a nucleotide sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to a nucleotide sequence encoding the amino acid sequence encoded by any one of SEQ ID NOs: 55-66.
The invention relates to transfer RNAs (tRNAs) that mediate the incorporation of unnatural amino acids into proteins.
During protein synthesis, a tRNA molecule delivers an amino acid to a ribosome for incorporation into a growing protein (polypeptide) chain. tRNAs typically are about 70 to 100 nucleotides in length. Active tRNAs contain a 3′ CCA sequence that may be transcribed into the tRNA during its synthesis or may be added later during post-transcriptional processing. During aminoacylation, the amino acid that is attached to a given tRNA molecule is covalently attached to the 2′ or 3′ hydroxyl group of the 3′-terminal ribose to form an aminoacyl-tRNA (aa-tRNA). It is understood that an amino acid can spontaneously migrate from the 2′-hydroxyl group to the 3′-hydroxyl group and vice versa, but it is incorporated into a growing protein chain at the ribosome from the 3′-OH position. A loop at the other end of the folded aa-tRNA molecule contains a sequence of three bases known as the anticodon. When this anticodon sequence hybridizes or base-pairs with a complementary three-base codon sequence in a ribosome-bound mRNA, the aa-tRNA binds to the ribosome and its amino acid is incorporated into the polypeptide chain being synthesized by the ribosome. Because all tRNAs that base-pair with a specific codon are aminoacylated with a single specific amino acid, the translation of the genetic code is effected by tRNAs. Each of the 61 non-termination codons in an mRNA directs the binding of its cognate aa-tRNA and the addition of a single specific amino acid to the growing polypeptide chain being synthesized by the ribosome. The term “cognate” refers to components that function together, e.g., a tRNA and an aminoacyl-tRNA synthetase.
Suppressor tRNAs are modified tRNAs that alter the reading of a mRNA in a given translation system. For example, a suppressor tRNA may read through a codon such as a stop codon, a four base codon, or a rare codon. The use of the word in suppressor is based on the fact, that under certain circumstance, the modified tRNA “suppresses” the typical phenotypic effect of the codon in the mRNA. Suppressor tRNAs typically contain a mutation (modification) in either the anticodon, changing codon specificity, or at some position that alters the aminoacylation identity of the tRNA. The term “suppression activity” refers to the ability of a tRNA, e.g., a suppressor tRNA, to read through a codon (e.g., a premature stop codon) that would not be read through by the endogenous translation machinery in a system of interest.
In certain embodiments, a tRNA (e.g., a suppressor tRNA) contains a modified anticodon region, such that the modified anticodon hybridizes with a different codon than the corresponding naturally occurring anticodon.
In certain embodiments, a tRNA comprises an anticodon that hybridizes to a codon selected from UAG (i.e., an “amber” termination codon), UGA (i.e., an “opal” termination codon), and UAA (i.e., an “ochre” termination codon).
In certain embodiments, a tRNA comprises an anticodon that hybridizes to a non-standard codon, e.g., a 4- or 5-nucleotide codon. Examples of four base codons include AGGA, CUAG, UAGA, and CCCU. Examples of five base codons include AGGAC, CCCCU, CCCUC, CUAGA, CUACU, and UAGGC. tRNAs comprising an anticodon that hybridizes to a non-standard codon, e.g., a 4- or 5-nucleotide codon, and methods of using such tRNAs to incorporate unnatural amino acids into proteins are described, for example, in Moore et al. (2000) J. M
As used herein, the term “tRNA” includes variants having one or more mutations (e.g., nucleotide substitutions, deletions, or insertions) relative to a reference (e.g., a wild-type) tRNA sequence. In certain embodiments, a tRNA may comprise, consist, or consist essentially of, a single mutation (e.g., a mutation contemplated herein), or a combination of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more than 15 mutations (e.g., mutations contemplated herein). It is contemplated that a tRNA may comprise, consist, or consist essentially 1-15, 1-10, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-15, 2-10, 2-7, 2-6, 2-5, 2-4, 2-3, 3-15, 3-10, 3-7, 3-6, 3-5, or 3-4 mutations (e.g., mutations contemplated herein).
In certain embodiments, a variant suppressor tRNA has increased activity to incorporate an unnatural amino acid (e.g., an unnatural amino acid contemplated herein) into a mammalian protein relative to a counterpart wild-type suppressor tRNA (in this context, a wild-type suppressor tRNA refers to a suppressor tRNA that corresponds to a wild-type tRNA molecule but for any modifications to the anti-codon region to impart suppression activity). The activity of the variant suppressor tRNA may be increased relative to the wild-type suppressor tRNA, for example, by about 2.5 to about 200 fold, about 2.5 to about 150 fold, about 2.5 to about 100 fold about 2.5 to about 80 fold, about 2.5 to about 60 fold, about 2.5 to about 40 fold, about 2.5 to about 20 fold, about 2.5 to about 10 fold, about 2.5 to about 5 fold, about 5 to about 200 fold, about 5 to about 150 fold, about 5 to about 100 fold, about 5 to about 80 fold, about 5 to about 60 fold, about 5 to about 40 fold, about 5 to about 20 fold, about 5 to about 10 fold, about 10 to about 200 fold, about 10 to about 150 fold, about 10 to about 100 fold, about 10 to about 80 fold, about 10 to about 60 fold, about 10 to about 40 fold, about 10 to about 20 fold, about 20 to about 200 fold, about 20 to about 150 fold, about 20 to about 100 fold, about 20 to about 80 fold, about 20 to about 60 fold, about 20 to about 40 fold, about 40 to about 200 fold, about 40 to about 150 fold, about 40 to about 100 fold, about 40 to about 80 fold, about 40 to about 60 fold, about 60 to about 200 fold, about 60 to about 150 fold, about 60 to about 100 fold, about 60 to about 80 fold, about 80 to about 200 fold, about 80 to about 150 fold, about 80 to about 100 fold, about 100 to about 200 fold, about 100 to about 150 fold, or about 150 to about 200 fold.
It is contemplated that the tRNA may function in vitro or in vivo and can be provided to a translation system (e.g., an in vitro translation system or a cell) as a mature tRNA (e.g., an aminoacylated tRNA), or as a polynucleotide that encodes the tRNA.
A tRNA may be derived from a bacterial source, e.g., Escherichia coli, Thermus thermophilus, or Bacillus stearothermophilus. A tRNA may also be derived from an archaeal source, e.g., from the Methanosarcinacaea or Desulfitobacterium families, any of the M. barkeri (Mb), M. alvus (Ma), M. mazei (Mm) or D. hafnisense (Dh) families, Methanohacterium thermoautotrophicum, Haloferax volcanii, Halobacterium species NRC-1, or Archaeoglobus fulgiidus. In other embodiments, eukaryotic sources can also be used, for example, plants, algae, protists, fungi, yeasts, or animals (e.g., mammals, insects, arthropods, etc.).
In certain embodiments, the tRNA is derived from an E. coli leucyl tRNA and, for example, is preferentially charged with a leucine analog over the naturally-occurring leucine amino acid by an aminoacyl-tRNA synthetase derived from an E. coli leucyl-tRNA synthetase, e.g., an aminoacyl-tRNA synthetase contemplated herein.
For example, the tRNA may comprise, consist essentially of, or consist of the nucleotide sequence of any one of SEQ ID NOs: 16-42 or 67, or a nucleotide sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one of SEQ ID NOs: 16-42 or 67.
In certain embodiments, the tRNA is derived from an E. coli tryptophanyl tRNA and, for example, is preferentially charged with a tryptophan analog over the naturally-occurring tryptophan amino acid by an aminoacyl-tRNA synthetase derived from an E. coli tryptophanyl-tRNA synthetase, e.g., an aminoacyl-tRNA synthetase contemplated herein.
For example, the tRNA may comprise, consist essentially of, or consist of the nucleotide sequence of any one of SEQ ID NOs: 49-53, or a nucleotide sequence that has at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one of SEQ ID NOs: 49-53.
Additional suppressor tRNAs, and methods of generating suppressor tRNAs, are described in International (PCT) Publication No. WO 2020/257668.
It is understood that, throughout the description, in each instance where a tRNA comprises, consists essentially of, or consists of a nucleotide sequence including one or more thymines (T), a tRNA is also contemplated that comprises, consists essentially of, or consists of the same nucleotide sequence including a uracil (U) in place of one or more of the thymines (T), or a uracil (U) in place of all the thymines (T). Similarly, in each instance where a tRNA comprises, consists essentially of, or consists of a nucleotide sequence including one or more uracils (U), a tRNA is also contemplated that comprises, consists essentially of, or consists of a nucleotide sequence including a thymine (T) in place of the one or more of the uracils (U), or a thymine (T) in place of all the uracils (U). In addition, additional modifications to the bases can be present.
Methods for producing recombinant tRNA are described in U.S. Patent Application Publication Nos. 2003/0108885 and 2005/0009049, Forster et al. (2003) P
A tRNA may be aminoacylated (i.e., charged) with a desired unnatural amino acid (UAA) by any method, including enzymatic or chemical methods.
Enzymatic molecules capable of charging a tRNA include aminoacyl-tRNA synthetases, e.g., aminoacyl-tRNA synthetases disclosed herein. Additional enzymatic molecules capable of charging tRNA include ribozymes, for example, as described in Illangakekare et al. (1995) S
Chemical aminoacylation methods include those described in Hecht (1992) A
The invention relates to unnatural amino acids (UAAs) and their incorporation into proteins.
As used herein, an unnatural amino acid refers to any amino acid, modified amino acid, or amino acid analogue other than the following twenty genetically encoded alpha-amino acids: alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine. See, e.g., Biochemistry by L. Stryer, 3rd ed. 1988, Freeman and Company, New York, for structures of the twenty natural amino acids. The term unnatural amino acid also includes amino acids that occur by modification (e.g. post-translational modifications) of a natural amino acid but are not themselves naturally incorporated into a growing polypeptide chain by the translation complex.
Because unnatural amino acids typically differ from natural amino acids only in the structure of the side chain, unnatural amino acids may, for example, form amide bonds with other amino acids in the same manner in which they are formed in naturally occurring proteins. However, the unnatural amino acids have side chain groups that distinguish them from the natural amino acids. For example, the side chain may comprise an alkyl-, aryl-, acyl-, keto-, azido-, hydroxyl-, hydrazine, cyano-, halo-, hydrazide, alkenyl, alkyl, ether, thiol, seleno-, sulfonyl-, borate, boronate, phospho, phosphono, phosphine, heterocyclic, enone, imine, aldehyde, ester, thioacid, hydroxylamine, amine, and the like, or any combination thereof. Other non-naturally occurring amino acids include, but are not limited to, amino acids comprising a photoactivatable cross-linker, spin-labeled amino acids, fluorescent amino acids, metal binding amino acids, metal-containing amino acids, radioactive amino acids, amino acids with novel functional groups, amino acids that covalently or noncovalently interact with other molecules, photocaged and/or photoisomerizable amino acids, amino acids comprising biotin or a biotin analogue, glycosylated amino acids such as a sugar substituted serine, other carbohydrate modified amino acids, keto-containing amino acids, amino acids comprising polyethylene glycol or polyether, heavy atom substituted amino acids, chemically cleavable and/or photocleavable amino acids, amino acids with an elongated side chains as compared to natural amino acids, including but not limited to, polyethers or long chain hydrocarbons, including but not limited to, greater than about 5 or greater than about 10 carbons, carbon-linked sugar-containing amino acids, redox-active amino acids, amino thioacid containing amino acids, and amino acids comprising one or more toxic moiety.
