Patent Grant
11760982
This application is a National Stage Application of International Application No. PCT/EP2018/070479, filed Jul. 27, 2018; which claims priority to European Application No. 17306006.2, filed Jul. 27, 2017.
The present invention relates to the field of expression systems, particularly in eukaryotic cells.
In particular, the invention relates to a chimeric enzyme useful for the production of RNA molecules with 5′-terminal cap structures and preferably with a 3′ poly(A) tail.
In the eukaryotes, precursors of messenger RNA (mRNA), i.e. the pre-mRNAs, are synthesized by the RNA polymerase II and then undergoes multiple post-transcriptional modifications, which are required for their biological activities including translation, stability or immune response modulation. Two of these modifications are particularly critical for mRNA metabolism and its translation: the addition of a cap at their 5′-end and a polyadenylation tail at their 3′-end.
The capping is a specialized structure found at the 5′-end of nearly all eukaryotic messenger RNAs. The simplest cap structure, cap-0, results of the addition of a guanine nucleoside methylated at N7 that is joined by 5′-5′ triphosphate bound to the end of primary RNA (i.e. m7GpppN where N is any base, p denotes a phosphate and m a methyl group). In the so called canonical pathway, the formation of the cap-0 involves a series of three enzymatic reactions: RNA triphosphatase (RTPase) removes the γ phosphate residue of 5′ triphosphate end of nascent pre-mRNA to diphosphate, RNA guanylyltransferase (GTase) transfers GMP from GTP to the diphosphate 5′ end of nascent RNA terminus, and RNA N7-guanine methyltransferase (N7-MTase) adds a methyl residue on azote 7 of guanine to the GpppN cap (Furuichi and Shatkin 2000). In higher eukaryotes and some viruses, the 2′-hydroxyl group of the ribose of the first (i.e. cap-1 structures; m7GpppNm2′-OpN) and second (i.e. cap2 structures; m7 GpppNm2′-OpNm2′-O) transcribed nucleotides can be methylated by two separate ribose-2′-O MTases, respectively named cap1- and cap2-specific MTases (Langberg and Moss 1981). However, In contrast to the cellular N7-MTase activity that is exclusively nuclear, cap-1 ribose-2′-O MTase activity has been detected in both the cytoplasm and nucleus of HeLa cells, whereas cap2 MTase activity is exclusively found in their cytoplasm (Langberg and Moss 1981).
The formation of the 5′-terminal m7GpppN cap is the first step of pre-mRNA processing. The m7GpppN cap plays important roles in mRNA stability and its transport from the nucleus to the cytoplasm (Huang and Steitz 2005, Kohler and Hurt 2007). In addition, the 5′-terminal m7GpppN cap is important for the translation of mRNA to protein by anchoring the eukaryotic translation initiation factor 4F (eIF4F) complex, which mediates the recruitment of the 16S portion of the small ribosomal subunit to mRNA (Furuichi, LaFiandra et al. 1977, Gingras, Raught et al. 1999, Rhoads 1999). The 5′-terminal m7GpppN cap therefore enhances drastically the translation of mRNA both in vitro (Lo, Huang et al. 1998), and in cellulo (Malone, Feigner et al. 1989, Gallie 1991, Lo, Huang et al. 1998, Kozak 2005). The cap-0, cap-1 and cap-2 modifications participate in the innate immune response, by distinguishing self from non-self RNA through the RNA sensor RIG-1 and MDAS, which in turn induce an interferon type-I response (Hornung, Ellegast et al. 2006, Daffis, Szretter et al. 2010).
Since they are widely used in the life sciences, biotechnology and medicines, many expression systems have been designed to efficiently produce proteins and/or RNAs particularly in eukaryotic cells.
The inventor has developed in the past an artificial expression system (i.e. a chimeric enzyme) for efficient transgenesis in eukaryotic cells, which autonomously generates mRNA molecules, in particular in the cytoplasm of said cells (WO 2011/128444). Using this system, RNA chains are synthesized by RNA polymerase moiety of this chimeric enzyme and are capped at 5′-end by its mRNA capping enzyme moiety. In addition, a poly(A) tail can be produced at the 3′-end of transcripts by transcription of a polyadenosine track from DNA templates. This system has notably the advantage of not using the endogenous RNA transcription machinery of eukaryotic cells, e.g. RNA polymerase II and associated factors involved in transcription and post-transcription.
Other attempts to couple capping to transcription and thus to improve the translatability of uncapped transcripts produced by the T7 RNA polymerase by fusing the carboxyl-terminal domain (CTD) of the largest subunit of the RNA polymerase II (POLR2A), have to enhance the capping of both constitutively and alternatively spliced substrates in cellulo (Kaneko, Chu et al. 2007, Natalizio, Robson-Dixon et al. 2009). The CTD comprises 25-52 heptapeptide repeats of the consensus sequence 1YSPTSPS7, which is highly conserved throughout evolution and subject to reversible phosphorylation during the transcription cycle (Palancade and Bensaude 2003). When phosphorylated, the CTD is thought to mediate the coupling of transcription and capping of nascent transcripts, by binding one or more subunits of the mRNA capping enzymes in yeast (Cho, Takagi et al. 1997, McCracken, Fong et al. 1997) and mammals (McCracken, Fong et al. 1997, Yue, Maldonado et al. 1997). Noticeably, RNA polymerase II with Ser5-phosphorylated CTD repeats undergoes promoter proximal pausing which is coincident with the co-transcriptional capping of the nascent transcripts (Komarnitsky, Cho et al. 2000, Schroeder, Schwer et al. 2000). However, in contrast to what could be expected intuitively, the fusion of the CTD to the single-unit T7 RNA polymerase is not sufficient to enhance the capping of both constitutively and alternatively spliced substrates in vivo (Kaneko, Chu et al. 2007, Natalizio, Robson-Dixon et al. 2009).
There remains therefore a significant need in the art for new and improved expression systems, in particular in eukaryotic cells, which are appropriate for gene therapy and large-scale protein production without cytotoxicity or induced-cytotoxicity. The present inventor has made a significant step forward with the invention disclosed herein.
The purpose of the invention is to fulfill this need by providing new chimeric enzymes, which make it possible to solve in whole or part the problems mentioned-above.
Unexpectedly, the inventor has notably demonstrated that monomeric or oligomeric chimeric (non-natural) enzymes comprising catalytic domains of a capping enzyme, particularly a catalytic domain of a RNA triphosphatase, a catalytic domain of a guanylyltransferase, a catalytic domain of a N7-guanine methyltransferase, and a RNA-binding domain of a protein-RNA tethering system, said RNA-binding domain binding specifically to a RNA element consisting of a specific RNA sequence and/or structure, allows to highly increase the capping rate of specific mRNAs produced by a RNA polymerase.
These results are surprising since the formation of the cap is a complex process and that the capping of exogenous transcripts cannot be achieved by most other approaches, such as the fusion enzyme CTD-T7 RNA polymerase (Kaneko, Chu et al. 2007, Natalizio, Robson-Dixon et al. 2009).
The U.S. Pat. No. 5,866,680 suggests but without any demonstration the use of the nuclear 70K RNA binding-domain to direct RNA modifying activity to specific site in RNAs including different enzymes such as RNA capping enzymes.
Unexpectedly, the inventor has also demonstrated that cytoplasmic monomeric or oligomeric chimeric enzymes comprising catalytic domains of a capping enzyme and a bacteriophage RNA-binding domain of a bacteriophage protein-RNA tethering system allows to highly increase the capping rate of specific mRNAs produced by a bacteriophage DNA-dependant RNA polymerase, compared to other RNA-binding domains of protein-RNA tethering systems, such as the U1-RNA 70K (also known as SNRNP70)-U1snRNA system described in said U.S. Pat. No. 5,866,680.
The inventor has also demonstrated that surprisingly monomeric or oligomeric chimeric enzymes comprising catalytic domains of a capping enzyme, a RNA-binding domain of a protein-RNA tethering system and catalytic domain of a poly(A) polymerase, allows to highly increase, synergistically, the capping rate of specific mRNAs produced by RNA polymerase, compared to the combination of a capping enzyme fused to a RNA-binding domain in presence of a poly(A) polymerase fused to a RNA-binding domain. These results are unexpected since capping enzymes and poly(A) polymerases are not physically linked in the nature and contain no known predicted binding domain for a specific RNA sequence. One skilled in the art could have expected to obtain the same expression rate since the components are the same.
Thus, in one aspect, the invention relates to a chimeric enzyme, in particular cytoplasmic, comprising or consisting of:
The chimeric enzyme according to the invention has in particular the following advantages:
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one skilled in the relevant art.
For convenience, the meaning of certain terms and phrases employed in the specification, examples, and claims are provided.
As used herein, the term “chimeric enzyme” refers to an enzyme that is not a native enzyme found in the nature (that is non-natural). Accordingly, a chimeric enzyme may comprise catalytic domains that are derived from different sources (e.g. from different enzymes) or catalytic domains derived from the same source (e.g. from the same enzyme), but arranged in a different manner than that found in nature.
The term “chimeric enzyme” encompasses monomeric (i.e. single-unit) enzyme but also oligomeric (i.e. multi-unit) enzyme, in particular hetero-oligomeric enzyme.
More specifically, the term “chimeric enzyme” may encompasses an enzyme that comprises or consists of a RNA-binding domain of a protein-RNA tethering system linked covalently or noncovalently with one (i.e. single unit) or several (i.e. multi-unit) catalytic domain(s) (at least one catalytic domain of a capping enzyme) or protein(s) (at least one capping enzyme).
The term “catalytic domain” of an enzyme relates to a protein domain, which is necessary and sufficient, in particular in its three-dimensional structure, to assure the enzymatic function. For example, a catalytic domain of a RNA triphosphatase is the domain, which is necessary and sufficient to assure the RNA triphosphatase function. The term “catalytic domain” encompasses catalytic domain of wild type or mutant enzyme.
The term “protein domain” defines distinct functional and/or structural building blocks and elements in a protein which folds and functions independently.