In addition to unnatural amino acids that contain novel side chains, unnatural amino acids also optionally comprise modified backbone structures.
Many unnatural amino acids are based on natural amino acids, such as tyrosine, glutamine, phenylalanine, and the like. Tyrosine analogs include para-substituted tyrosines, ortho-substituted tyrosines, and meta substituted tyrosines, wherein the substituted tyrosine comprises a keto group (including but not limited to, an acetyl group), a benzoyl group, an amino group, a hydrazine, an hydroxyamine, a thiol group, a carboxy group, an isopropyl group, a methyl group, a C6-C20 straight chain or branched hydrocarbon, a saturated or unsaturated hydrocarbon, an O-methyl group, a polyether group, a nitro group, or the like. In addition, multiply substituted aryl rings are also contemplated. Glutamine analogs include, but are not limited to, α-hydroxy derivatives, γ-substituted derivatives, cyclic derivatives, and amide substituted glutamine derivatives. Exemplary phenylalanine analogs include, but are not limited to, para-substituted phenylalanines, ortho-substituted phenylalanines, and meta-substituted phenylalanines, wherein the substituent comprises a hydroxy group, a methoxy group, a methyl group, an allyl group, an aldehyde, an azido, an iodo, a bromo, a keto group (including but not limited to, an acetyl group), or the like. Specific examples of unnatural amino acids include, but are not limited to, a p-acetyl-L-phenylalanine, a p-propargyl-phenylalanine, O-methyl-L-tyrosine, an L-3-(2-naphthyl)alanine, a 3-methyl-phenylalanine, an O-4-allyl-L-tyrosine, a 4-propyl-L-tyrosine, a tri-O-acetyl-GlcNAcβ-serine, an L-Dopa, a fluorinated phenylalanine, an isopropyl-L-phenylalanine, a p-azido-L-phenylalanine, a p-acyl-L-phenylalanine, a p-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, a phosphonotyrosine, a p-iodo-phenylalanine, a p-bromophenylalanine, a p-amino-L-phenylalanine, an isopropyl-L-phenylalanine, and a p-propargyloxy-phenylalanine, and the like.
Examples of structures of a variety of unnatural amino acids are provided in U.S. Patent Application Publication Nos. 2003/0082575 and 2003/0108885, PCT Publication No. WO 2002/085923, and Kiick et al. (2002) P
An unnatural amino acid in a polypeptide may be used to attach another molecule to the polypeptide, including but not limited to, a label, a dye, a polymer, a water-soluble polymer, a derivative of polyethylene glycol, a photoactivatable crosslinker, a radionuclide, a cytotoxic compound, a drug, an affinity label, a photoaffinity label, a reactive compound, a resin, a second protein or polypeptide or polypeptide analog, an antibody or antibody fragment, a metal chelator, a cofactor, a fatty acid, a carbohydrate, a polynucleotide, a DNA, a RNA, an antisense polynucleotide, a saccharide, a water-soluble dendrimer, a cyclodextrin, an inhibitory ribonucleic acid, a biomaterial, a nanoparticle, a spin label, a fluorophore, a metal-containing moiety, a radioactive moiety, a novel functional group, a group that covalently or noncovalently interacts with other molecules, a photocaged moiety, an actinic radiation excitable moiety, a photoisomerizable moiety, biotin, a derivative of biotin, a biotin analogue, a moiety incorporating a heavy atom, a chemically cleavable group, a photocleavable group, an elongated side chain, a carbon-linked sugar, a redox-active agent, an amino thioacid, a toxic moiety, an isotopically labeled moiety, a biophysical probe, a phosphorescent group, a chemiluminescent group, an electron dense group, a magnetic group, an intercalating group, a chromophore, an energy transfer agent, a biologically active agent, a detectable label, a small molecule, a quantum dot, a nanotransmitter, an immunomodulatory molecule, or any combination of the above.
Any suitable unnatural amino acid can be used with the methods described herein for incorporation into a protein of interest.
The unnatural amino acid may be a leucine analog. The invention provides a leucine analog depicted in
In certain embodiments, the unnatural amino acid is a tryptophan analog (also referred to herein as a derivative). Exemplary tryptophan analogs include 5-azidotryptophan, 5-propargyloxytryptophan, 5-aminotryptophan, 5-methoxytryptophan, 5-O-allyltryptophan or 5-bromotryptophan. Additional exemplary tryptophan analogs are depicted in
In addition, the UAAs set forth in
C5AzMe (Compound 5 as shown in
AzW (Compound 15 as shown in
LCA (Compound 21 as shown in
Many unnatural amino acids are commercially available, e.g., from Sigma-Aldrich (St. Louis, Mo., USA), Novabiochem (Darmstadt, Germany), or Peptech (Burlington, Mass., USA). Those that are not commercially available can be synthesized using standard methods known to those of ordinary skill in the art. For organic synthesis techniques, see, e.g., Organic Chemistry by Fessendon and Fessendon, (1982, Second Edition, Willard Grant Press, Boston Mass.); Advanced Organic Chemistry by March (Third Edition, 1985, Wiley and Sons, New York); and Advanced Organic Chemistry by Carey and Sundberg (Third Edition, Parts A and B, 1990, Plenum Press, New York). Additional exemplary publications describing the synthesis of unnatural amino acids appear in PCT Publication No. WO2002/085923, U.S. Patent Application Publication No. 2004/0198637, Matsoukas el al. (1995) J. M
tRNAs, aminoacyl-tRNA synthetases, or any other molecules of interest may be expressed in a cell of interest by incorporating a gene encoding the molecule into an appropriate expression vector. As used herein, “expression vector” refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression: other elements for expression can be supplied by the host cell or in an in vitro expression system.
tRNAs, aminoacyl-tRNA synthetases, or any other molecules of interest may be introduced to a cell of interest by incorporating a gene encoding the molecule into an appropriate transfer vector. The term “transfer vector” refers to a vector comprising a recombinant polynucleotide which can be used to deliver the polynucleotide to the interior of a cell. It is understood that a vector may be both an expression vector and a transfer vector.
Vectors (e.g., expression vectors or transfer vectors) include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes), retrotransposons (e.g. piggyback, sleeping beauty), and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide of interest.
Typical vectors contain transcription and translation terminators, transcription and translation initiation sequences, and promoters useful for regulation of the expression of the particular target nucleic acid. The vectors optionally comprise generic expression cassettes containing at least one independent terminator sequence, sequences permitting replication of the cassette in eukaryotes, or prokaryotes, or both (including but not limited to, shuttle vectors) and selection markers for both prokaryotic and eukaryotic systems.
In certain embodiments, the vector comprises a regulatory sequence or promoter operably linked to the nucleotide sequence encoding the suppressor tRNA and/or the tRNA synthetase. The term “operably linked” refers to a linkage of polynucleotide elements in a functional relationship. A nucleic acid sequence is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For instance, a promoter or enhancer is operably linked to a gene if it affects the transcription of the gene. Operably linked nucleotide sequences are typically contiguous. However, as enhancers generally function when separated from the promoter by several kilobases and intronic sequences may be of variable lengths, some polynucleotide elements may be operably linked but not directly flanked and may even function in trans from a different allele or chromosome.
Exemplary promoters which may be employed include, but are not limited to, the retroviral LTR, the SV40 promoter, the human cytomegalovirus (CMV) promoter, the U6 promoter, the EF1α promoter, the CAG promoter, the H1 promoter, the UbiC promoter, the PGK promoter, the 7SK promoter, a pol II promoter, a pol III promoter, or any other promoter (e.g., cellular promoters such as eukaryotic cellular promoters including, but not limited to, the histone, pol III, and β-actin promoters). Other viral promoters which may be employed include, but are not limited to, adenovirus promoters, TK promoters, and B19 parvovirus promoters. The selection of a suitable promoter will be apparent to those skilled in the art from the teachings contained herein. In certain embodiments, a vector comprises a nucleotide sequence encoding an aminoacyl-tRNA synthetase operably linked to a CMV or an EF1α promoter and/or a nucleotide sequence encoding a suppressor tRNA operably linked to a U6 or an H1 promoter.
In certain embodiments, a vector (e.g., an expression vector or a transfer vector) comprises a nucleic acid encoding a suppressor tRNA (e.g., a suppressor tRNA disclosed herein) and nucleic acid encoding a tRNA synthetase mutein (e.g., a tRNA synthetase mutein disclosed herein) and the nucleic acid encoding the suppressor tRNA and the nucleic acid encoding the tRNA synthetase mutein are present in a ratio selected from 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 12:1, 14:1, 16:1, 18:1, 20:1, 24:1, 28:1, 32:1, 36:1, 40:1, 44:1, 48:1, 54:1, and 64:1. In certain embodiments, the nucleic acid encoding the suppressor tRNA and the tRNA synthetase mutein are present in a ratio between 1:1 and 64:1, 1:1 and 32:1, 1:1 and 16:1, 1:1 and 8:1, 1:1 and 4:1, 4:1 and 64:1, 4:1 and 32:1, 4:1 and 16:1, 4:1 and 8:1, 8:1 and 64:1, 8:1 and 32:1, 8:1 and 16:1, 16:1 and 64:1, 16:1 and 32:1, or 32:1 and 64:1.
In certain embodiments, the vector is a viral vector. The term “virus” is used herein to refer to an obligate intracellular parasite having no protein-synthesizing or energy-generating mechanism. Exemplary viral vectors include retroviral vectors (e.g., lentiviral vectors), adenoviral vectors, adeno-associated viral vectors, herpesviruses vectors, epstein-barr virus (EBV) vectors, polyomavirus vectors (e.g., simian vacuolating virus 40 (SV40) vectors), poxvirus vectors, and pseudotype virus vectors.
The virus may be a RNA virus (having a genome that is composed of RNA) or a DNA virus (having a genome composed of DNA). In certain embodiments, the viral vector is a DNA virus vector. Exemplary DNA viruses include parvoviruses (e.g., adeno-associated viruses), adenoviruses, asfarviruses, herpesviruses (e.g., herpes simplex virus 1 and 2 (HSV-1 and HSV-2), epstein-barr virus (EBV), cytomegalovirus (CMV)), papillomoviruses (e.g., HPV), polyomaviruses (e.g., simian vacuolating virus 40 (SV40)), and poxviruses (e.g., vaccinia virus, cowpox virus, smallpox virus, fowlpox virus, sheeppox virus, myxoma virus). In certain embodiments, the viral vector is a RNA virus vector. Exemplary RNA viruses include bunyaviruses (e.g., hantavirus), coronaviruses, flaviviruses (e.g., yellow fever virus, west nile virus, dengue virus), hepatitis viruses (e.g., hepatitis A virus, hepatitis C virus, hepatitis E virus), influenza viruses (e.g., influenza virus type A, influenza virus type B, influenza virus type C), measles virus, mumps virus, noroviruses (e.g., Norwalk virus), poliovirus, respiratory syncytial virus (RSV), retroviruses (e.g., human immunodeficiency virus-1 (HIV-1)) and toroviruses.
Adeno-Associated Virus (AAV) Vectors
In certain embodiments, a vector is an adeno-associated virus (AAV) vector. AAV is a small, nonenveloped icosahedral virus of the genus Dependoparvovirus and family Parvovirus. AAV has a single-stranded linear DNA genome of approximately 4.7 kb. AAV is capable of infecting both dividing and quiescent cells of several tissue types, with different AAV serotypes exhibiting different tissue tropism.
AAV includes numerous serologically distinguishable types including serotypes AAV-1 to AAV-12, as well as more than 100 serotypes from nonhuman primates (See, e.g., Srivastava (2008) J. C
The wild-type AAV genome contains two 145 nucleotide inverted terminal repeats (ITRs), which contain signal sequences directing AAV replication, genome encapsidation and integration. In addition to the ITRs, three AAV promoters, p5, p19, and p40, drive expression of two open reading frames encoding rep and cap genes. Two rep promoters, coupled with differential splicing of the single AAV intron, result in the production of four rep proteins (Rep 78, Rep 68, Rep 52, and Rep 40) from the rep gene. Rep proteins are responsible for genomic replication. The Cap gene is expressed from the p40 promoter, and encodes three capsid proteins (VP1, VP2, and VP3) which are splice variants of the cap gene. These proteins form the capsid of the AAV particle.
Because the cis-acting signals for replication, encapsidation, and integration are contained within the ITRs, some or all of the 4.3 kb internal genome may be replaced with foreign DNA, for example, an expression cassette for an exogenous gene of interest. Accordingly, in certain embodiments, the AAV vector comprises a genome comprising an expression cassette for an exogenous gene flanked by a 5′ ITR and a 3′ ITR. The ITRs may be derived from the same serotype as the capsid or a derivative thereof. Alternatively, the ITRs may be of a different serotype from the capsid, thereby generating a pseudotyped AAV. In certain embodiments, the ITRs are derived from AAV-2. In certain embodiments, the ITRs are derived from AAV-5. At least one of the ITRs may be modified to mutate or delete the terminal resolution site, thereby allowing production of a self-complementary AAV vector.
The rep and cap proteins can be provided in trans, for example, on a plasmid, to produce an AAV vector. A host cell line permissive of AAV replication must express the rep and cap genes, the ITR-flanked expression cassette, and helper functions provided by a helper virus, for example adenoviral genes E1a, E1b55K, E2a, E4orf6, and VA (Weitzman et al., Adeno-associated virus biology. Adeno-Associated Virus: Methods and Protocols, pp. 1-23, 2011). Methods for generating and purifying AAV vectors have been described in detail (See e.g., Mueller et al., (2012) CURRENT PROTOCOLS IN MICROBIOLOGY, 14D.1.1-14D.1.21, Production and Discovery of Novel Recombinant Adeno-Associated Viral Vectors). Numerous cell types are suitable for producing AAV vectors, including HEK293 cells, COS cells, HeLa cells, BHK cells, Vero cells, as well as insect cells (See e.g. U.S. Pat. Nos. 6,156,303, 5,387,484, 5,741,683, 5,691,176, 5,688,676, and 8,163,543, U.S. Patent Publication No. 20020081721, and PCT Publication Nos. WO00/47757, WO00/24916, and WO96/17947). AAV vectors are typically produced in these cell types by one plasmid containing the ITR-flanked expression cassette, and one or more additional plasmids providing the additional AAV and helper virus genes.
AAV of any serotype may be used in the present invention. Similarly, it is contemplated that any adenoviral type may be used, and a person of skill in the art will be able to identify AAV and adenoviral types suitable for the production of their desired recombinant AAV vector (rAAV). AAV particles may be purified, for example by affinity chromatography, iodixonal gradient, or CsCl gradient.
AAV vectors may have single-stranded genomes that are 4.7 kb in size, or are larger or smaller than 4.7 kb, including oversized genomes that are as large as 5.2 kb, or as small as 3.0 kb. Thus, where the exogenous gene of interest to be expressed from the AAV vector is small, the AAV genome may comprise a stuffer sequence. Further, vector genomes may be substantially self-complementary thereby allowing for rapid expression in the cell. In certain embodiments, the genome of a self-complementary AAV vector comprises from 5′ to 3′: a 5′ ITR; a first nucleic acid sequence comprising a promoter and/or enhancer operably linked to a coding sequence of a gene of interest; a modified ITR that does not have a functional terminal resolution site; a second nucleic acid sequence complementary or substantially complementary to the first nucleic acid sequence; and a 3′ ITR. AAV vectors containing genomes of all types are suitable for use in the method of the present invention.
Non-limiting examples of AAV vectors include pAAV-MCS (Agilent Technologies), pAAVK-EF1α-MCS (System Bio Catalog #AAV502A-1), pAAVK-EF1α-MCS1-CMV-MCS2 (System Bio Catalog #AAV503A-1), pAAV-ZsGreen1 (Clontech Catalog #6231), pAAV-MCS2 (Addgene Plasmid #46954), AAV-Stuffer (Addgene Plasmid #106248), pAAVscCBPIGpluc (Addgene Plasmid #35645), AAVS1_Puro_PGK1_3×FLAG Twin_Strep (Addgene Plasmid #68375), pAAV-RAM-d2TTA::TRE-MCS-WPRE-pA (Addgene Plasmid #63931), pAAV-UbC (Addgene Plasmid #62806), pAAVS1-P-MCS (Addgene Plasmid #80488), pAAV-Gateway (Addgene Plasmid #32671), pAAV-Puro_siKD (Addgene Plasmid #86695), pAAVS1-Nst-MCS (Addgene Plasmid #80487), pAAVS1-Nst-CAG-DEST (Addgene Plasmid #80489), pAAVS1-P-CAG-DEST (Addgene Plasmid #80490), pAAVf-EnhCB-lacZnls (Addgene Plasmid #35642), and pAAVS1-shRNA (Addgene Plasmid #82697). These vectors can be modified to be suitable for therapeutic use. For example, an exogenous gene of interest can be inserted in a multiple cloning site, and a selection marker (e.g., puro or a gene encoding a fluorescent protein) can be deleted or replaced with another (same or different) exogenous gene of interest. Further examples of AAV vectors are disclosed in U.S. Pat. Nos. 5,871,982, 6,270,996, 7,238,526, 6,943,019, 6,953,690, 9,150,882, and 8,298,818, U.S. Patent Publication No. 2009/0087413, and PCT Publication Nos. WO2017075335A1, WO2017075338A2, and WO2017201258A1.
Lentivirus Vectors
In certain embodiments, the viral vector can be a retroviral vector. Examples of retroviral vectors include moloney murine leukemia virus vectors, spleen necrosis virus vectors, and vectors derived from retroviruses such as rous sarcoma virus, harvey sarcoma virus, avian leukosis virus, human immunodeficiency virus, myeloproliferative sarcoma virus, and mammary tumor virus. Retroviral vectors are useful as agents to mediate retroviral-mediated gene transfer into eukaryotic cells.
In certain embodiments, the retroviral vector is a lentiviral vector. Exemplary lentiviral vectors include vectors derived from human immunodeficiency virus-1 (HIV-1), human immunodeficiency virus-2 (HIV-2), simian immunodeficiency virus (SIV), feline immunodeficiency virus (FIV), bovine immunodeficiency virus (BIV), Jembrana Disease Virus (JDV), equine infectious anemia virus (EIAV), and caprine arthritis encephalitis virus (CAEV).
Retroviral vectors typically are constructed such that the majority of sequences coding for the structural genes of the virus are deleted and replaced by the gene(s) of interest. Often, the structural genes (i.e., gag, pol, and env), are removed from the retroviral backbone using genetic engineering techniques known in the art. Accordingly, a minimum retroviral vector comprises from 5′ to 3′: a 5′ long terminal repeat (LTR), a packaging signal, an optional exogenous promoter and/or enhancer, an exogenous gene of interest, and a 3′ LTR. If no exogenous promoter is provided, gene expression is driven by the 5′ LTR, which is a weak promoter and requires the presence of Tat to activate expression. The structural genes can be provided in separate vectors for manufacture of the lentivirus, rendering the produced virions replication-defective. Specifically, with respect to lentivirus, the packaging system may comprise a single packaging vector encoding the Gag, Pol, Rev, and Tat genes, and a third, separate vector encoding the envelope protein Env (usually VSV-G due to its wide infectivity). To improve the safety of the packaging system, the packaging vector can be split, expressing Rev from one vector, Gag and Pol from another vector. Tat can also be eliminated from the packaging system by using a retroviral vector comprising a chimeric 5′ LTR, wherein the U3 region of the 5′ LTR is replaced with a heterologous regulatory element.
The genes can be incorporated into the proviral backbone in several general ways. The most straightforward constructions are ones in which the structural genes of the retrovirus are replaced by a single gene that is transcribed under the control of the viral regulatory sequences within the LTR. Retroviral vectors have also been constructed which can introduce more than one gene into target cells. Usually, in such vectors one gene is under the regulatory control of the viral LTR, while the second gene is expressed either off a spliced message or is under the regulation of its own, internal promoter.
Accordingly, the new gene(s) are flanked by 5′ and 3′ LTRs, which serve to promote transcription and polyadenylation of the virion RNAs, respectively. The term “long terminal repeat” or “LTR” refers to domains of base pairs located at the ends of retroviral DNAs which, in their natural sequence context, are direct repeats and contain U3, R and U5 regions. LTRs generally provide functions fundamental to the expression of retroviral genes (e.g., promotion, initiation and polyadenylation of gene transcripts) and to viral replication. The LTR contains numerous regulatory signals including transcriptional control elements, polyadenylation signals, and sequences needed for replication and integration of the viral genome. The U3 region contains the enhancer and promoter elements. The U5 region is the sequence between the primer binding site and the R region and contains the polyadenylation sequence. The R (repeat) region is flanked by the U3 and U5 regions. In certain embodiments, the R region comprises a trans-activation response (TAR) genetic element, which interacts with the trans-activator (tat) genetic element to enhance viral replication. This element is not required in embodiments wherein the U3 region of the 5′ LTR is replaced by a heterologous promoter.
In certain embodiments, the retroviral vector comprises a modified 5′ LTR and/or 3′ LTR. Modifications of the 3′ LTR are often made to improve the safety of lentiviral or retroviral systems by rendering viruses replication-defective. In specific embodiments, the retroviral vector is a self-inactivating (SIN) vector. As used herein, a SIN retroviral vector refers to a replication-defective retroviral vector in which the 3′ LTR U3 region has been modified (e.g., by deletion or substitution) to prevent viral transcription beyond the first round of viral replication. This is because the 3′ LTR U3 region is used as a template for the 5′ LTR U3 region during viral replication and, thus, the viral transcript cannot be made without the U3 enhancer-promoter. In a further embodiment, the 3′ LTR is modified such that the U5 region is replaced, for example, with an ideal polyadenylation sequence. It should be noted that modifications to the LTRs such as modifications to the 3′ LTR, the 5′ LTR, or both 3′ and 5′ LTRs, are also included in the invention.
In certain embodiments, the U3 region of the 5′ LTR is replaced with a heterologous promoter to drive transcription of the viral genome during production of viral particles. Examples of heterologous promoters which can be used include, for example, viral simian virus 40 (SV40) (e.g., early or late), cytomegalovirus (CMV) (e.g., immediate early), Moloney murine leukemia virus (MoMLV), Rous sarcoma virus (RSV), and herpes simplex virus (HSV) (thymidine kinase) promoters. Typical promoters are able to drive high levels of transcription in a Tat-independent manner. This replacement reduces the possibility of recombination to generate replication-competent virus, because there is no complete U3 sequence in the virus production system.
Adjacent the 5′ LTR are sequences necessary for reverse transcription of the genome (the tRNA primer binding site) and for efficient packaging of viral RNA into particles (the Psi site). As used herein, the term “packaging signal” or “packaging sequence” refers to sequences located within the retroviral genome which are required for encapsidation of retroviral RNA strands during viral particle formation (see e.g., Clever et al., 1995 J. VIROLOGY, 69(4):2101-09). The packaging signal may be a minimal packaging signal (also referred to as the psi [Ψ] sequence) needed for encapsidation of the viral genome.