In particular, the chimeric enzyme according to the invention is a monomeric or oligomeric non-natural enzyme.
As used herein, the term “monomeric enzyme” relates to a single-unit enzyme that consists of only one polypeptide chain.
As used herein, the term “oligomeric enzyme” refers to a multi-unit enzyme that consists of at least two polypeptides chains, linked together covalently or noncovalently. The term “oligomeric enzyme” encompasses a multi-unit enzyme, wherein at least two units of said enzyme are linked together covalently or noncovalently. The term “oligomeric enzyme” encompasses homo-oligomeric enzyme that is a multi-unit enzyme consisting of only one type of monomers (subunits) and hetero-oligomeric enzyme consisting of different types of monomers (subunits).
As used herein, the term “protein-RNA tethering system” refers to a system wherein a protein (or a peptide) recognizes and specifically binds (with high affinity) via its RNA-binding domain to a specific RNA element consisting of a specific RNA sequence and/or structure, therefore making possible to tether this protein (or peptide) with this RNA element. The specific binding between the protein (or the peptide) via its RNA binding domain and the specific RNA element implies that the protein (or peptide) and the specific RNA element interact with high affinity. Interaction with high affinity includes interaction with an affinity of about 10−6 M or stronger, in particular at least 10−7M, at least 10−8M, at least 10−9M and more particularly at least 10−10 M. Whether a RNA-binding domain specifically binds with high affinity to a specific RNA element can be tested readily by, inter alia, comparing the reaction of said RNA-binding domain with a specific RNA element with the reaction of said RNA-binding domain with RNA other than the specific RNA element.
The RNA-protein affinity can be determined by various methods, well known by one skilled in the art. These methods include, but are not limited to, steady-state fluorescence or electrophoretic measurements, RNA electrophoretic mobility shift assay.
As used herein, the term “RNA-binding domain of a protein-RNA tethering system” refers to the domain of a protein (or a peptide) which is necessary and sufficient, in particular in its three-dimensional structure, to assure the recognition and the interaction with high affinity with a specific RNA element consisting of a specific RNA sequence and/or structure, therefore making possible to tether this protein (or peptide) via said RNA-binding domain with this RNA element. Thus, said “RNA-binding domain” (RNA-tethering domain) binds to RNA with sequence and/or structure specificity, i.e. binds specifically to a RNA element consisting of a specific RNA sequence and/or structure. The term “RNA-binding domain of a protein-RNA tethering system” encompasses RNA-biding domain of wild type or mutant protein (or peptide).
The chimeric enzyme according to the invention comprises at least said RNA-binding domain but can further comprise the whole or part of the protein (or peptide) containing said RNA-binding domain. In fact, according to one embodiment of the chimeric enzyme according to the invention, said RNA-binding domain of a protein-RNA tethering system can be included in the whole or part of a protein (or a peptide) of a protein-RNA tethering system.
Some characterized protein-RNA tethering systems include bacteriophage protein-RNA tethering systems such as the MS2 coat protein-RNA tethering system, the R17 coat protein-RNA tethering system and the lambdoid N antitermination protein-RNA tethering systems. The MS2 coat protein and the R17 coat protein recognize and interact with high affinity with specific RNA elements consisting of stem-loop RNA structures (Valegard, Murray et al. 1994, Valegard, Murray et al. 1997). The lambdoid N antitermination protein-RNA tethering systems recognize and interact with high affinity with specific RNA elements consisting of boxBL and boxBR stem loop RNA structures (Das 1993, Greenblatt, Nodwell et al. 1993, Friedman and Court 1995). The bacteriophages characterized so far that belong either to the lambdoid family (i.e. λ, P22, ϕ21, HK97 and 933W viruses) or the MS2-related family (i.e. MS2, and R17).
Other well-characterized protein-RNA tethering systems include: (a) TAT binding domain from the Human immunodeficiency virus-1 (HIV-1; e.g. NCBI reference sequence ABY50660.1) (Dingwall, Ernberg et al. 1990, Weeks, Ampe et al. 1990, Karn, Dingwall et al. 1991, Puglisi, Tan et al. 1992, Frankel and Young 1998) and Bovine Immunodeficiency Virus (Puglisi, Chen et al. 1995), (b) Rev protein from HIV-1 and mutants (e.g. UniProtKB P69718) bind to the Rev-binding element (RBE), a short stem-internal stem-loop structure (Karn, Dingwall et al. 1991, Tan and Frankel 1995, Battiste, Mao et al. 1996, Frankel and Young 1998), (c) Jembrana disease virus Tat protein (UniProtKB Q82854) bind its own TAR protein, as well as TAR proteins from human and bovine immunodeficiency viruses (Smith, Calabro et al. 2000), (d) Iron regulatory proteins, such as the iron-responsive element-binding protein 1 (IREB1, e.g. UniProtKB P21399) and 2 (IREB2, e.g. UniProtKB P48200), which bind iron-responsive elements within 5′UTR or 3′UTR of iron metabolism mRNAs (Theil 1994, Rouault 2006), (e) Brome mosaic virus (BMV) coat protein (UniProtKB Q5KSV1_BMV) binds an hairpin of the MP coding region required for packaging of viral RNA (Sacher and Ahlquist 1989, Choi and Rao 2003), (f) U1A small nuclear ribonucleoprotein subunit 70K (SNRNP70), which binds with high specificity and affinity to a 30-nucleotide RNA hairpin within the 3′UTR of U1snRNA (Keene, Query et al. 1999), (g) SLBP (stem-loop binding protein UniProtKB Q14493) that binds the stem-loop structure in the 3′UTR of histone pre-mRNAs (Marzluff, Wagner et al. 2008), (h) 60S ribosomal protein L7 (e.g. UniProtKB P18124) that binds to G-rich structures in 28S rRNA (Hemmerich, Bosbach et al. 1997), (i) Cowpea chlorotic mottle virus capsid protein (UniProtKB P03601) that binds an hairpin required for packaging of viral RNA (Annamalai, Apte et al. 2005), (j) human T-cell leukemia virus type I (HTLV-1) rex protein and related mutants (e.g. HTLV-1 isolate Caribbea HS-35 subtype A, UniProtKB P0C206), which bind to rex-response element (RxRE) located in the 3′ long terminal repeat of all human T-cell leukemia virus type I-specific mRNAs (Ballaun, Farrington et al. 1991, Jiang, Gorin et al. 1999), (j) HTLV-2 Rex protein (UniProtKB Q85601) that binds 5′ long terminal repeat RNA (Yip, Dynan et al. 1991), (m) RNA splicing component U2 snRNP auxiliary factor U2AF65 (e.g. UniProtKB P26368) that binds a polypyrimidine tract that precedes 3′ splice sites of pre-mRNA (Zamore, Patton et al. 1992, Banerjee, Rahn et al. 2004), (n) bacterial ribosomal protein S7 (UniProtKB P02359) that binds to the lower half of the 3′ major domain of 16S ribosomal RNA (Robert, Gagnon et al. 2000), (o) the archeal L7Ae protein binds to RNA containing a kink-turn with nanomolar affinity (Turner, Melcher et al. 2005, Ye, Yang et al. 2013), (p) RNA binding dormain from the SELENBP2 gene product (Selenium Binding Protein 2, SBP2) binds to the SECIS element in the 3′-UTR of some mRNAs encoding selenoproteins (Mix, Lobanov et al. 2007), (q) the N-terminal domain of Brome mosaic virus (BMV) that can bind a BoxB (Yi, Vaughan et al. 2009), (r) the N-terminus of gp10 head-tail connector which binds ϕ29 pRNA sequence (Xiao, Moll et al. 2005), (s) Streptavidin that binds the artificial RNA aptamer (Leppek and Stoecklin 2014).
In one embodiment of the chimeric enzyme according to the invention, said RNA-binding domain is a bacteriophage RNA-binding domain of a bacteriophage protein-RNA tethering system, in particular selected in the group consisting of: the MS2 coat protein-RNA tethering system, the R17 coat protein-RNA tethering system and the lambdoid N antitermination protein-RNA tethering systems, more particularly the lambdoid N antitermination protein-RNA tethering systems selected from the group consisting of the lambda N antitermination protein-RNA tethering system, the phi21 N antitermination protein-RNA tethering system, the HK97 N antitermination protein-RNA tethering system and the p22 N antitermination protein-RNA tethering system, and even more particularly the lambda N antitermination protein-RNA tethering system.
Particularly, when the chimeric enzyme of the invention is used to add a 5′-terminal cap to an RNA molecule synthetized by a bacteriophage DNA-dependent polymerase (comprised or not in said chimeric enzyme), said RNA-binding domain is a bacteriophage RNA-binding domain of a bacteriophage protein-RNA tethering system.
In fact, unexpectedly, the inventor has demonstrated that cytoplasmic monomeric or oligomeric chimeric enzymes comprising catalytic domains of a capping enzyme and a bacteriophage RNA-binding domain of a bacteriophage protein-RNA tethering system allows to highly increase the capping rate of specific mRNAs produced by a bacteriophage DNA-dependant RNA polymerase, compared to other RNA-binding domains of protein-RNA tethering systems, including the U1-RNA 70K system described in the U.S. Pat. No. 5,866,680.
In particular, said RNA-binding domain is a bacteriophage RNA-binding domain of a bacteriophage protein selected in the group consisting of: the wild type MS2 coat protein (NCBI accession number NC_001417.2, UniProtKB/Swiss-Prot P03612), the wild type R17 coat protein (NCBI accession numbers EF108465.1, UniProtKB/Swiss-Prot P69170) and the wild type lambdoid N antitermination proteins and mutants and derivatives thereof which are able to recognize and interact with high affinity with the specific RNA element, more particularly the wild type lambdoid N antitermination proteins selected from the group consisting of the wild type lambda N antitermination protein (NCBI accession number NC_001416.1, complete genome sequence; UniProtKB/Swiss-Prot accession number P03045), the wild type phi21 N antitermination protein (NCBI accession number AH007390.1, partial genome sequence; UniProtKB/Swiss-Prot accession number P07243), the wild type HK97 N antitermination protein-RNA tethering system (NCBI accession number NC_002167.1, complete genome sequence; NCBI protein accession number NP_037732.1) and the wild type p22 N antitermination protein (particularly NCBI sequence (NCBI accession number NC_002371.2, complete genome sequence; UniProtKB/Swiss-Prot accession number P04891), and even more particularly the wild type lambda N antitermination protein (NCBI accession number NC_001416.1, complete genome sequence; UniProtKB/Swiss-Prot accession number P03045).