In certain embodiments, the retroviral vector (e.g., lentiviral vector) further comprises a FLAP. As used herein, the term “FLAP” refers to a nucleic acid whose sequence includes the central polypurine tract and central termination sequences (cPPT and CTS) of a retrovirus, e.g., HIV-1 or HIV-2. Suitable FLAP elements are described in U.S. Pat. No. 6,682,907 and in Zennou et al. (2000) CELL, 101:173. During reverse transcription, central initiation of the plus-strand DNA at the cPPT and central termination at the CTS lead to the formation of a three-stranded DNA structure: a central DNA flap. While not wishing to be bound by any theory, the DNA flap may act as a cis-active determinant of lentiviral genome nuclear import and/or may increase the titer of the virus. In particular embodiments, the retroviral vector backbones comprise one or more FLAP elements upstream or downstream of the heterologous genes of interest in the vectors. For example, in particular embodiments, a transfer plasmid includes a FLAP element. In one embodiment, a vector of the invention comprises a FLAP element isolated from HIV-1.
In certain embodiments, the retroviral vector (e.g., lentiviral vector) further comprises an export element. In one embodiment, retroviral vectors comprise one or more export elements. The term “export element” refers to a cis-acting post-transcriptional regulatory element which regulates the transport of an RNA transcript from the nucleus to the cytoplasm of a cell. Examples of RNA export elements include, but are not limited to, the human immunodeficiency virus (HIV) RRE (see e.g., Cullen et al., (1991) J. V
In certain embodiments, the retroviral vector (e.g., lentiviral vector) further comprises a posttranscriptional regulatory element. A variety of posttranscriptional regulatory elements can increase expression of a heterologous nucleic acid, e.g., woodchuck hepatitis virus posttranscriptional regulatory element (WPRE; see Zufferey et al., (1999) J. VIROL., 73:2886); the posttranscriptional regulatory element present in hepatitis B virus (HPRE) (Huang et al., M
Elements directing the efficient termination and polyadenylation of the heterologous nucleic acid transcripts increase heterologous gene expression. Transcription termination signals are generally found downstream of the polyadenylation signal. Accordingly, in certain embodiments, the retroviral vector (e.g., lentiviral vector) further comprises a polyadenylation signal. The term “polyadenylation signal” or “polyadenylation sequence” as used herein denotes a DNA sequence which directs both the termination and polyadenylation of the nascent RNA transcript by RNA polymerase H. Efficient polyadenylation of the recombinant transcript is desirable as transcripts lacking a polyadenylation signal are unstable and are rapidly degraded. Illustrative examples of polyadenylation signals that can be used in a vector of the invention, includes an ideal polyadenylation sequence (e.g., AATAAA, ATTAAA, AGTAAA), a bovine growth hormone polyadenylation sequence (BGHpA), a rabbit β-globin polyadenylation sequence (rpgpA), or another suitable heterologous or endogenous polyadenylation sequence known in the art.
In certain embodiments, a retroviral vector further comprises an insulator element. Insulator elements may contribute to protecting retrovirus-expressed sequences, e.g., therapeutic genes, from integration site effects, which may be mediated by cis-acting elements present in genomic DNA and lead to deregulated expression of transferred sequences (i.e., position effect; see, e.g., Burgess-Beusse et al., (2002) P
Non-limiting examples of lentiviral vectors include pLVX-EF1alpha-AcGFP1-C1 (Clontech Catalog #631984), pLVX-EF1alpha-IRES-mCherry (Clontech Catalog #631987), pLVX-Puro (Clontech Catalog #632159), pLVX-IRES-Puro (Clontech Catalog #632186), pLenti6/V5-DEST™ (Thermo Fisher), pLenti6.2/V5-DEST™ (Thermo Fisher), pLKO.1 (Plasmid #10878 at Addgene), pLKO.3G (Plasmid #14748 at Addgene), pSico (Plasmid #11578 at Addgene), pLJM1-EGFP (Plasmid #19319 at Addgene), FUGW (Plasmid #14883 at Addgene), pLVTHM (Plasmid #12247 at Addgene), pLVUT-tTR-KRAB (Plasmid #11651 at Addgene), pLL3.7 (Plasmid #11795 at Addgene), pLB (Plasmid #11619 at Addgene), pWPXL (Plasmid #12257 at Addgene), pWPI (Plasmid #12254 at Addgene), EF.CMV.RFP (Plasmid #17619 at Addgene), pLenti CMV Puro DEST (Plasmid #17452 at Addgene), pLenti-puro (Plasmid #39481 at Addgene), pULTRA (Plasmid #24129 at Addgene), pLX301 (Plasmid #25895 at Addgene), pHIV-EGFP (Plasmid #21373 at Addgene), pLV-mCherry (Plasmid #36084 at Addgene), pLionII (Plasmid #1730 at Addgene), pInducer10-mir-RUP-PheS (Plasmid #44011 at Addgene). These vectors can be modified to be suitable for therapeutic use. For example, a selection marker (e.g., puro, EGFP, or mCherry) can be deleted or replaced with a second exogenous gene of interest. Further examples of lentiviral vectors are disclosed in U.S. Pat. Nos. 7,629,153, 7,198,950, 8,329,462, 6,863,884, 6,682,907, 7,745,179, 7,250,299, 5,994,136, 6,287,814, 6,013,516, 6,797,512, 6,544,771, 5,834,256, 6,958,226, 6,207,455, 6,531,123, and 6,352,694, and PCT Publication No. WO2017/091786.
Adenoviral Vectors
In certain embodiments, the viral vector can be an adenoviral vector. Adenoviruses are medium-sized (90-100 nm), non-enveloped (naked), icosahedral viruses composed of a nucleocapsid and a double-stranded linear DNA genome. The term “adenovirus” refers to any virus in the genus Adenoviridiae including, but not limited to, human, bovine, ovine, equine, canine, porcine, murine, and simian adenovirus subgenera. Typically, an adenoviral vector is generated by introducing one or more mutations (e.g., a deletion, insertion, or substitution) into the adenoviral genome of the adenovirus so as to accommodate the insertion of a non-native nucleic acid sequence, for example, for gene transfer, into the adenovirus.
A human adenovirus can be used as the source of the adenoviral genome for the adenoviral vector. For instance, an adenovirus can be of subgroup A (e.g., serotypes 12, 18, and 31), subgroup B (e.g., serotypes 3, 7, 11, 14, 16, 21, 34, 35, and 50), subgroup C (e.g., serotypes 1, 2, 5, and 6), subgroup D (e.g., serotypes 8, 9, 10, 13, 15, 17, 19, 20, 22-30, 32, 33, 36-39, and 42-48), subgroup E (e.g., serotype 4), subgroup F (e.g., serotypes 40 and 41), an unclassified serogroup (e.g., serotypes 49 and 51), or any other adenoviral serogroup or serotype. Adenoviral serotypes 1 through 51 are available from the American Type Culture Collection (ATCC, Manassas, Virginia). Non-group C adenoviral vectors, methods of producing non-group C adenoviral vectors, and methods of using non-group C adenoviral vectors are disclosed in, for example, U.S. Pat. Nos. 5,801,030, 5,837,511, and 5,849,561, and PCT Publication Nos. WO1997/012986 and WO1998/053087.
Non-human adenovirus (e.g., ape, simian, avian, canine, ovine, or bovine adenoviruses) can be used to generate the adenoviral vector (i.e., as a source of the adenoviral genome for the adenoviral vector). For example, the adenoviral vector can be based on a simian adenovirus, including both new world and old world monkeys (see, e.g., Virus Taxonomy: VHIth Report of the International Committee on Taxonomy of Viruses (2005)). A phylogeny analysis of adenoviruses that infect primates is disclosed in, e.g., Roy et al. (2009) PLoS P
The adenoviral vector can be replication-competent, conditionally replication-competent, or replication-deficient. A replication-competent adenoviral vector can replicate in typical host cells, i.e., cells typically capable of being infected by an adenovirus. A conditionally-replicating adenoviral vector is an adenoviral vector that has been engineered to replicate under pre-determined conditions. For example, replication-essential gene functions, e.g., gene functions encoded by the adenoviral early regions, can be operably linked to an inducible, repressible, or tissue-specific transcription control sequence, e.g., a promoter. Conditionally-replicating adenoviral vectors are further described in U.S. Pat. No. 5,998,205. A replication-deficient adenoviral vector is an adenoviral vector that requires complementation of one or more gene functions or regions of the adenoviral genome that are required for replication, as a result of, for example, a deficiency in one or more replication-essential gene function or regions, such that the adenoviral vector does not replicate in typical host cells, especially those in a human to be infected by the adenoviral vector.
Preferably, the adenoviral vector is replication-deficient, such that the replication-deficient adenoviral vector requires complementation of at least one replication-essential gene function of one or more regions of the adenoviral genome for propagation (e.g., to form adenoviral vector particles). The adenoviral vector can be deficient in one or more replication-essential gene functions of only the early regions (i.e., E1-E4 regions) of the adenoviral genome, only the late regions (i.e., L1-L5 regions) of the adenoviral genome, both the early and late regions of the adenoviral genome, or all adenoviral genes (i.e., a high capacity adenovector (HC-Ad)). See, e.g., Morsy et al. (1998) PROC. NATL. ACAD. SC. USA 95: 965-976, Chen et al. (1997) P
The replication-deficient adenoviral vector of the invention can be produced in complementing cell lines that provide gene functions not present in the replication-deficient adenoviral vector, but required for viral propagation, at appropriate levels in order to generate high titers of viral vector stock. Such complementing cell lines are known and include, but are not limited to, 293 cells (described in, e.g., Graham el al. (1977) J. GEN. VIROL. 36: 59-72), PER.C6 cells (described in, e.g., PCT Publication No. WO1997/000326, and U.S. Pat. Nos. 5,994,128 and 6,033,908), and 293-ORF6 cells (described in, e.g., PCT Publication No. WO1995/034671 and Brough el al. (1997) J. V
Additional exemplary adenoviral vectors, and/or methods for making or propagating adenoviral vectors are described in U.S. Pat. Nos. 5,559,099, 5,837,511, 5,846,782, 5,851,806, 5,994,106, 5,994,128, 5,965,541, 5,981,225, 6,040,174, 6,020,191, 6,083,716, 6,113,913, 6,303,362, 7,067,310, and 9,073,980.
Commercially available adenoviral vector systems include the ViraPower™ Adenoviral Expression System available from Thermo Fisher Scientific, the AdEasy™ adenoviral vector system available from Agilent Technologies, and the Adeno-X™ Expression System 3 available from Takara Bio USA, Inc.
Also encompassed by the invention are host cells or cell lines (e.g., prokaryotic or eukaryotic host cells or cell lines) that include a tRNA, aminoacyl-tRNA synthetase, unnatural amino acid, nucleic acid, and/or vector disclosed herein. The nucleic acid encoding the engineered tRNA and aminoacyl-tRNA synthetase can be expressed in an expression host cell either as an autonomously replicating vector within the expression host cell (e.g., a plasmid, or viral particle) or via a stable integrated element or series of stable integrated elements in the genome of the expression host cell, e.g., a mammalian host cell.
Host cells are genetically engineered (including but not limited to, transformed, transduced or transfected), for example, using nucleic acids or vectors disclosed herein. For example, in certain embodiments, one or more vectors include coding regions for an orthogonal tRNA, an orthogonal aminoacyl-tRNA synthetase, and, optionally, a protein to be modified by the inclusion of one or more UAAs, which are operably linked to gene expression control elements that are functional in the desired host cell or cell line. For example, the genes encoding tRNA synthetase and tRNA and an optional selectable marker (e.g., an antibiotic resistance gene, e.g., a puromycin resistance cassette) can be integrated in a transfer vector (e.g., a plasmid, which can be linearized prior to transfection), where for example, the genes encoding the tRNA synthetase can be under the control of a polymerase II promoter (e.g., CMV, EF1α, UbiC, or PGK, e.g., CMV or EF1α) and the genes encoding the tRNA can be under the control of a polymerase III promoter (e.g., U6, 7SK, or H1, e.g., U6). The vectors are transfected into cells and/or microorganisms by standard methods including electroporation or infection by viral vectors, and clones can selected via expression of the selectable marker (for example, by antibiotic resistance).
Exemplary prokaryotic host cells or cell lines include cells derived from a bacteria, e.g., Escherichia coli, Thermus thermophilus, Bacillus stearothermophilus, Pseudomonas fluorescens, Pseudomonas aeruginosa, and Pseudomonas putida. Exemplary eukaryotic host cells or cell lines include cells derived from a plant (e.g., a complex plant such as a monocot or dicot), an algae, a protist, a fungus, a yeast (including Saccharomyces cerevisiae), or an animal (including a mammal, an insect, an arthropod, etc.). Additional exemplary host cells or cell lines include HEK293, HEK293T, Expi293, CHO, CHOK1, Sf9, Sf21, HeLa, U20S, A549, HT1080, CAD, P19, NIH 3T3, L929, N2a, MCF-7, Y79, SO-RB50, HepG2, DUKX-X11, J558L, BHK, COS, Vero, NSO, or ESCs. It is understood that a host cell or cell line can include individual colonies, isolated populations (monoclonal), or a heterogeneous mixture of cells.
A contemplated cell or cell line includes, for example, one or multiple copies of an orthogonal tRNA/aminoacyl-tRNA synthetase pair, optionally stably maintained in the cell's genome or another piece of DNA maintained by the cell. For example, the cell or cell line may contain one or more copies of (i) a tryptophanyl tRNA/aminoacyl-tRNA synthetase pair (wild-type or engineered) stably maintained by the cell, and/or (ii) a leucyl tRNA/aminoacyl-tRNA synthetase pair (wild-type or engineered) stably maintained by the cell.
For example, in certain embodiments, the cell line is a stable cell line and the cell line comprises a genome having stably integrated therein (i) a nucleic acid sequence encoding an aminoacyl-tRNA synthetase (e.g., a prokaryotic tryptophanyl-tRNA synthetase mutein capable of charging a tRNA with an unnatural amino acid or a prokaryotic leucyl-tRNA synthetase mutein capable of charging a tRNA with an unnatural amino acid, e.g., a tRNA synthetase mutein disclosed herein); and/or (ii) a nucleic acid sequence encoding a suppressor tRNA (e.g., prokaryotic suppressor tryptophanyl-tRNA capable of being charged with an unnatural amino acid or prokaryotic suppressor leucyl-tRNA capable of being charged with an unnatural amino acid, e.g., a suppressor tRNA disclosed herein).
It is contemplated that the nucleic acid sequence encoding the aminoacyl-tRNA synthetase (e.g., a prokaryotic tryptophanyl-tRNA synthetase mutein capable of charging a tRNA with an unnatural amino acid or a prokaryotic leucyl-tRNA synthetase mutein capable of charging a tRNA with an unnatural amino acid, e.g., a tRNA synthetase mutein disclosed herein), when integrated into the genome of the host cell, has a copy number in the range from about 1 to about 50, from about 5 to about 50, from about 10 to about 50, from about 15 to about 50, from about 20 to about 50, from about 25 to about 50, from about 30 to about 50, from about 35 to about 50, from about 40 to about 50, from about 1 to about 40, from about 5 to about 40, from about 10 to about 40, from about 15 to about 40, from about 20 to about 40, from about 25 to about 40, from about 30 to about 40, from about 35 to about 40, from about 1 to about 30, from about 5 to about 30, from about 10 to about 30, from about 15 to about 30, from about 20 to about 30, from about 25 to about 30, from about 1 to about 20, from about 5 to about 20, from about 10 to about 20, from about 15 to about 20. Copy number may be determined by, for example, full genome sequencing.
In a contemplated stable cell line, the nucleic acid sequence encoding the suppressor tRNA (e.g., prokaryotic suppressor tryptophanyl-tRNA capable of being charged with an unnatural amino acid or prokaryotic suppressor leucyl-tRNA capable of being charged with an unnatural amino acid, e.g., a suppressor tRNA disclosed herein), when integrated into the genome of the host cell, has a copy number in the range from about 1 to about 500, from about 5 to about 500, from about 10 to about 500, from about 15 to about 500, from about 20 to about 500, from about 25 to about 500, from about 50 to about 500, from about 75 to about 500, from about 100 to about 500, from about 125 to about 500, from about 150 to about 500, from about 175 to about 500, from about 200 to about 500, from about 225 to about 500, from about 250 to about 500, from about 1 to about 450, from about 5 to about 450, from about 10 to about 450, from about 15 to about 450, from about 20 to about 450, from about 25 to about 450, from about 50 to about 450, from about 75 to about 450, from about 100 to about 450, from about 125 to about 450, from about 150 to about 450, from about 175 to about 450, from about 200 to about 450, from about 225 to about 450, from about 250 to about 450, from about 1 to about 400, from about 5 to about 400, from about 10 to about 400, from about 15 to about 400, from about 20 to about 400, from about 25 to about 400, from about 50 to about 400, from about 75 to about 400, from about 100 to about 400, from about 125 to about 400, from about 150 to about 400, from about 175 to about 400, from about 200 to about 400, from about 225 to about 400, from about 250 to about 400, from about 1 to about 350, from about 5 to about 350, from about 10 to about 350, from about 15 to about 350, from about 20 to about 350, from about 25 to about 350, from about 50 to about 350, from about 75 to about 350, from about 100 to about 350, from about 125 to about 350, from about 150 to about 350, from about 175 to about 350, from about 200 to about 350, from about 225 to about 350, or from about 250 to about 350, from about 1 to about 300, from about 5 to about 300, from about 10 to about 300, from about 15 to about 300, from about 20 to about 300, from about 25 to about 300, from about 50 to about 300, from about 75 to about 300, from about 100 to about 300, from about 125 to about 300, from about 150 to about 300, from about 175 to about 300, from about 200 to about 300, from about 225 to about 300, or from about 250 to about 300, from about 1 to about 200, from about 5 to about 200, from about 10 to about 200, from about 15 to about 200, from about 20 to about 200, from about 25 to about 200, from about 50 to about 200, from about 75 to about 200, from about 100 to about 200, from about 125 to about 200, from about 150 to about 200, from about 175 to about 200, from about 1 to about 175, from about 5 to about 175, from about 10 to about 175, from about 15 to about 175, from about 20 to about 175, from about 25 to about 175, from about 50 to about 175, from about 75 to about 175, from about 100 to about 175, from about 125 to about 175, from about 150 to about 175, from about 1 to about 150, from about 5 to about 150, from about 10 to about 150, from about 15 to about 150, from about 20 to about 150, from about 25 to about 150, from about 50 to about 150, from about 75 to about 150, from about 100 to about 150, from about 125 to about 150, from about 1 to about 125, from about 5 to about 125, from about 10 to about 125, from about 15 to about 125, from about 20 to about 125, from about 25 to about 125, from about 50 to about 125, from about 75 to about 125, from about 100 to about 125, from about 1 to about 100, from about 5 to about 100, from about 10 to about 100, from about 15 to about 100, from about 20 to about 100, from about 25 to about 100, from about 50 to about 100, from about 75 to about 100, from about 1 to about 75, from about 5 to about 75, from about 10 to about 75, from about 15 to about 75, from about 20 to about 75, from about 25 to about 75, from about 50 to about 75, from about 1 to about 50, from about 5 to about 50, from about 10 to about 50, from about 15 to about 50, from about 20 to about 50, from about 25 to about 50, from about 1 to about 25, from about 5 to about 25, from about 10 to about 25, from about 15 to about 25, from about 20 to about 25, from about 1 to about 20, from about 5 to about 20, from about 10 to about 20, from about 15 to about 20, from about 1 to about 15, from about 5 to about 15, from about 10 to about 15, from about 1 to about 10, from about 5 to about 10, or from about 1 to about 5. In certain embodiments, the nucleic acid sequence encoding the suppressor tRNA has a copy number greater than 500 (e.g., a copy number in the range from about 500 to about 2000, from about 500 to about 1800, from about 500 to about 1600, from about 500 to about 1400, from about 500 to about 1200, from about 500 to about 1000, from about 500 to about 900, from about 500 to about 800, from about 500 to about 700, or from about 500 to about 600). In certain embodiments, the nucleic acid sequence encoding the suppressor tRNA has a copy number less than 500, less than 450, less than 400, less than 350, less than 300, less than 250, less than 200, less than 175, less than 150, less than 125, less than 100, less than 75, less than 50, less than 25, less than 10, or less than 5. Copy number may be determined by, for example, full genome sequencing.
In certain embodiments, the suppressor tRNA and the tRNA synthetase mutein are present in a ratio selected from 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 12:1, 14:1, 16:1, 18; 1, 20:1, 24:1, 28:1, 32:1, 36:1, 40:1, 44:1, 48:1, 54:1, and 64:1. In certain embodiments, the suppressor tRNA and the tRNA synthetase mutein are present in a ratio between 1:1 and 64:1, 1:1 and 32:1, 1:1 and 16:1, 1:1 and 8:1, 1:1 and 4:1, 4:1 and 64:1, 4:1 and 32:1, 4:1 and 16:1, 4:1 and 8:1, 8:1 and 64:1, 8:1 and 32:1, 8:1 and 16:1, 16:1 and 64:1, 16:1 and 32:1, or 32:1 and 64:1.
In certain embodiments, the cell line is capable of expressing the target protein (e.g., continuously) for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150 or 180 days (e.g., when the cells are maintained in continuous culture). In certain embodiments, the cell line is capable of expressing the target protein (e.g., continuously) for from 5 to 120, 5 to 100, 5 to 75, 5 to 50, 5 to 40, 5 to 30, 5 to 20, 5 to 10, 10 to 120, 10 to 100, 10 to 75, 10 to 50 days, 10 to 40 days, 10 to 30 days, 10 to 20 days, 20 to 120, 20 to 100, 20 to 75, 20 to 50 days, 20 to 40 days, 20 to 30 days, 30 to 120, 30 to 100, 30 to 75, 30 to 50 days, 30 to 40, 40 to 120, 40 to 100, 40 to 75, 40 to 50, 50 to 120, 50 to 100, 50 to 75, 75 to 120, 75 to 100, or 100 to 120 days (e.g., when the cells are maintained in continuous culture).
In certain embodiments, the cell line is capable of expressing the target protein (e.g., continuously) for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150 or 180 passages (e.g., when the cells are passaged once per day). In certain embodiments, the cell line is capable of expressing the target protein (e.g., continuously) for from 5 to 120, 5 to 100, 5 to 75, 5 to 50, 5 to 40, 5 to 30, 5 to 20, 5 to 10, 10 to 120, 10 to 100, 10 to 75, 10 to 50, 10 to 40, 10 to 30, 10 to 20, 20 to 120, 20 to 100, 20 to 75, 20 to 50, 20 to 40, 20 to 30, 30 to 120, 30 to 100, 30 to 75, 30 to 50, 30 to 40, 40 to 120, 40 to 100, 40 to 75, 40 to 50, 50 to 120, 50 to 100, 50 to 75, 75 to 120, 75 to 100, or 100 to 120 passages (e.g., when the cells are passaged once per day).