The entire or nearly entire MS2/R17 proteins are needed for proficient binding to the tethered RNA, since multiple amino-acid residues spread in these proteins are involved in stem-loop interaction (Valegard, Murray et al. 1994, Valegard, Murray et al. 1997).
So, in one embodiment, the chimeric enzyme of the invention comprises the wild type MS2 coat protein (NCBI accession number NC_001417.2, UniProtKB/Swiss-Prot P03612) or its isolate the wild type R17 coat protein (NCBI accession numbers EF108465.1, UniProtKB/Swiss-Prot P69170), or a mutant or derivative thereof which is able to recognize and interact with high affinity with the specific RNA element.
Importantly, the 18- to 22-amino-acid region from the N-terminal sequences of the lambdoid N-proteins bind to cognate RNA sequences with an affinity and specificity similar to that of the full-length N-proteins (Franklin 1985, Cilley and Williamson 1997).
In one embodiment of the chimeric of the invention, said RNA-binding domain of a protein-RNA tethering system comprising or consisting of the peptide consisting of amino acids at position 1 to 22, in particular 1 to 18 of the wild type lambda N antitermination protein (NCBI accession number NC_001416.1, complete genome sequence; UniProtKB/Swiss-Prot accession number P03045), or of the wild type phi21 N antitermination protein (NCBI accession number AH007390.1, partial genome sequence; UniProtKB/Swiss-Prot accession number P07243), or of the wild type HK97 N antitermination protein-RNA tethering system (NCBI accession number NC_002167.1, complete genome sequence; NCBI protein accession number NP_037732.1) or of the wild type P22 N antitermination protein (NCBI accession number NC_002371.2, complete genome sequence; UniProtKB/Swiss-Prot accession number P04891) or a mutant or derivative thereof which is able to recognize and interact with high affinity with the specific RNA element, particularly of the wild type lambda N antitermination protein (NCBI accession number NC_001416.1, complete genome sequence; UniProtKB/Swiss-Prot accession number P03045).
In particular, said RNA-binding domain of a protein-RNA tethering system comprising or consisting of the peptide consisting of amino acids at position 1 to 22, of the wild type lambda N antitermination protein (NCBI accession number NC_001416.1, complete genome sequence; UniProtKB/Swiss-Prot accession number P03045), in particular SEQ ID No 2, preferably encoded by SEQ ID No 1.
In particular, said RNA-binding domain of a protein-RNA tethering system does not derive from the same source (e.g. from the same enzyme) than the different catalytic domains of the chimeric enzyme of the invention.
The chimeric enzyme according to the invention can be a nuclear enzyme, a subcellular compartment enzyme or a cytoplasmic enzyme. Thus, the chimeric enzyme according to the invention can comprise a signal peptide well known by one skilled in the art, which directs the transport of the enzyme in cells. For example, the chimeric enzyme according to the invention can comprise a nuclear localization signal (NLS), which directs the enzyme to the nucleus. Such NLS is often a unit consisting of five basic, plus-charged amino acids. The NLS can be located anywhere on the peptide chain.
Preferably, the chimeric enzyme according to the invention is a cytoplasmic chimeric enzyme. In particular, it does not comprise signal peptide that directs the transport of the enzyme, except to the cytoplasm.
The cytoplasmic localization of the chimeric enzyme according to the invention has the advantage that it optimizes the levels of transgene expression by avoiding the active transfer of large DNA molecules (i.e. transgene) from the cytoplasm to the nucleus of eukaryotic cells and the export of RNA molecules from the nucleus to the cytoplasm.
These cytoplasmic chimeric enzymes according to the invention can thus be useful to generate a host-independent, eukaryotic gene expression system that is able to work in the cytoplasm in which significantly higher amounts of transfected DNA are usually found as compared to the nucleus.
There is no competition between the endogenous gene transcription and the transgene transcription, since the endogenous gene transcription occurs in the nucleus of eukaryotic cells in contrast to the transgene transcription, which occurs in the cytoplasm.
The cytoplasmic chimeric enzyme according to the invention is thus notably appropriate for large-scale assays and protein production.
As used herein, the term “capping enzyme” refers to any enzyme able to add a m7 GpppG cap at 5′-end of mRNA and/or to modify the ultimate or penultimate bases of a RNA sequence, including cap-0 canonical or non-canonical capping enzymes and cap-1 or cap-2 nucleoside 2′ methyltransferases, N6-methyl-adenosine transferase.
As used herein, the term “cap-0 canonical capping enzymes” refers to enzymes able to add cap-0 structure at the 5′end of RNA molecules by involving a series of three enzymatic reactions: RNA triphosphatase (RTPase) that removes the γ phosphate residue of 5′ triphosphate end of nascent pre-mRNA to diphosphate ppRNA, RNA guanylyltransferase (GTase) that transfers GMP from GTP to the diphosphate ppRNA nascent RNA terminus, and RNA N7-guanine methyltransferase (N7-MTase) that adds a methyl residue on nitrogen 7 of guanine to the GpppRNA cap (Furuichi and Shatkin 2000).
The enzymatic domains of eukaryotic organisms and viruses, which are involved in the canonical formation of cap-0 structure, can be assembled in a variable number of protein subunits:
As used herein, the term “cap-0 non canonical capping enzymes” refers to enzymes able to add a cap-0 structure at the 5′ end of RNA molecules but in a pathway which differs from the canonical enzymatic process. As of today, three non-canonical 5′ RNA cap synthesis mechanisms have been described:
As used herein, the term “cap-1 capping enzymes” refers to enzymes able to add cap-1 structure at the 5′end of RNA molecules.
As used herein, the term “cap-2 capping enzymes” refers to enzymes able to add cap-2 structure at the 5′end of RNA molecules.
In mammalians, higher eukaryotes and some viruses, two cap modifications are found, which are lacking in yeast and plant mRNAs (Langberg and Moss 1981) and are generated by methylation of the 2′ hydroxy-groups of the ribose moiety of nucleotides at the 5′ end of the mRNA: cap-1 at the first mRNA nucleotide, and cap-2 at the second one. Cap-1 methylation is found on nearly all mammalian mRNA molecules, while only half of the mRNA contain a 2′-O-methylated residue on the second transcribed nucleotide.
In mammalians, cap-1 and cap-2 modifications are performed by two ribose-2′-O methyltransferases, (also named nucleoside-2′-methyltransferase or 2′-O-MTases) (Belanger, Stepinski et al. 2010). Firstly, MTR1 (cap-1 ribose-2′-O MTase activity, also named FTSJD2, KIAA0082 or ISG95; UniProtKB/Swiss-Prot accession number Q8N1G2), which is exclusively found in the nucleus and contains a putative nuclear localization signal and a G-patch domain that is potentially involved in RNA binding (Haline-Vaz, Silva et al. 2008). Noticeably, MRT1 associates with the CTD of RNA polymerase II, which indicate that cap-1 formation occurs early in the synthesis of mRNA (Langberg and Moss 1981). Secondly, MTR2 (cap 2 ribose-2′-O MTase, also named FTSJD1 or FLJ11171; UniProtKB/Swiss-Prot accession number Q8IYT2) transfers a methyl group from S-adenosylmethionine to the 2′-O-ribose of the second nucleotide of mRNA and small nuclear RNA. Nor N7 methylation of the guanosine cap-0 or cap-1 modification is required for MTR2, but the presence of cap-1 increases MTR2 activity. The MTR2 protein is distributed throughout the nucleus and cytosol, in contrast to the nuclear MTR1 (Keith, Ensinger et al. 1978).
Some eukaryotic viruses have their own cap-1 and/or cap-2 2′-O-MTases, including:
In one embodiment, the chimeric enzyme according to the invention comprises or consists of:
As used herein, the term “RNA triphosphatase” (RTPase) relates to the enzyme, which removes the γ phosphate residue of 5′ triphosphate end of nascent pre-mRNA to diphosphate (Furuichi and Shatkin 2000).
As used herein, the term “RNA guanylyltransferase” (GTase) refers to the enzyme, which transfers GMP from GTP to the diphosphate nascent RNA terminus (Furuichi and Shatkin 2000).
As used herein, the term “N7-guanine methyltransferase” (N7-MTase) relates to the enzyme, which adds a methyl residue on azote 7 of guanine to the GpppN cap (Furuichi and Shatkin 2000).
Said catalytic domains of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase, can be of the same or of different capping enzymes.
Preferably, said catalytic domains of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase are from one or several cytoplasmic enzymes, which have advantageously relatively simple structure and well-characterized enzymatic activities. Thus, in particular, said catalytic domains of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase can be catalytic domains of one or several virus capping enzymes, or of capping enzymes of cytoplasmic episomes.
In one embodiment, said catalytic domains of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase are from one or several virus capping enzymes, in particular selected in the group consisting of the wild type vaccinia virus capping enzyme, the wild type bluetongue virus capping enzyme, the wild type bamboo mosaic virus capping enzyme, the wild type African swine fever virus capping enzyme, the wild type Acanthamoeba polyphaga mimivirus capping enzyme, the wild type Organic Lake phycodnavirus 1 (OLPV1) capping enzyme, the wild type Organic Lake phycodnavirus 2 (OLPV2) capping enzyme, the wild type Phaeocystis globosa virus capping enzyme, the wild type Chrysochromulina ericina virus capping enzyme and mutants or derivatives thereof which are able respectively to remove the γ phosphate residue of 5′ triphosphate end of nascent pre-mRNA to diphosphate or transfer GMP from GTP to the diphosphate nascent RNA terminus or add a methyl residue on azote 7 of guanine to the GpppN cap, more particularly of the wild type African swine fever virus capping enzyme and mutants or derivatives thereof which are able respectively to remove the γ phosphate residue of 5′ triphosphate end of nascent pre-mRNA to diphosphate or transfer GMP from GTP to the diphosphate nascent RNA terminus or add a methyl residue on azote 7 of guanine to the GpppN cap.