In certain embodiments, the cell line maintains genomic copy number (GCN) of the suppressor tRNA and/or the tRNA synthetase for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150 or 180 days (e.g., when the cells are maintained in continuous culture). In certain embodiments, the cell line maintains genomic copy number (GCN) of the suppressor tRNA and/or the tRNA synthetase for from 5 to 120, 5 to 100, 5 to 75, 5 to 50, 5 to 40, 5 to 30, 5 to 20, 5 to 10, 10 to 120, 10 to 100, 10 to 75, 10 to 50, 10 to 40, 10 to 30, 10 to 20, 20 to 120, 20 to 100, 20 to 75, 20 to 50, 20 to 40, 20 to 30, 30 to 120, 30 to 100, 30 to 75, 30 to 50, 30 to 40, 40 to 120, 40 to 100, 40 to 75, 40 to 50, 50 to 120, 50 to 100, 50 to 75, 75 to 120, 75 to 100, or 100 to 120 days (e.g., when the cells are maintained in continuous culture).
In certain embodiments, the cell line maintains genomic copy number (GCN) of the suppressor tRNA and/or the tRNA synthetase for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150 or 180 passages (e.g., when the cells are passaged once per day). In certain embodiments, the cell line the cell line maintains genomic copy number (GCN) of the suppressor tRNA and/or the tRNA synthetase for from 5 to 120, 5 to 100, 5 to 75, 5 to 50, 5 to 40, 5 to 30, 5 to 20, 5 to 10, 10 to 120, 10 to 100, 10 to 75, 10 to 50, 10 to 40, 10 to 30, 10 to 20, 20 to 120, 20 to 100, 20 to 75, 20 to 50, 20 to 40, 20 to 30, 30 to 120, 30 to 100, 30 to 75, 30 to 50, 30 to 40, 40 to 120, 40 to 100, 40 to 75, 40 to 50, 50 to 120, 50 to 100, 50 to 75, 75 to 120, 75 to 100, or 100 to 120 passages (e.g., when the cells are passaged once per day).
In certain embodiments, the cell line is capable of expressing the target protein at a level of expression that is at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or about 100% of the level of expression of the template protein expressed in a corresponding cell line from the gene lacking a premature stop codon, for example, the cell line is capable of expressing the target protein (e.g., continuously) at the level of expression for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150 or 180 days (e.g., when the cells are maintained in continuous culture).
In certain embodiments, (i) the cell line is capable of expressing the target protein at a level of expression that is at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%, or about 100% of the level of expression of the template protein expressed in a corresponding cell line from the gene lacking a premature stop codon, for example, the cell line is capable of expressing the target protein at the level of expression (e.g., continuously) for at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 150 or 180 days (e.g., when the cells are maintained in continuous culture), and (ii) the nucleic acid sequence encoding the suppressor tRNA has a copy number less than 500, less than 450, less than 400, less than 350, less than 300, less than 250, less than 200, less than 175, less than 150, less than 125, less than 100, less than 75, less than 50, less than 25, less than 10, or less than 5. Copy number may be determined by, for example, full genome sequencing.
Methods to introduce a nucleic acid encoding a tRNA and/or an aminoacyl-tRNA synthetase into the genome of a cell of interest, or to stably maintain the nucleic acid in DNA replicated by the cell that is outside of the genome, are well known in the art. 1001801 The nucleic acid encoding the tRNA and/or an aminoacyl-tRNA synthetase can be provided to the cell in an expression vector, transfer vector, or DNA cassette, e.g., an expression vector, transfer vector, or DNA cassette disclosed herein. The expression vector transfer vector, or DNA cassette encoding the tRNA and/or aminoacyl-tRNA synthetase can contain one or more copies of the tRNA and/or aminoacyl-tRNA synthetase optionally under the control of an inducible or constitutively active promoter. The expression vector, transfer vector, or DNA cassette may, for example, contain other standard components (enhancers, terminators, etc.). It is contemplated that the nucleic acid encoding the tRNA and the nucleic acid encoding the aminoacyl-tRNA synthetase may be on the same or different vector, may be present in the same or different ratios, and may be introduced into the cell, or stably integrated in the cellular genome, at the same time or sequentially.
One or multiple copies of a DNA cassette encoding the tRNA and/or aminoacyl-tRNA synthetase can be integrated into a host cell genome or stably maintained in the cell using a transposon system (e.g., PiggyBac), a viral vector (e.g., a lentiviral vector or other retroviral vector), CRISPR/Cas9 based recombination, electroporation and natural recombination, a BxB1 recombinase system, or using a replicating/maintained piece of DNA (such as one derived from Epstein-Barr virus).
In order to select for cell lines which stably maintain the nucleic acid encoding the tRNA and/or aminoacyl-tRNA synthetase and/or are efficient at incorporating UAAs into a protein of interest, a selectable marker can be used. Exemplary selectable markers include zeocin, puromycin, neomycin, dihydrofolate reductase (DHFR), glutamine synthetase (GS), mCherry-EGFP fusion, or other fluorescent proteins. In certain embodiments, a gene encoding a selectable marker protein (or a gene encoding a protein required for a detectable function, e.g., viability, in the presence of the selectable marker) may include a premature stop codon, such that the protein will only be expressed if the cell line is capable of incorporating a UAA at the site of the premature stop codon. In certain embodiments, the selection of a stable cell line comprises incubating cells with puromycin, for example, at about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 μg/ml, greater than or equal to 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 μg/ml, less than or equal to 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 μg/mI, or from 1 to 10, 2 to 10, 4 to 10, 6 to 10, 8 to 10, 1 to 8, 2 to 8, 4 to 8, 6 to 8, 1 to 6, 2 to 6, 4 to 6, 1 to 4, 2 to 4, or 1 to 2 μg/ml.
In certain embodiments, to develop a host cell or cell line including two or more tRNA/aminoacyl-tRNA synthetase pairs, one can use multiple identical or distinct UAA directing codons in order to identify host cells or cell lines which have incorporated multiple copies of the two or more tRNA/aminoacyl-tRNA synthetase pairs through iterative rounds of genomic integration and selection. Host cells or cell lines which contain enhanced UAA incorporation efficiency, low background, and decreased toxicity can first be isolated via a selectable marker containing one or more stop codons. Subsequently, the host cells or cell lines can be subjected to a selection scheme to identify host cells or cell lines which contain the desired copies of tRNA/aminoacyl-tRNA synthetase pairs and express a gene of interest (either genomically integrated or not) containing one or more stop codons. Protein expression may be assayed using any method known in the art, including for example, Western blot using an antibody that binds the protein of interest or a C-terminal tag.
The host cells or cell lines be cultured in conventional nutrient media modified as appropriate for such activities as, for example, screening steps, activating promoters or selecting transformants. These cells can optionally be cultured into transgenic organisms. Other useful references, e.g. for cell isolation and culture (e.g., for subsequent nucleic acid isolation) include Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique, third edition, Wiley-Liss, New York; Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips (eds.) (1995) Plant Cell, Tissue and Organ Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg N.Y.) and Atlas and Parks (eds.) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, Fla.
The production of an exemplary cell line capable of producing antibodies incorporating a UAA is described in Roy et al. (2020) MABS 12(1), e1684749). Additional exemplary methods to generate stable cell lines for the incorporation of a UAA into a protein are described in Example 2 and
In certain embodiments, a method for the generation of a stable cell line for the incorporation of a UAA into a protein comprises one or more of the following steps: (i) transfecting cells with one or more plasmids encoding a suppressor tRNA and an aminoacyl-tRNA synthetase, wherein the one or more plasmids include a selectable marker (e.g., an antibiotic resistance gene) (ii) selecting cells that contain the one or more plasmids using the selectable marker, (iii) transiently transfecting cells with a reporter construct (e.g., a fluorescent reporter construct) that gives a detectable signal upon UAA incorporation into a protein, (iv) selecting cells that are capable of UAA incorporation using the reporter construct, and (v) further propagating the cells. In certain embodiments, the method further comprises (vi) transiently transfecting cells with the reporter construct again, and selecting cells that have maintained capability of UAA incorporation using the reporter construct.
In certain embodiments, a method for the generation of a stable cell line comprises contacting the cell with one or more vectors (e.g., expression vectors or transfers vector), wherein the one or more vectors comprise a nucleic acid encoding a suppressor tRNA (e.g., a suppressor tRNA disclosed herein) and a nucleic acid encoding a tRNA synthetase mutein (e.g., a tRNA synthetase mutein disclosed herein) and the nucleic acid encoding the suppressor tRNA and the nucleic acid encoding the tRNA synthetase mutein are present in a ratio selected from 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 12:1, 14:1, 16:1, 18:1, 20:1, 24:1, 28:1, 32:1, 36:1, 40:1, 44:1, 48:1, 54:1, and 64:1. In certain embodiments, the nucleic acid encoding the suppressor tRNA and the tRNA synthetase mutein are present in a ratio between 1:1 and 64:1, 1:1 and 32:1, 1:1 and 16:1, 1:1 and 8:1, 1:1 and 4:1, 4:1 and 64:1, 4:1 and 32:1, 4:1 and 16:1, 4:1 and 8:1, 8:1 and 64:1, 8:1 and 32:1, 8:1 and 16:1, 16:1 and 64:1, 16:1 and 32:1, or 32:1 and 64:1.
In certain embodiments, a method for the generation of a stable cell line comprises contacting the cell with a single vector (e.g., a single expression vector or transfer vector), wherein the single vector comprises a nucleic acid encoding a suppressor tRNA (e.g., a suppressor tRNA disclosed herein) and a nucleic acid encoding a tRNA synthetase mutein (e.g., a tRNA synthetase mutein disclosed herein). In certain embodiments, a method for the generation of a stable cell line comprises contacting the cell with a first vector (e.g., a first expression vector or transfer vector), wherein the first vector comprises a nucleic acid encoding a suppressor tRNA (e.g., a suppressor tRNA disclosed herein) and a second vector (e.g., a second expression vector or transfer vector), wherein the second vector comprises a nucleic acid encoding a tRNA synthetase (e.g., a tRNA synthetase mutein, e.g., a tRNA synthetase mutein disclosed herein). In certain embodiments, the cell is contacted with the first and second vector simultaneously. In certain embodiments, the cell is contacted with the first and second vector sequentially (e.g., the cell is first contacted with the first vector and then contacted with the second vector, or the cell is first contacted with the second vector and then contacted with the first vector).
Also encompassed by the invention are proteins including unnatural amino acids (UAAs) and methods of making the same.
The incorporation of an unnatural amino acid can be done for a variety of purposes, including tailoring changes in protein structure and/or function, changing size, acidity, nucleophilicity, hydrogen bonding, hydrophobicity, accessibility of protease target sites, targeting to a moiety (e.g., for a protein array), adding a biologically active molecule, attaching a polymer, attaching a radionuclide, modulating serum half-life, modulating tissue penetration (e.g. tumors), modulating active transport, modulating tissue, cell or organ specificity or distribution, modulating immunogenicity, modulating protease resistance, etc. Proteins that include an unnatural amino acid can have enhanced or even entirely new catalytic or biophysical properties. For example, the following properties are optionally modified by inclusion of an unnatural amino acid into a protein: toxicity, biodistribution, structural properties, spectroscopic properties, chemical and/or photochemical properties, catalytic ability, half-life (including but not limited to, serum half-life), ability to react with other molecules, including but not limited to, covalently or noncovalently, and the like. The compositions including proteins that include at least one unnatural amino acid are useful for, including but not limited to, novel therapeutics, diagnostics, enzymes, and binding proteins (e.g., therapeutic antibodies).