As used herein the term “vaccinia virus capping enzyme” relates to the heterodimeric D1R/D12L capping enzyme of vaccinia virus. The D1R gene product having RTPase, GTase and N7-MTase enzymatic domains (Cong and Shuman 1993, Niles and Christen 1993, Mao and Shuman 1994, Cong and Shuman 1995, Mao and Shuman 1996, Myette and Niles 1996, Yu and Shuman 1996, Yu, Martins et al. 1997, Gong and Shuman 2003) (genomic sequence strain Western Reserve NC_006998.1; UniProtKB/Swiss-Prot accession number P04298) and D12L gene product that has no intrinsic enzymatic activity but enhances drastically the RNA N7-MTase activity of the D1R subunit (Higman, Bourgeois et al. 1992, Higman, Christen et al. 1994, Mao and Shuman 1994, Schwer, Hausmann et al. 2006, De la Pena, Kyrieleis et al. 2007) (genomic sequence strain Western Reserve NC_006998.1; Gene 3707515; UniProtKB/Swiss-Prot accession number P04318).
As used herein the term “bluetongue virus capping enzyme” relates to the single-unit VP4 capping enzyme of Bluetongue virus (BTV), which is a 76 kDa protein (644 amino-acids; for sequence, see for instance NCBI BTV serotype 10 genomic sequence Y00421; Gene 2943157; UniProtKB/Swiss-Prot P07132). This capping enzyme is likely able to homodimerize through the leucine zipper located near its carboxyl-terminus (Ramadevi, Rodriguez et al. 1998). VP4 catalyze all three enzymatic steps required for mRNA m7GpppN capping synthesis: RTPase (Martinez-Costas, Sutton et al. 1998), GTase (Martinez-Costas, Sutton et al. 1998, Ramadevi, Burroughs et al. 1998) and N7-MTase (Ramadevi, Burroughs et al. 1998).
As used herein, the term “bamboo mosaic virus capping enzyme” relates to ORF1, the Bamboo Mosaic Virus (BMV) mRNA capping enzyme, which is a single-unit 155-kDa protein (1365-amino acids; NCBI BMV isolate BaMV-O genomic sequence NC_001642; Gene 1497253; UniProtKB/Swiss-Prot Q65005). ORF1 protein has all the enzymatic activities required to generate m7GpppN mRNA capping, i.e. RTPase (Li, Shih et al. 2001, Han, Tsai et al. 2007), GTase and N7-MTase (Li, Chen et al. 2001, Li, Shih et al. 2001).
As used herein, the term “African swine fever virus capping enzyme” (ASFV) relates to the NP868R capping enzyme (G4R), which is a single-unit 100 kDa protein (868 amino-acids; NCBI ASFV genomic sequence strain BA71V NC_001659; Gene 1488865; UniProtKB/Swiss-Prot P32094), which has all the enzymatic activities required to generate m7GpppN mRNA capping, i.e. RTPase, GTase and N7-MTase (Pena, Yanez et al. 1993, Jais 2011, Dixon, Chapman et al. 2013, Jais, Decroly et al. 2018).
As used herein, the term “Acanthamoeba Polyphaga mimivirus capping enzyme” relates to R382, (APMV), which is another single-unit 136.5 kDa protein (1170 amino-acids; NCBI APMV genomic sequence NC_006450; Gene 3162607; UniProtKB/Swiss-Prot Q5UQX1).
As used herein, the term “Organic Lake phycodnavirus 1 (OLPV1) capping enzyme” refers to a 889 single-unit amino-acids, as referenced with NCBI accession number ADX05869.1.
As used herein, the term “Organic Lake phycodnavirus 2 (OLPV2) capping enzyme” refers to a 942 single-unit amino-acids, as referenced with NCBI accession number ADX06468.1.
As used herein, the term “Phaeocystis globosa virus capping enzyme” refers to a 1066 single-unit amino-acids as referenced with UniProtKB/Swiss-Prot YP_008052553.1.
As used herein, the term “Chrysochromulina ericina virus capping enzyme” refers to a 965 single-unit amino-acids as referenced with UniProtKB/Swiss-Prot YP_009173557.1.
In one embodiment, said catalytic domains of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase are from the capping enzymes of cytoplasmic episomes, like pGKL2. In particular, said catalytic domains of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase are included in the whole or part of the capping enzyme of the yeast linear extra-chromosomal episome pGKL2 encoded by the ORF3 gene of Kluyveromyces lactis pGKL2 (NCBI Kluyveromyces lactis CB 2359 pGKL2 genomic sequence NC_010187; UniProtKB/Swiss-Prot P05469) and which is a 594 amino-acid protein (70.6 kDa protein).
In one embodiment of the chimeric enzyme according to the invention, said catalytic domain of a RNA triphosphatase, said catalytic domain of a guanylyltransferase, said catalytic domain of a N7-guanine methyltransferase, are included in a monomer, i.e. in one polypeptide. For example, said monomer can be a monomeric capping enzyme or a monomeric chimeric enzyme according to the invention.
In particular, said catalytic domain of a RNA triphosphatase, said catalytic domain of a guanylyltransferase, and said catalytic domain of a N7-guanine methyltransferase are included in a monomeric capping enzyme. In this case, the chimeric enzyme according to the invention comprise a monomeric capping enzyme, which includes said catalytic domain of a RNA triphosphatase, said catalytic domain of a guanylyltransferase, and said catalytic domain of a N7-guanine methyltransferase. Said monomeric capping enzyme can be a monomeric virus capping enzyme, in particular selected in the group consisting of the wild type bluetongue virus capping enzyme, the wild type bamboo mosaic virus capping enzyme, the wild type African swine fever virus capping enzyme, the wild type Acanthamoeba polyphaga mimivirus capping enzyme, the wild type OLPV1 capping enzyme, the wild type OLPV2 capping enzyme, the wild type Phaeocystis globosa virus capping enzyme, the wild type Chrysochromulina ericina virus capping enzyme and mutants and derivatives thereof which are able to add a m7GpppN cap at the 5′-terminal end of RNA molecules and, more particularly of the wild type African swine fever virus capping enzyme and mutants and derivatives thereof which are able to add a m7GpppN cap at the 5′-terminal end of RNA molecules, and even more particularly the wild type African swine fever virus capping enzyme
The chimeric enzyme according to the invention can also further comprise a domain, which enhances the activity of at least one catalytic domain of the chimeric enzyme of the invention, in particular of at least one catalytic domain of a capping enzyme, more particularly of at least one catalytic domain selected in the group consisting of a catalytic domain of a RNA triphosphatase, a catalytic domain of a guanylyltransferase, a catalytic domain of a N7-guanine methyltransferase, preferably of a N7-guanine methyltransferase.
For example said domain, which enhance the activity of at least one catalytic domain of the chimeric enzyme of the invention, can be a 31-kDa subunit encoded by the vaccinia virus D12L gene (genomic sequence NC_006998.1; Gene3707515; UniProtKB/Swiss-Prot YP_232999.1), which has no intrinsic enzymatic activity, but enhances drastically the RNA N7-guanine methyltransferase activity of the D1R subunit of the vaccinia mRNA capping enzyme (Higman, Bourgeois et al. 1992, Higman, Christen et al. 1994, Mao and Shuman 1994).
In one embodiment, the chimeric enzyme according to the invention further comprises at least one catalytic domain of a 5′-end RNA processing enzyme other than cap-0, cap-1 and cap-2 capping enzymes.
As used herein, the term “5′-end RNA processing enzyme other than cap-0, cap-1 and cap-2 capping enzymes” relates to enzymes able to modify the ultimate or penultimate bases of a mRNA sequence, other than cap-0, cap-1 and cap-2 capping enzymes, including N6-methyl-adenosine transferase and enzymes able to add 2,2,7-trimethylguanosine (TMG) and 2,7-trimethylguanosine (DMG) cap modifications at the 5′end of RNA molecules.
Other capping modifications than cap-0, cap-1, cap-2 modifications have been characterized in eukaryotes or viruses mRNA. For instance, the m6A methylation by N6-methyl-adenosine transferase of the first base is a reversible modification that influences cellular mRNA fate (Mauer, Luo et al. 2017). 2,2,7-trimethylguanosine (TMG) and 2,7-trimethylguanosine (DMG) cap modifications, which are present on snRNAs, telomerase RNAs, trans-spliced nematode mRNAs and certain viral mRNAs, can confer an advantage of translation (Darzynkiewicz, Stepinski et al. 1988, Cai, Jankowska-Anyszka et al. 1999). TMG and DMG are performed by specialized enzymes from viruses (e.g. L320 from DNA mimivirus, UniProtKB/Swiss-Prot accession number Q5UQR2 (Benarroch, Qiu et al. 2009); protozoan (e.g. Giardia lamblia trimethylguanosine synthase (NCBI accession number EAA46438 (Hausmann and Shuman 2005); lower eukaryotes (e.g. Schizosaccharomyces pombe trimethylguanosine synthase, UniProtKB/Swiss-Prot accession number Q09814 (Hausmann and Shuman 2005, Hausmann, Zheng et al. 2008, Benarroch, Jankowska-Anyszka et al. 2010) and mammalian (e.g. human trimethylguanosine synthase 1 UniProtKB/Swiss-Prot accession number Q96RS0 (Zhu, Qi et al. 2001, Hausmann, Zheng et al. 2008, Benarroch, Jankowska-Anyszka et al. 2010).
In one embodiment, the chimeric enzyme according to the invention further comprises at least one catalytic domain of a poly(A) polymerase.
In fact, unexpectidely, the inventor has demonstrated that monomeric or oligomeric chimeric enzymes comprising at least one catalytic domain of a capping enzyme, at least one RNA-binding domain of a protein-RNA tethering system and at least one catalytic domain of a poly(A) polymerase allows to highly increase, synergistically, the capping rate of specific mRNAs produced by RNA polymerase, compared to the combination of a capping enzyme fused to a RNA-binding domain in presence of a poly(A) polymerase fused to a RNA-binding domain. These results are unexpected since capping enzymes and poly(A) polymerases are not physically linked in the nature and contain no binding domain for a specific RNA sequence. One skilled in the art could have expected to obtain the same expression rate since the components are the same.
As used herein, the term “poly(A) polymerase” relates to any enzyme able to catalyze the non-templated addition of adenosine residues from ATP onto the 3′ end of RNA molecules.
In one embodiment, said catalytic domain of a poly(A) polymerase is a catalytic domain of a canonical poly(A) polymerase including mammalian (such as PAPOLA, PAPOLG), yeast, (such as Saccharomyces cerevisiae PAP1, Schizosaccharomyces pombe PLA1, Candida albicans PAP, Pneumocystis carinii PAP), protozoan, viral and bacterial canonical poly(A) polymerases.
In particular said catalytic domain of a poly(A) polymerase is a cytoplasmic canonical poly(A) polymerase, more particularly selected in the group consisting of:
In still another embodiment, said catalytic domain of a poly(A) polymerase is a catalytic domain of a non-canonical poly(A) polymerase, in particular of a cytoplasmic non-canonical poly(A) polymerase. “noncanonical poly(A) polymerases”, refers to enzymes, that do not have a tripartite structure involving a N-terminal nucleotidyltransferase (NT) catalytic domain, a central domain, and a C-terminal domain corresponding to the RNA binding domain (RBD) (Trippe, Sandrock et al. 1998). As of today, the following non-canonical poly(A) polymerases have been described in mammalians:
In an embodiment, said catalytic domain of a poly(A) polymerase is a catalytic domain of a yeast or protozoan poly(A) polymerase, in particular selected in the group consisting of the wild type Saccharomyces cerevisiae PAP1 poly(A) polymerase, Schizosaccharomyces pombe PLA1, Candida albicans PAP (UniProtKB/Swiss-Prot accession number Q9UW26), Pneumocystis carinii PAP (UniProtKB/Swiss-Prot accession number A0A0W4ZDF2), the cytoplasmic mutants of the Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans or Pneumocystis carinii poly(A) polymerases (wherein the nuclear localization signal is non-functional or deleted) and mutants or derivatives thereof, which are able to catalyze the non-templated addition of adenosine residues from ATP onto the 3′ end of RNA molecules.
The yeast or protozoan poly(A) polymerases have notably the advantage of its reduced molecular weight in comparison to mammalian canonical poly(A) polymerases (e.g. 568 and 566 amino-acids vs. 745 amino-acids for the Saccharomyces cerevisiae PAP1 and Schizosaccharomyces pombe PLA1 poly(A) polymerases vs. the human PAPOLA, UniProtKB/Swiss-Prot accession number P51003, respectively), as well as high processivity in tethering assays (Dickson, Thompson et al. 2001), As used herein, the term “PAP1 poly(A) polymerase” refers to the Saccharomyces cerevisiae PAP1 poly(A) polymerase (UniProtKB/Swiss-Prot accession number P29468),
As used herein, the term “PLA1 poly(A) polymerase” refers to the Schizosaccharomyces pombe PLA1 poly(A) polymerase, UniProtKB/Swiss-Prot accession number Q10295),
Said catalytic domain of a poly(A) polymerase can be a catalytic domain of a virus poly(A) polymerase, in particular selected in the group consisting of the wild type VP55 poly(A) polymerase, the wild type C475L poly(A) polymerase, the wild type R341 poly(A) polymerase and the wild type MG561 poly(A) polymerase and mutants or derivatives thereof, which are able to catalyze the non-templated addition of adenosine residues from ATP onto the 3′ end of RNA molecules.
The virus poly(A) polymerases have notably the advantage of their reduced molecular weight in comparison to mammalian poly(A) polymerases, their strong enzymatic activity and presence in the cytoplasmic compartment when expressed in mammalian cells. In addition, some of these enzymes, such as R341 and MG561 poly(A) polymerases do not require any know accessory protein cofactor.
As used herein, the term “VP55 poly(A) polymerase” relates to the catalytic subunit (UniProtKB/Swiss-Prot accession number strain Western Reserve P23371) of the heterodimeric vaccinia virus poly(A) polymerase. VP39, the second subunit, acts as a processivity factor (UniProtKB/Swiss-Prot accession number strain Western Reserve P07617).
As used herein, the term “C475L poly(A) polymerase” relates to the African Swine Fever Virus poly(A) polymerase (UniProtKB/Swiss-Prot accession number A0A0A1E081).
As used herein, the term “R341 poly(A) polymerase” relates to the Acanthamoeba polyphaga mimivirus R341 poly(A) polymerase (UniProtKB/Swiss-Prot accession number E3VZZ8).
As used herein, the term “MG561 poly(A) polymerase” relates to the Megavirus chilensis MG561 poly(A) polymerases (NCBI Accession number: YP_004894612).
In one embodiment, the chimeric enzyme according to the invention further comprises at least one catalytic domain of a DNA-dependent RNA polymerase.
As used herein, the term “DNA-dependent RNA polymerase” (RNAPs) relates to nucleotidyl transferases that synthesize complementary strand of RNA from a single- or double-stranded DNA template in the 5′→3′ direction.
Preferably, said catalytic domain of a DNA-dependent RNA polymerase is a catalytic domain of an enzyme, which have a relatively simple structure and more preferably, which have characterized genomic enzymatic regulation elements (i.e. promoter and transcription termination signal). Thus, in particular, said catalytic domain of a DNA-dependent RNA polymerase can be a catalytic domain of a bacteriophage DNA-dependent RNA polymerase, of a bacterial DNA-dependent RNA polymerase or of a DNA-dependent RNA polymerase of various eukaryotic organelles (e.g. mitochondria, chloroplast and proplastids).
In one embodiment, said catalytic domain of a DNA-dependent RNA polymerase is a catalytic domain of a bacteriophage DNA-dependent RNA polymerase.
The bacteriophage DNA-dependent RNA polymerases have notably the advantage that they optimize the levels of transgene expression, in particular by having a higher processivity than the eukaryotic RNA polymerases. The bacteriophage DNA-dependent RNA polymerases have also a much simpler structure than most nuclear eukaryotic polymerases, which consist of multiple subunits (e.g. RNA polymerase II) and transcription factors. Most of the bacteriophage DNA-dependent RNA polymerases characterized so far are single-subunit enzymes, which require no accessory proteins for initiation, elongation, or termination of transcription (Chen and Schneider 2005). Several of these enzymes, which are named for the bacteriophages from which they have been cloned, have also well-characterized regulation genomic elements (i.e. promoter and termination signals), which are important for transgenesis.
There is also no competition between the endogenous gene transcription and the transgene transcription. The chimeric enzymes according to the invention, which comprise bacteriophage DNA-dependent RNA-polymerase moieties, allow the production of RNA transcripts in any eukaryotic species (e.g. yeast, rodents, and humans). They are not expensive, quick and easy to implement and thus appropriate for large-scale assays and protein productions; it allows the production of RNA transcripts in any biological system (e.g. acellular reaction mix, cultured cells, and living organisms), since in contrast to eukaryotic RNA polymerase such as RNA polymerase II, most of bacteriophage DNA-dependent RNA polymerases do not require associated factors for initiation, elongation or termination of transcription.
Said catalytic domain of a bacteriophage DNA-dependent RNA polymerase can be a catalytic domain of a bacteriophage DNA-dependent RNA polymerase, in particular selected in the group consisting of the wild type T7 RNA polymerase (NCBI genomic sequence NC_001604; Gene 1261050; UniProtKB/Swiss-Prot P00573), the wild type T3 RNA polymerase (NCBI genomic sequence NC_003298; Gene 927437; UniProtKB/Swiss-Prot Q778M8), the wild type K1E RNA polymerase (NCBI genome sequence AM084415.1, UniProtKB/Swiss-Prot Q2WC24), the wild type K1-5 RNA polymerase (NCBI genome sequence AY370674.1, NCBI YP_654105.1), the wild type K11 RNA polymerase (NCBI genomic K11 RNAP sequence NC_004665; Gene 1258850; UniProtKB/Swiss-Prot Q859H5), the wild type φA1122 RNA polymerase (NCBI genomic sequence NC_004777; Gene 1733944; UniProtKB/Swiss-Prot protein Q858N4), the wild type φYeo3-12 RNA polymerase (NCBI genomic sequence NC_001271; Gene 1262422; UniProtKB/Swiss-Prot Q9T145) and the wild type gh-1 RNA polymerase (NCBI genomic sequence NC_004665; Gene 1258850; UniProtKB/Swiss-Prot protein Q859H5), the wild type SP6 RNA polymerase (NCBI genomic sequence NC_004831; Gene 1481778; UniProtKB/Swiss-Prot protein Q7Y5R1), and mutants or derivatives thereof, which are able to synthesize single-stranded RNA complementary in sequence to the double-stranded template DNA in the 5′→3′ direction, more particularly the wild type T7 RNA polymerase, the wild type T3 RNA polymerase, the wild type SP6 RNA polymerase, the wild type K1-5 RNA polymerase and the wild type K1E RNA polymerase and mutants or derivatives thereof, which are able to synthesize single-stranded RNA complementary in sequence to the double-stranded template DNA in the 5′→3′ direction.
The prototype of bacteriophage RNA polymerases, i.e. the bacteriophage T7 RNA polymerase, has in particular the advantage that, in vitro, the enzyme is extremely processive and elongates 240-250 nucleotides/s at 37° C. in the 5′→3′ direction (Golomb and Chamberlin 1974, Lyakhov, He et al. 1997, Zhang and Studier 1997, Finn, MacLachlan et al. 2005). Moreover, when expressed in eukaryotic cells, the bacteriophage T7 RNA polymerase, remains largely in the cytoplasm (Elroy-Stein and Moss 1990, Gao and Huang 1993, Brisson, He et al. 1999, Jais, Decroly et al. 2018), and thus optimizes the levels of transgene expression by avoiding the active transfer of large DNA molecules (i.e. transgene) from the cytoplasm to the nucleus of eukaryotic cells and the export of RNA molecules from the nucleus to the cytoplasm.