A protein may have at least one, for example, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten or more UAAs. The UAAs can be the same or different. For example, there can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more different sites in the protein that comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more different UAAs. A protein may have at least one, but fewer than all, of a particular amino acid present in the protein substituted with the UAA. For a given protein with more than one UAA, the UAA can be identical or different (for example, the protein can include two or more different types of UAAs, or can include two of the same UAA). For a given protein with more than two UAAs, the UAAs can be the same, different or a combination of a multiple unnatural amino acid of the same kind with at least one different UAA.
In certain embodiments, the protein is an antibody (or a fragment thereof), bispecific antibody, nanobody, affibody, viral protein, chemokine, antigen, blood coagulation factor, hormone, growth factor, enzyme, or any other polypeptide or protein.
As used herein, unless otherwise indicated, the term “antibody” is understood to mean an intact antibody (e.g., an intact monoclonal antibody), or a fragment thereof, such as a Fc fragment of an antibody (e.g., an Fc fragment of a monoclonal antibody), or an antigen-binding fragment of an antibody (e.g., an antigen-binding fragment of a monoclonal antibody), including an intact antibody, antigen-binding fragment, or Fc fragment that has been modified, engineered, or chemically conjugated. Examples of antigen-binding fragments include Fab, Fab′, (Fab′)2, Fv, single chain antibodies (e.g., scFv), minibodies, and diabodies. Examples of antibodies that have been modified or engineered include chimeric antibodies, humanized antibodies, and multispecific antibodies (e.g., bispecific antibodies). An example of a chemically conjugated antibody is an antibody conjugated to a toxin moiety.
Additional examples of therapeutic, diagnostic, and other proteins that can be modified to comprise one or more unnatural amino acids are described in U.S. Patent Application Publication Nos. 2003/0082575 and 2005/0009049.
tRNAs, aminoacyl-tRNA synthetases, and/or unnatural amino acids disclosed herein may be used to incorporate an unnatural amino acid into a protein of interest using any appropriate translation system.
The term “translation system” refers to a system including components necessary to incorporate an amino acid into a growing polypeptide chain (protein). Components of a translation system can include, e.g., ribosomes, tRNA's, synthetases, mRNA and the like. Translation systems may be cellular or cell-free, and may be prokaryotic or eukaryotic. For example, translation systems may include, or be derived from, a non-eukaryotic cell, e.g., a bacterium (such as E. coli), a eukaryotic cell, e.g., a yeast cell, a mammalian cell, a plant cell, an algae cell, a fungus cell, or an insect cell.
Translation systems include host cells or cell lines, e.g., host cells or cell lines contemplated herein. To express a polypeptide of interest with an unnatural amino acid in a host cell, one may clone a polynucleotide encoding the polypeptide into an expression vector that contains, for example, a promoter to direct transcription, a transcription/translation terminator, and if for a nucleic acid encoding a protein, a ribosome binding site for translational initiation.
Translation systems also include whole cell preparations such as permeabilized cells or cell cultures wherein a desired nucleic acid sequence can be transcribed to mRNA and the mRNA translated. Cell-free translation systems are commercially available and many different types and systems are well-known. Examples of cell-free systems include, but are not limited to, prokaryotic lysates such as Escherichia coli lysates, and eukaryotic lysates such as wheat germ extracts, insect cell lysates, rabbit reticulocyte lysates, rabbit oocyte lysates and human cell lysates. Reconstituted translation systems may also be used. Reconstituted translation systems may include mixtures of purified translation factors as well as combinations of lysates or lysates supplemented with purified translation factors such as initiation factor-1 (IF-1), IF-2, IF-3 (a or p), elongation factor T (EF-Tu), or termination factors. Cell-free systems may also be coupled transcription/translation systems wherein DNA is introduced to the system, transcribed into mRNA and the mRNA is translated.
The invention provides methods of expressing a protein containing an unnatural amino acid and methods of producing a protein with one, or more, unnatural amino acids at specified positions in the protein. The methods comprise incubating a translation system (e.g., culturing or growing a host cell or cell line, e.g., a host cell or cell line disclosed herein) under conditions that permit incorporation of the unnatural amino acid into the protein being expressed in the cell. The translation system may be contacted with (e.g. the cell culture medium may be contacted with) one, or more, unnatural amino acids (e.g., leucyl or tryptophanyl analogs) under conditions suitable for incorporation of the one, or more, unnatural amino acids into the protein.
In certain embodiments, the protein is expressed from a nucleic acid sequence comprising a premature stop codon. The translation system (e.g., host cell or cell line) may, for example, contain a leucyl-tRNA synthetase mutein (e.g., a leucyl-tRNA synthetase mutein disclosed herein) capable of charging a suppressor leucyl tRNA (e.g., a suppressor leucyl tRNA disclosed herein) with an unnatural amino acid (e.g., a leucyl analog) which is incorporated into the protein at a position corresponding to the premature stop codon. In certain embodiments, the leucyl suppressor tRNA comprises an anticodon sequence that hybridizes to the premature stop codon and permits the unnatural amino to be incorporated into the protein at the position corresponding to the premature stop codon.
In certain embodiments, the protein is expressed from a nucleic acid sequence comprising a premature stop codon. The translation system (e.g., host cell or cell line) may, for example, contain a tryptophanyl-tRNA synthetase mutein (e.g., a tryptophanyl-tRNA synthetase mutein disclosed herein) capable of charging a suppressor tryptophanyl tRNA (e.g., a suppressor tryptophanyl tRNA disclosed herein) with an unnatural amino acid (e.g., a tryptophan analog) which is incorporated into the protein at a position corresponding to the premature stop codon. In certain embodiments, the tryptophanyl suppressor tRNA comprises an anticodon sequence that hybridizes to the premature stop codon and permits the unnatural amino to be incorporated into the protein at the position corresponding to the premature stop codon.
Throughout the description, where compositions are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are compositions of the present invention that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the present invention that consist essentially of, or consist of, the recited processing steps.
In the application, where an element or component is said to be included in and/or selected from a list of recited elements or components, it should be understood that the element or component can be any one of the recited elements or components, or the element or component can be selected from a group consisting of two or more of the recited elements or components.
Further, it should be understood that elements and/or features of a composition or a method described herein can be combined in a variety of ways without departing from the spirit and scope of the present invention, whether explicit or implicit herein. For example, where reference is made to a particular compound, that compound can be used in various embodiments of compositions of the present invention and/or in methods of the present invention, unless otherwise understood from the context. In other words, within this application, embodiments have been described and depicted in a way that enables a clear and concise application to be written and drawn, but it is intended and will be appreciated that embodiments may be variously combined or separated without parting from the present teachings and invention(s). For example, it will be appreciated that all features described and depicted herein can be applicable to all aspects of the invention(s) described and depicted herein.
It should be understood that the expression “at least one of” includes individually each of the recited objects after the expression and the various combinations of two or more of the recited objects unless otherwise understood from the context and use. The expression “and/or” in connection with three or more recited objects should be understood to have the same meaning unless otherwise understood from the context.
The use of the term “include,” “includes,” “including,” “have,” “has,” “having,” “contain,” “contains,” or “containing,” including grammatical equivalents thereof, should be understood generally as open-ended and non-limiting, for example, not excluding additional unrecited elements or steps, unless otherwise specifically stated or understood from the context.
Where the use of the term “about” is before a quantitative value, the present invention also includes the specific quantitative value itself, unless specifically stated otherwise. As used herein, the term “about” refers to a ±10% variation from the nominal value unless otherwise indicated or inferred.
It should be understood that the order of steps or order for performing certain actions is immaterial so long as the present invention remain operable. Moreover, two or more steps or actions may be conducted simultaneously.
The use of any and all examples, or exemplary language herein, for example, “such as” or “including,” is intended merely to illustrate better the present invention and does not pose a limitation on the scope of the invention unless claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the present invention.
E. coli
E. coli
E. coli Trp-
E. coli
The following Examples are merely illustrative and are not intended to limit the scope or content of the invention in any way.
This Example describes the construction of leucyl tRNA-synthetase muteins.
Wild-type E. coli leucyl tRNA-synthetase (SEQ ID NO: 1) was cloned into a plasmid under control of a CMV promoter. The plasmid also contained a 4×U6-LeutRNACUA DNA cassette encoding a suppressor tRNA (E. coli leucyl tRNA h1 with a CUA anticodon, SEQ ID NO: 19). The plasmid, encoding the leucyl-trRNA synthetase and leucyl suppressor tRNA was used as a library template construct and is referred to as pBBK-LeuRS.wt-LtR-TAG.
Leucyl synthetase muteins V2 (SEQ ID NO: 3) and V3 (SEQ ID NO: 4) were generated via standard mutagenesis of wild-type active site residues (see, Zheng et al. (2018) supra) Leucyl synthetase mutein V1 (SEQ ID NO: 2) was designed by combining distinct active site mutations of the V2 and V3 muteins.
The plasmid encoding leucyl tRNA-synthetase mutein V1 (SEQ ID NO: 2; referred to herein as LeuRS.v1) was then used as a template for the generation of a library of plasmids encoding additional leucyl tRNA-synthetases variants. The library included plasmids encoding leucyl tRNA-synthetase variants with individual substitutions of each of Q2, E20, M40, L41, T252, Y499, Y527, and H537 with each of the twenty natural amino acids.
A sGFP-39TAG reporter fluorescence assay, which utilizes a reporter plasmid encoding the GFP protein with an amber codon at Y39 and fused to a His-tag at the C-terminal (GFP39-TAG), was used to assess the leucyl synthetase mutein activity in mammalian cells. HEK293T cells were cultured in Dulbecco's modified Eagle's Medium (DMEM) supplemented with 10% FBS and 0.5× penicillin-streptomycin in a humidified incubator at 37° C. in the presence of 8% CO2. 0.7×106 HEK293T cells were seeded per well 24 hours prior to transfection in a 12 well plate. Polyethylamine and DNA were mixed at a ratio of 4 μL PEI (1 mg/mL) to 1 μg DNA in DMEM. For each transfection mixture, 500 ng GFP39-TAG reporter plasmid was mixed with pBBK-LeuRS.v#-LtR-TAG. Unnatural amino acids (UAAs) were added or excluded from the media at concentrations of 0.5 mM LCA, 1 mM LKET, or 1 mM ACA. Fluorescence images were obtained at 48 hours with an Olympus microscope through a 488 bandpass filter set. To obtain GFP39-TAG expression data, cells were harvested at 12,000×g. Cells were washed with PBS and lysed with CelLytic M lysis buffer supplemented with 1× Halt protease inhibitor and 0.01% Pierce universal nuclease. After a 20 minute incubation, the lysate was clarified at 15,000×g for 10 minutes and transferred to a clear bottom 96-well assay plate. Fluorescence was measured using a Fluoroskan Ascent II (Ex. 485 nm; Em. 535 nm).
Variants of LeuRS.v1 (SEQ ID NOs: 5-14) were assayed for LCA incorporation as described above. Point mutations in variants of LeuRS.v1 are shown in
The LeuRS variants depicted in
Leucyl synthetase muteins described in this Example with enhanced activity to wild-type are summarized in TABLE 1.
Example 2—Construction of Stable Cell Lines Expressing Leucyl tRNAs and Leucyl tRNA-Synthetase Muteins
This Example describes the construction of cell lines, e.g., stable cell lines, expressing leucyl suppressor tRNAs and leucyl tRNA-synthetases (schematically depicted in
CHO-dhFr adherent cells were acquired from ATCC. CHO-dhFr cells were chosen as a parental cell line due to the flexibility of their inherent metabolic dhFr selection strategy for future integration of target genes of interest (i.e., post-platform cell line generation). CHO-dhFr cells were maintained according to the ATCC protocol in Gibcor™ IMDM, supplemented with 10% Fetal Bovine Serum, 0.1 mM hypoxanthine, 0.016 mM thymidine, and 0.002 mM Methotrexate. For stable cell line generation, CHO-dhFr cells under passage 15 were cultured for pCLD plasmid transfection either using Lipofectamine 2000 (Thermo Fisher Scientific) or Nucleofector 4D-X unit and associated kits (Lonza).
For Lipofectamine 2000 transfections, 2 mL of 2.5×105 per mL CHO-dhFr cells were plated per well of a 6 well plate 24 hours prior to transfection. 24 hours later, cells were transfected with 3 μg of a plasmid containing (i) a 4×U6 promoter, leucyl suppressor tRNA h1 repeat cassette and (ii) an EF1α promoter, LeuRS.v1-IRES-puromycin cassette (plasmid 2, TABLE 2) using Lipofectamine 2000 following the Thermo Fisher Scientific standard protocol.
For Lonza Nucleofector 4D-X transfections, 1×106 CHO-dhFr cells transfected with 2-4 μg of plasmid containing (i) a 4×U6 promoter, leucyl suppressor tRNA repeat cassette and (ii) an EF1α promoter, LeuRS.v1-IRES-puromycin cassette (plasmid 2, TABLE 2) using the Lonza kit SE according to the manufacturer's instructions. Cells post-transfection were plated into a 6 well plate. After Lipofectamine 2000-based transfection or Nucleofection, plates were incubated at 37° C. with 5% CO2 to recover for 24-48 hours prior to application of 1.5 μg-6 μg puromycin for selection (steps 1-2 of
The leucyl suppressor tRNA in plasmid 2 is depicted in SEQ ID NO: 19 and the LeuRS.v1 leucyl-tRNA synthetase in plasmid 2 is depicted in SEQ ID NO: 2.
Two weeks post-puromycin selection, the cells were transfected with a dual reporter construct comprising both GFP and mCherry fluorescent reporters using Lipofectamine 2000, as described in the manufacturer's protocol. Said dual reporter constitutively produces mCherry (red) and is connected via a linker comprising a stop codon to GFP, such that the reporter conditionally produces GFP (green) if the tRNA/aaRS pair are active (step 3 of
Isolated clones were then individually prepared for transfection and recharacterization via the same mCherry-GFP conditional reporter described above, which served as a representative readout of UAA incorporation (step 5 of
The fluorescence intensity of the transfected cells was quantified by FACS. Histogram analysis of the MG* reporter expressed in clonal populations (
The histogram depicted in
Productivity analysis of stable clones was performed with the use of a GFP* reporter, comparing the parental cell line or clone 1.L1w.6 (
Stability of the clonal cell lines for UAA incorporation capability is further assayed via the above methods over a 30-60 day period. Clones are thawed and cultured over two months according to the protocol as described above. Every two weeks, clonal population timepoints are banked in liquid nitrogen according to standard ATCC protocol. At the end of the two-month culture period, cells are thawed and fluorescence analysis is repeated as described above for each timepoint, followed by the general productivity analysis as described above (step 6 of
Additional constructs for the construction of stable cell lines expressing leucyl suppressor tRNAs and leucyl-tRNA synthetases include plasmids 1, and 3-7 (TABLE 2). Relative to plasmid 2, these additional constructs include, for example, different tRNA or aaRS copy number or different resistance gene.
A summary of the constructs for construction of stable cell lines expressing leucyl suppressor tRNAs and leucyl-tRNA synthetases described in this Example is depicted in TABLE 2.
Parallel cell line pools were generated with nucleofection as described in Example 2 above using pCLD-4×LeutRwt-LeuRS.v1-Puro (plasmid 1 of TABLE 2) or pCLD-4×LeutR.h1-LeuRS.v1-Puro (plasmid 1 of TABLE 2), with “wild-type” (wild-type other than any mutations in the anticodon region) or mutein tRNA h1, each engineered to contain the CUA anticodon, in order to compare the effect of the “wild-type” versus h1 leucyl tRNAs, respectively, on the efficiency of stable clone generation (the process as shown in steps 1-3 of
Cell line pools were generated by nucleofection as described above in Example 2 using pCLD-4×TrptR-TGA-TrpRS.h14-Puro (plasmid 1 of TABLE 3). This version of the pCLD plasmid contains (i) a 4×U6 promoter, Trp-tRNA-UCA repeat cassette and (ii) an EF1α promoted TrpRS.h14-IRES-puromycin cassette. The tryptophanyl suppressor tRNA Trp-tRNA-UCA in plasmid 1 is depicted in SEQ ID NO: 50, and the TrpRS.h14 tryptophanyl-tRNA synthetase in plasmid 1 is depicted in SEQ ID NO: 44.
A shortened puromycin selection of 7-10 days, in either 1.5 μg/mL or 4 μg/mL, was used, and an mCherry-GFP* reporter was used, with a TGA stop codon rather than a TAG stop codon. The TGA stop codon displays higher efficiency than the TAG stop codon in mammalian cells for tryptophanyl pairs. Pools of stable tryptophan cell lines were subjected to the same selection conditions and analyzed via FACS analysis using the modified MG* (TGA) reporter as described above in Example 2 in the presence of 1 mM 5-hydroxytryptophan, HTP, the UAA for the tryptophanyl pair (
Further characterization of clonal isolates, for example, as was performed with the leucyl clonal isolates described in Example 2 above, is conducted to determine protein production and stability characteristics of the stable tryptophanyl cell lines.
Additional constructs for the construction of stable cell lines expressing tryptophanyl suppressor tRNAs and tryptophanyl-tRNA synthetases include plasmids 2-6 (TABLE 3). Relative to plasmid 1, these additional constructs include, for example, different tRNA or aaRS copy number.
A summary of the constructs for construction of stable cell lines expressing tryptophanyl suppressor tRNAs and tryptophanyl-tRNA synthetases described in this Example is depicted in TABLE 3.
This Example describes the construction of stable cell lines expressing leucyl suppressor tRNAs and leucyl tRNA-synthetases, including by (i) transfecting cells with a single plasmid encoding both the leucyl suppressor tRNA and leucyl tRNA-synthetase, and (ii) transfecting cells sequentially with separate plasmids encoding the leucyl suppressor tRNA and leucyl tRNA-synthetase.
Stable CHO-dhFr cell lines were generated by transfection of plasmid 2 (TABLE 2) using Lipofectamine 2000 or nucleofection. Selection was performed at 1.5, 2, 4, or 6 μg/mL puromycin. Post-puromycin selection, cells were transfected with the MG* dual GFP and mCherry fluorescent reporter. Transfected cells were cultured in the presence of UAA (LCA), and UAA incorporation activity was determined by fluorescence activated cell sorting (FACS) and fluorescent microscopy. Except where indicated otherwise, all experimental steps and reagents were generally as described in Example 2 above.
Results for select, top-performing clones are shown in
In
Further stable CHO-dhFr cells lines were generated using a sequential selection method, where the leucyl suppressor tRNA was first integrated into the genome under a puromycin selectable marker and the leucyl tRNA-synthetase was then integrated into the genome under a zeocin selectable marker.
In brief, plasmid 2 (TABLE 2) was subcloned to remove the LeuRS.v1, resulting in a 4×LeutR.h1 only plasmid which contained a puromycin selectable marker. Plasmid 2 was also subcloned to remove the 4×LeutR.h1 and replace the puromycin selectable marker with a zeocin selectable marker, resulting in a 1×LeuRS.v1 only plasmid which contained a zeocin selectable marker. First, the 4×LeutR.h1 only plasmid was transfected into CHO-dhFr cells using Lipofectamine 2000 and a puromycin resistant pool was selected. Selected pools were transiently transfected with a plasmid encoding LeuRS.v1 and assayed for activity using the MG* reporter. Stable clones with UAA incorporation activity were isolated. Next, these stable clones were further transfected with the 1×LeuRS.v1 only plasmid using Lipofectamine 2000 and 0.05-2 μg/mL zeocin for selection. Cells were assayed again for activity using the MG* reporter, and stable clones with UAA incorporation activity were isolated. This sequential approach would hypothetically allow for stable cell lines with varying copies of the suppressor tRNA and/or tRNA-synthetase genes, thereby not constraining the cell lines to the 4:1 copy number ratio of the genes in plasmid 2. Except where indicated otherwise, all experimental steps and reagents were generally as described in Example 2 above. It is expected that similar results would be obtained using, for example, nucleofection in place of Lipofectamine 2000.
Results for select, top-performing clones are shown in
This Example describes the construction of stable cell lines expressing leucyl suppressor tRNAs (including “wild-type” tRNA and h1 mutant leucyl tRNA) and leucyl tRNA-synthetases, and a comparison of their UAA incorporation activity.
Parallel cell line pools were generated with nucleofection as described in Example 2 above using pCLD-4×LeutRwt-LeuRS.v1-Puro (plasmid 1 of TABLE 2) or pCLD-4×LeutR.h1-LeuRS.v1-Puro (plasmid 1 of TABLE 2), with “wild-type” (wild-type other than any mutations in the anticodon region) leucyl tRNA or h1 mutant leucyl tRNA, each engineered to contain the CUA anticodon, in order to compare the effect of the “wild-type” versus h1 mutant leucyl tRNAs, respectively, on the efficiency of stable clone generation. Both pools were subjected to the same selection conditions (2 μg/mL puromycin). Clones were isolated without bias and analyzed via FACS analysis using an MG* reporter as described in Example 2 above.
Relative activity of the clones is shown in
This Example describes genomic copy number (GCN) analysis of stable cell lines expressing leucyl suppressor tRNAs (including “wild-type” tRNA and h1 mutant leucyl tRNA) and leucyl tRNA-synthetases, and a comparison of GCN and UAA incorporation activity in the cell lines.
A select group of clones from Examples 5 and 6 were analyzed for genomic copy number (GCN) by qPCR. Primers were designed to measure GCN of the leucyl suppressor tRNA (either “wild-type” or h1 mutant leucyl tRNA) or LeuRS.v1 synthetase, using B2M as a genomic control. GCN was measured at day 0 (t0) and day 60 (t60), with cells passaged routinely. Results are shown in
Together, these results demonstrate that stable cell lines expressing h1 mutant leucyl tRNA have higher UAA incorporation activity at lower GCN relative to stable cell lines expressing “wild-type” leucyl tRNA. It is expected that higher UAA incorporation activity at lower GCN has advantages for cell line development. For example, fewer integration sites result in less perturbation to the host genome, which is expected to result in improvements in cell growth and UAA incorporation/recombinant protein product.
The entire disclosure of each of the patent and scientific documents referred to herein is incorporated by reference for all purposes.
The invention may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. Scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.
This application claims the benefit of and priority to U.S. Provisional Patent Application Nos. 63/063,065, filed Aug. 7, 2020, and 63/210,593, filed Jun. 15, 2021, each of which are incorporated herein by reference in their entirety for all purposes.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/045088 | 8/6/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63210593 | Jun 2021 | US | |
| 63063065 | Aug 2020 | US |