The catalytic domain of a DNA-dependent RNA polymerase can be the one of the wild type of the K1E or K1-5 RNA polymerase but also of mutants of the K1E or K1-5 RNA polymerases, which are able to synthesize single-stranded RNA complementary in sequence to the double-stranded template DNA in the 5′→3′ direction, even with processivity. For example, said mutants can be selected in the group consisting of the K1E RNA polymerase mutants R551S (Jais, Decroly et al. 2018), F644A, Q649S, G645A, R627S, 1810S, D812E (Makarova, Makarov et al. 1995), and K631M (Osumi-Davis, de Aguilera et al. 1992, Osumi-Davis, Sreerama et al. 1994), in particular R551 S (Jais, Decroly et al. 2018).
Preferably, said catalytic domain of the DNA-dependent RNA-polymerase of the chimeric enzyme according to the invention is from different enzymes than those of the host cell to prevent the competition between the endogenous gene transcription and said DNA sequence transcription.
The chimeric enzyme according to the invention comprises at least said catalytic domains but can further comprise the whole or part of the enzymes containing said catalytic domains. In fact, according to one embodiment of the chimeric enzyme according to the invention, said catalytic domain of a RNA triphosphatase, said catalytic domain of a guanylyltransferase and said catalytic domain of a N7-guanine methyltransferase can be included in the whole or part of a capping enzyme, preferably of a monomeric capping enzyme. Said catalytic domain of a poly(A) polymerase can also be included in the whole or part of a poly(A) polymerase. Said catalytic domain of a DNA-dependent RNA polymerase can also be included in the whole or part of a DNA-dependent RNA polymerase, preferably of a monomeric DNA-dependent RNA polymerase.
Unexpectedly, the inventor has demonstrated that a chimeric enzyme of the invention is able to generate translatable RNA in the cells, therefore generating the key modifications required for its recognition and use by the host-cell ribosomal machinery.
As used herein, the terms «link» and «bound» encompass covalent and non-covalent linkage.
Said RNA-binding domain can be linked by covalent (directly or indirectly by a linking peptide) linkage to one catalytic domain of the chimeric enzyme according to the invention, in particular selected in the group consisting of:
Linking peptide has the advantage of generating fusion proteins in which steric hindrance is minimizes and enough space is provided for the components of the fusion protein to remain in their native conformation.
Said linking peptide of the invention can be selected from the group consisting of:
The flexible linker peptides of formula (GlymSerp)n have the advantages that the glycine residues confer peptide flexibility, while the serine provide some solubility (Huston, Levinson et al. 1988). Furthermore, the absence of sensitive sites for chymotrypsin I, factor Xa, papain, plasmin, thrombin and trypsin in the (GlymSerp)n linker sequences is supposed to increase the overall stability of the resulting fusion proteins.
(GlymSerp)n linkers of variable lengths are commonly used to engineer single-chain Fv fragment (sFv) antibodies (Huston, Levinson et al. 1988). In addition, (GlymSerp)n linkers have been used to generate various fusion proteins, which frequently retain the biological activities of each of their components (Newton, Xue et al. 1996, Lieschke, Rao et al. 1997, Shao, Zhang et al. 2000, Hu, Li et al. 2004).
Other types of peptide linkers can be also considered to generate chimeric enzymes according to the invention, such as GGGGIAPSMVGGGGS (SEQ ID No 48) (Turner, Ritter et al. 1997), SPNGASNSGSAPDTSSAPGSQ (SEQ ID No 49) (Hennecke, Krebber et al. 1998), EGKSSGSGSESKSTE (SEQ ID No 50) (Bird, Hardman et al. 1988), EGKSSGSGSESKEF (SEQ ID No 51) (Newton, Xue et al. 1996), GGGSGGGSGGGTGGGSGGG (SEQ ID No 52) (Robinson and Sauer 1998), GSTSGSGKSSEGKG (SEQ ID No 53) (Bedzyk, Weidner et al. 1990), YPRSIYIRRRHPSPSLTT (SEQ ID No 54) (Tang, Jiang et al. 1996), GSTSGSGKPGSGEGS (SEQ ID No 55) (Ting, Kain et al. 2001), SSADDAKKDAAKKDDAKKDDAKKDA (SEQ ID No 56) (Pantoliano, Bird et al. 1991), GSADDAXXDAAXKDDAKKDDAKKDGS (SEQ ID No 57) (Gregoire, Lin et al. 1996), LSADDAKKDAAKKDDAKKDDAKKDL (SEQ ID No 58) (Pavlinkova, Beresford et al. 1999), AEAAAKEAAAKEAAAKA (SEQ ID No 59) (Wickham, Carrion et al. 1995), GSTSGSGKPGSGEGSTGAGGAGSTSGSGKPSGEG (SEQ ID No 60) (Ting, Kain et al. 2001), LSLEVAEEIARLEAEV (SEQ ID No 61) (Ting, Kain et al. 2001), GTPTPTPTPTGEF (SEQ ID No 62) (Gustaysson, Lehtio et al. 2001), GSTSGSGKPGSGEGSTKG (SEQ ID No 63) (Whitlow, Bell et al. 1993) and GSHSGSGKP (SEQ ID No 64) (Ting, Kain et al. 2001) as described previously in the patent application WO 2011/128444.
Said RNA-binding domain of a protein-RNA tethering system and said catalytic domains can also be assembled by specific protein elements, like leucine zippers.
The C-terminal end or the N-terminal end of said RNA-binding domain can be linked to the N-terminal end or the C-terminal end of one of said catalytic domain of the chimeric enzyme of the invention, respectively.
Preferably, the C-terminal end of said RNA binding domain is linked by covalent (directly or indirectly by a linking peptide preferably of formula Gly4, (Gly4Ser)1 (Gly4Ser)2 or (Gly4Ser)4, even more preferably of formula (Gly4Ser)1 or a Gly4) linkage to the N-terminal end of one of the catalytic domain selected in the group consisting of:
In one embodiment, the C-terminal end of said RNA binding domain is linked by covalent (directly or indirectly by a linking peptide preferably of formula Gly4, (Gly4Ser)1 (Gly4Ser)2 or (Gly4Ser)4, even more preferably of formula (Gly4Ser)1 or a Gly4) linkage to the N-terminal end of one of the catalytic domain selected in the group consisting of:
In one embodiment, the chimeric enzyme of the invention is a fusion protein.
As used herein, the term “fusion protein” relates to artificial proteins created through the joining of two or more proteins or protein domains that originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins.
In one embodiment, the chimeric enzyme of the invention is a fusion protein, wherein:
In one embodiment, the chimeric enzyme of the invention is a fusion protein, wherein:
In one embodiment of the chimeric enzyme according to the invention, at least two, in particularly at least three, at least four and more particularly the whole catalytic domains can be assembled, fused, or bound directly or indirectly by a linking peptide (particularly by a linking peptide of formula Gly4, (Gly4Ser)1, (Gly4Ser)2 or (Gly4Ser)4, more particularly of formula (Gly4Ser)2.
In particular, at least two, particularly at least three and more particularly the whole catalytic domains selected in the group consisting of:
Preferably, at least said catalytic domain of a DNA-dependent RNA polymerase is bound by a linking peptide (particularly selected in the group consisting of linking peptide of formula Gly4, (Gly4Ser)1, (Gly4Ser)2 and (Gly4Ser)4, more particularly of formula (Gly4Ser)2) to at least one of the catalytic domain of a capping enzyme in particular selected in the group consisting of:
Particularly, the linking peptide can be located N-terminally with respect to said catalytic domain of a DNA-dependent RNA polymerase, in particular of a bacteriophage DNA-dependent RNA polymerase selected in the group consisting of T7, T3, SP6, K1-5 and K1E RNA polymerases, and C-terminally with respect to said catalytic domain of a RNA triphosphatase, said catalytic domain of a guanylyltransferase, and said catalytic domain of a N7-guanine methyltransferase.
In particular, the N-terminal end of said catalytic domain of a DNA-dependent RNA polymerase, in particular of a bacteriophage DNA-dependent RNA polymerase selected in the group consisting of T7, T3, SP6, K1-5 and K1E-RNA polymerases, is linked by covalent linkage, in particular by a linking peptide, to the C-terminal end of one of the catalytic domain selected in the group consisting of:
Preferably, at least said catalytic domain of a poly(A) polymerase is bound by a linking peptide to at least one of the catalytic domain of a capping enzyme in particular selected in the group consisting of:
Particularly, the linking peptide can be located C-terminally with respect to said catalytic domain of a poly(A) polymerase and N-terminally with respect to said catalytic domain of a capping enzyme, in particular said catalytic domain of a RNA triphosphatase, said catalytic domain of a guanylyltransferase, and said catalytic domain of a N7-guanine methyltransferase, more particularly said catalytic domain of a RNA triphosphatase.
Said catalytic domains of a capping enzyme (in particular of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase), of a DNA-dependent RNA polymerase and of a poly(A) polymerase can also be assembled by specific protein elements, like leucine zippers, like biotinylation domain to one of the catalytic domain (e.g. Avi-tag II (Cronan 1990) or PFB-tag (Wu, Yeung et al. 2002)) and a biotin binding domain to one of the other catalytic domain (e.g. Strep-tag II (Schmidt and Skerra 1993) or Nano-tag (Lamla and Erdmann 2004)) in the chimeric enzyme according to the invention.
In one embodiment of the chimeric enzyme according to the invention, at least two of said catalytic domains can be assembled, by non-covalent linkage, in particular by leucine zippers.
Preferably, at least said catalytic domain of a DNA-dependent RNA polymerase or of a poly(A) polymerase is assembled by non-covalent linkage, in particular by leucine zippers, to at least one of the catalytic domain of a capping enzyme, preferably to at least one of the catalytic domain selected in the group consisting of:
In one embodiment, at least said catalytic domain of a poly(A) polymerase is assembled by non-covalent linkage, in particular by leucine zippers, preferably at its C-terminal end, to at least one of the catalytic domain of a capping enzyme, particularly to at least one of the catalytic domain selected in the group consisting of:
The leucine zippers, which are dimeric coiled-coil protein structures composed of two amphipathic α-helices that interact with each other, are commonly used to homo- or hetero-dimerize proteins (O'Shea, Klemm et al. 1991). Each helices consist of repeats of seven amino acids, in which the first amino-acid (residue a) is hydrophobic, the fourth (residue d) is usually a leucine, while the other residues are polar. The leucine zippers VELCRO ACID-p1 and BASE-p1, which form a parallel heterodimeric two-stranded coiled coil structures, have high propensity to form parallel protein hetero-dimers (O'Shea, Lumb et al. 1993). They have been used to heterodimerize membrane proteins (Chang, Bao et al. 1994, Pashine, Busch et al. 2003), as well as several soluble proteins (Busch, Reich et al. 1998, Busch, Pashine et al. 2002).
Other types of oligomerisation peptide domains can be also considered to generate chimeric enzyme according to the invention, to assemble at least two of said catalytic domains of the chimeric enzyme according to the invention, especially leucine zippers that form antiparallel heteromeric structures, such as the ACID-a1/BASE-a1 (Oakley and Kim 1998), ACID-Kg/BASE-Eg (McClain, Woods et al. 2001), NZ/CZ (Ghosh, Hamilton et al. 2000), ACID-pLL/BASE-pLL (Lumb and Kim 1995), and EE1234L and RR1234L (Moll, Ruvinov et al. 2001) leucine zippers. Disulfide-linked versions of leucine zippers can be also used to generate disulfide coiled coil-bound heterodimeric chimeric enzyme according to the invention (O'Shea, Lumb et al. 1993), as well as interchain disulfide bridges between cysteine residues under oxidizing conditions (Wells and Powers 1986).
At least two of said catalytic domains of a poly(A) polymerase, of a capping enzyme (in particular of a RNA triphosphatase, of a guanylyltransferase, of a N7-guanine methyltransferase), and of a DNA-dependent RNA polymerase can thus be assembled by leucine zippers, in particular leucine zippers that form antiparallel heteromeric structures, such as the ACID-a1/BASE-a1 (Oakley and Kim 1998), ACID-Kg/BASE-Eg (McClain, Woods et al. 2001), NZ/CZ (Ghosh, Hamilton et al. 2000), and ACID-pLL/BASE-pLL leucine zippers, disulfide coiled coil-bound (O'Shea, Lumb et al. 1993), as well as disulfide bridges between cysteine residues (Wells and Powers 1986).
In one embodiment, the chimeric enzyme according to the invention comprises:
In another embodiment, the chimeric enzyme according to the invention comprises:
The invention also relates to an isolated nucleic acid molecule or a group of isolated nucleic acid molecules, said nucleic acid molecule(s) encoding a chimeric enzyme according to the invention or an isolated nucleic acid molecule encoding a chimeric enzyme, characterized in that its sequence comprises a nucleic acid sequence encoding a RNA-binding domain of a protein-RNA tethering system fused in frame, in particular in the order, to:
Said group of isolated nucleic molecules encoding a chimeric enzyme according to the invention comprises or consists of all the nucleic acid molecules which are necessary and sufficient to obtain a chimeric enzyme according to the invention by their expression.
As used herein, the term “nucleic acid molecule” any molecules composed of linked nucleotides, encompassing DNA and RNA molecules.
In one embodiment, said group of isolated nucleic acid molecules encoding a chimeric enzyme according to the invention comprises or consists of:
In another embodiment, said group of isolated nucleic acid molecules encoding a chimeric enzyme according to the invention comprises or consists of:
In one embodiment, the isolated nucleic acid molecule of the invention comprises or consists of a nucleic acid sequence encoding said RNA-binding domain of a protein-RNA tethering system fused in frame, in particular in the order, to:
Such single nucleic acid sequence has the advantage of facilitating the subunit assembly, since there is only a single open-reading frame.
In one embodiment of the isolated nucleic acid molecule of the invention, its sequence comprises at least one nucleic acid sequence encoding a ribosome skipping motif.
As used herein, the term “ribosome skipping motif” relates to alternate mechanism of translation in which a specific viral peptide prevents the ribosome from covalently linking a new inserted amino-acid, and let it continue translation. This results in apparent co-translational cleavage of the polyprotein.
In particular, said ribosome skipping motif is selected in the group consisting of the 2A sequences from the Foot-and-mouth disease virus Aphtovirus (UniProtKB/Swiss-Prot AAT01756), Avisivirua A (UniProtKB/Swiss-Prot M4PJD6), Duck hepatitis A Avihepatovirus (UniProtKB/Swiss-Prot QOZQM1), Encephalomyocarditis Cardiovirus (UniProtKB/Swiss-Prot Q66765), Cosavirus A (UniProtKB/Swiss-Prot B8XTP8), Equine rhinitis B Erbovirus 1 (UniProtKB/Swiss-Prot Q66776), Seneca Valley Erbovirus (UniProtKB/Swiss-Prot Q155Z9), Hunnivirus A (UniProtKB/Swiss-Prot F4YYF3), Kunsagivirus A (UniProtKB/Swiss-Prot S4VD62), Mischivirus A (UniProtKB/Swiss-Prot I3VR62), Mosavirus A2 (UniProtKB/Swiss-Prot X2L6K2), Pasivirus A1 (UniProtKB/Swiss-Prot 16YOK4), Porcine teschovirus 1 (UniProtKB/Swiss-Prot Q9WJ28), Infectious flacherie Iflavirus (UniProtKB/Swiss-Prot Q70710), Thosea asigna Betatetravirus (UniProtKB/Swiss-Prot Q9YK87), Cricket paralysis Cripavirus (UniProtKB/Swiss-Prot Q9IJX4), Human rotavirus C (UniProtKB/Swiss-Prot Q9PY95), and Lymantria dispar cypovirus 1 (UniProtKB/Swiss-Prot 0911D7),
In particular, said nucleic acid sequence encoding a ribosome skipping motif is selected in the group consisting of the 2A sequences from the Foot-and-mouth disease virus Aphtovirus (also designated as “F2A”, UniProtKB/Swiss-Prot AAT01756) or Porcine teschovirus 1 (also designated as “T2A”, UniProtKB/Swiss-Prot Q9WJ28).
Said nucleic acid sequence encoding a ribosome skipping motif can be localized between any of the sequence encoding said catalytic domain of the chimeric enzyme of the invention.
In one embodiment, said nucleic acid sequence encoding a ribosome skipping motif can be localized between the sequence encoding said catalytic domain of a poly(A) polymerase fused in frame with the sequence encoding:
In another embodiment, said nucleic acid sequence encoding a ribosome skipping motif can be localized between the sequence encoding said catalytic domain of a DNA-dependent RNA polymerase fused in frame with the sequence encoding said catalytic domain of a capping enzyme, in particular selected in the group consisting of said catalytic domain of a RNA triphosphatase, said catalytic domain of a guanylyltransferase and said catalytic domain of a N7-guanine methyltransferase, more particularly fused in frame with the sequence encoding said catalytic domain of a N7-guanine methyltransferase.
In one embodiment, the isolated nucleic acid molecule according to the invention is characterized in that its sequence comprises or consists of
In one embodiment, the isolated nucleic acid molecule according to the invention is characterized in that its sequence comprises or consists of
In one embodiment, the isolated nucleic acid molecule of the invention encoding a chimeric enzyme, is characterized in that its sequence comprises a nucleic acid sequence encoding a RNA-binding domain of a protein-RNA tethering system fused in frame in the order to:
In fact, unexpectedly, the inventor has demonstrated (as illustrated in Example 8) that such nucleic acid molecule allows higher expression rate by a DNA-dependent RNA polymerase than the combination of a nucleic acid molecule encoding a chimeric enzyme comprising at least one domain of a capping enzyme and a DNA-dependent RNA polymerase associated with a nucleic acid molecule encoding a RNA-binding domain of a protein-RNA tethering system fused in frame to a nucleic acid sequence encoding at least one catalytic domain of a poly(A) polymerase.
These results are really surprising and one skilled in the art could have expected to obtain the same expression rate since the components are the same.
In particular, the nucleic acid molecule according to the invention can be operatively linked to at least one, preferably the whole promoter(s) selected from the group consisting of:
The link of the nucleic acid to a promoter for a eukaryotic DNA-dependent RNA polymerase, preferably for RNA polymerase II has notably the advantage that when the chimeric enzyme of the invention is expressed in an eukaryotic host cell, the expression of the chimeric enzymes is driven by the eukaryotic RNA polymerase, preferably the RNA polymerase II. These chimeric enzymes, in turn, can initiate transcription of the transgene. If tissue-specific RNA polymerase II promoters are used, the chimeric enzyme of the invention can be selectively expressed in the targeted tissues/cells.
Said promoter can be a constitutive promoter or an inducible promoter well known by one skilled in the art. The promoter can be developmentally regulated, inducible or tissue specific.
The invention also relates to a vector comprising a nucleic acid molecule according to the invention. Said vector can be appropriated for semi-stable or stable expression.
The invention also relates to a group of vectors comprising said group of isolated nucleic acid molecules according to the invention.
Particularly said vector according to the invention is a cloning or an expression vector.
The invention also relates to a host cell comprising a nucleic acid molecule according to the invention or a vector according to the invention or a group of vectors according to the invention.
The host cell according to the invention can be useful for large-scale protein production.
Preferably, said catalytic domains of the DNA-polymerase RNA polymerase chimeric enzyme according to the invention are from different enzymes than those of the host cell to prevent the competition between the endogenous gene transcription and the transgene transcription.
The invention also relates to a genetically engineered non-human eukaryotic organism, which expresses a chimeric enzyme encoded by the nucleic acid molecule or the group of isolated nucleic acid molecules according to the invention, in particular a chimeric enzyme according to the invention. Said non-human eukaryotic organism can be any non-human animals, plants.
The invention also relates to the use, particularly in vitro or ex vivo, of a chimeric enzyme according to the invention, for the production of RNA molecule with 5′-terminal cap, in particular 5′-terminal m7GpppN cap and preferably with 3′ poly(A) tail and optionally comprising at least one chemical modification.
The invention also relates to the use, particularly in vitro or ex vivo, of a nucleic acid molecule or a group of isolated nucleic acid molecules according to the invention, for the production of RNA molecule with 5′-terminal cap, in particular 5′-terminal m7GpppN cap and preferably with 3′ poly(A) tail and optionally comprising at least one chemical modification.
Particularly said RNA molecule is synthetized by a bacteriophage DNA-dependant RNA polymerase.
In fact, the chimeric enzyme according to the invention is suitable for synthetizing a capped RNA with at least one chemical modification.
In particular, the invention relates to the use, particularly in vitro or ex vivo, of a chimeric enzyme according to the invention, for the production of RNA molecule with 5′-terminal cap, in particular 5′-terminal m7GpppN cap and preferably with 3′ poly(A) tail and comprising at least one chemical modification selected from the group consisting of pyridin-4-one ribonucleoside, 5-aza-uridine, 2-thio-5-aza-uridine, 2-thiouridine, 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxyuridine, 3-methyluridine, 5-carboxymethyl-uridine, 1-carboxymethyl-pseudouridine, 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyluridine, 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine, l-taurinomethyl-4-thio-uridine, pseudouridine, 5-methyl-cytidine, 5-methyl-uridine, 1-methyl-pseudouridine, 4-thio-1-methyl-pseudouridine, 2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine, dihydropseudouridine, 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxyuridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, 5-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine, N4-acetylcytidine, 5-formylcytidine, N4-methylcytidine, 5-hydroxymethylcytidine, 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine, 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, 2-aminopurine, 2, 6-diaminopurine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza-2-aminopurine, 7-deaza-8-aza-2-aminopurine, 7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1-methyladenosine, N6-methyladenosine, N6-isopentenyladenosine, N6-(cis-hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine, N6-glycinylcarbamoyladenosine, N6-threonylcarbamoyladenosine, 2-methylthio-N6-threonyl carbamoyladenosine, N6,N6-dimethyladenosine, 7-methyladenine, 2-methylthio-adenine, 2-methoxy-adenine, inosine, 1-methyl-inosine, wyosine, wybutosine, 7-deaza-guanosine, 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine, 6-thio-7-methyl-guanosine, 7-methylinosine, 6-methoxy-guanosine, 1-methylguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, I-methyl-6-thio-guanosine, N2-methyl-6-thio-guanosine, and N2,N2-dimethyl-6-thio-guanosine.
The invention also relates to the in vitro or ex vivo use of a chimeric enzyme according to the invention or an isolated nucleic acid molecule or a group of isolated nucleic acid molecules according to the invention, for the production of protein, in particular protein of therapeutic interest like antibody, particularly in eukaryotic systems, such as in vitro synthesized protein assay or cultured cells.
The invention also relates to an in vitro or ex vivo method for producing a RNA molecule with a 5′-terminal cap, in particular a 5′-terminal m7 GpppN cap and preferably a 3′ poly(A) tail encoded by a DNA sequence, in a host cell, said method comprising the step of expressing in the host cell a nucleic acid molecule or a group of isolated nucleic acid molecules according to the invention, wherein said DNA sequence is covalently linked to at least one sequence encoding the RNA element of said protein-RNA tethering system, which specifically binds to said RNA-binding domain. As used herein the term “the RNA element of a protein-RNA tethering system which specifically binds to said RNA-binding domain” relates to a RNA sequence, usually forming a stem-loop, which is able to bind with high affinity to the corresponding RNA-binding domain of a protein-RNA tethering system.
Particularly, said DNA sequence is operatively linked to the promoter for a bacteriophage DNA-dependant RNA polymerase or to the promoter for said DNA-dependent RNA polymerase of the chimeric of the invention.
In particular, when the RNA-binding domain of a protein-RNA tethering system is the RNA-binding domain of the lambdoid N antitermination protein-RNA tethering systems, the element, which specifically binds to said RNA-binding domain can be a boxBL and/or a boxBR stem loop RNA structure (Das 1993, Greenblatt, Nodwell et al. 1993, Friedman and Court 1995), including the elements encoded by SEQ ID No 7 and SEQ ID No 38.
In particular, when the RNA-binding domain of a protein-RNA tethering system is the RNA-binding domain of the MS2 coat protein-RNA tethering system, the element, which specifically binds to said RNA-binding domain can be the 19 nucleotide or the 21 nucleotide stem-loop sequences, including the element encoded by SEQ ID No 39 (Peabody 1993, Valegard, Murray et al. 1994, LeGuyer, Behlen et al. 1996, Valegard, Murray et al. 1997) (nucleotides 1748-766 from enterobacteriophage MS2 isolate DL52, NCBI accession number J0966307.1), which contains the initiation codon of the gene for the viral replicase (Valegard, Murray et al. 1994, Valegard, Murray et al. 1997).
In particular, when the RNA-binding domain of a protein-RNA tethering system is the RNA-binding domain of the R17 isolate coat protein-RNA tethering system, the element, which specifically binds to said RNA-binding domain can be the 19 nucleotide or the 21 nucleotides stem-loop (nucleotides 1746-764 from enterobacteriophage R17, NCBI accession number EF108465.1), which contains the initiation codon of the gene for the viral replicase (Carey and Uhlenbeck 1983).
In particular, said DNA sequence is operatively linked to the promoter for a bacteriophage DNA-dependant RNA polymerase or to the promoter for said DNA-dependent RNA polymerase of the chimeric of the invention and covalently linked at its 3′ terminal end to at least one, preferably at least two, at least three and more preferably at least four sequences encoding the element which specifically binds to said RNA-binding domain.
In particular, said method according to the invention further comprises the step of contacting said DNA sequence encoding the RNA molecule with the enzyme of the invention.
In particular, said DNA sequence is operatively linked to the promoter for a bacteriophage DNA-dependant RNA polymerase or to the promoter for said DNA-dependent RNA polymerase of the chimeric of the invention and covalently linked at its 3′ terminal end to at least one sequence encoding the element which specifically binds to said RNA-binding domain covalently linked to a poly(A) track sequence consisting of at least 10, in particular at least 20, 30, and more particularly at least 40 deoxyadenosine residues.
In particular, said poly(A) track sequence can be covalently linked at its 3′ terminal end to a self-cleaving RNA sequence and optionally to a transcription stop sequence.
In particular, said self-cleaving RNA sequence can be the self-cleaving RNA sequence from the group comprising the genomic pseudoknot ribozyme of the hepatitis D virus (Genbank accession number AJ000558.1), antigenomic hepatitis-D Virus pseudoknot ribozyme (Genbank accession number AJ000558.1), tobacco Ringspot Virus satellite hairpin ribozyme (Genbank accession number NC_003889.1) or artificial short hairpin RNA (shRNA).
In particular, said transcription stop sequence can be the bacteriophageT7 phi10 transcription stop sequence (Genbank accession number GU071091.1) or E. coli RNA polymerase rrnB t1 stop (Genbank accession number LN832404.1).
In particular, said method according to the invention can further comprise the step of introducing in the host cell said DNA sequence and/or the nucleic acid according to the invention, using well-known methods by one skilled in the art like by transfection using calcium phosphate, by electroporation or by mixing a cationic lipid with DNA to produce liposomes.
In one embodiment, said method according to the invention further comprises the step of inhibiting, in particular silencing, preferably by siRNA (small interfering RNA), miRNA (microRNA) or shRNA, the cellular transcription and post-transcriptional machineries of said host cell.
In one embodiment, said method according to the invention further comprises the step of inhibiting the expression of the endogenous DNA-dependent RNA polymerase and/or the endogenous capping enzyme in said host cell.
As used herein the term “endogenous DNA-dependent RNA polymerase” relates to the endogenous DNA-dependent RNA polymerase of said host cell. When the host cell is a eukaryotic cell, said endogenous DNA-dependent RNA polymerase is the RNA polymerase II.
As used herein the term “endogenous capping enzyme” refers to the endogenous capping enzyme of said host cell.
As used herein the term “inhibiting the expression of a protein” relates to a decrease of at least 20%, particularly at least 35%, at least 50% and more particularly at least 65%, at least 80%, at least 90% of expression of said protein. Inhibition of protein expression can be determined by techniques well known to one skilled in the art, including but not limiting to Northern-Blot, Western-Blot, RT-PCR.
The step of inhibiting the expression of the endogenous DNA-dependent RNA polymerase and/or the endogenous capping enzyme in said host cell can be implemented by any techniques well known to one skilled in the art, including but not limiting to siRNA techniques that target said endogenous DNA-dependent RNA polymerase and/or the endogenous capping enzyme, antisense RNA techniques that target said endogenous DNA-dependent RNA polymerase and/or the endogenous capping enzyme, shRNA techniques that target said endogenous DNA-dependent RNA polymerase and/or the endogenous capping enzyme.
In addition to siRNA (or shRNA), other inhibitory sequences might be also considered for the same purpose including DNA or RNA antisense (Liu and Carmichael 1994, Dias and Stein 2002), hammerhead ribozyme (Salehi-Ashtiani and Szostak 2001), hairpin ribozyme (Lian, De Young et al. 1999) or chimeric snRNA U1-antisense targeting sequence (Fortes, Cuevas et al. 2003). In addition, other cellular target genes might be considered for inhibition, including other genes involved in the cellular transcription (e.g. other subunits of the RNA polymerase II or transcription factors), post-transcriptional processing (e.g. other subunit of the capping enzyme, as well as polyadenylation or spliceosome factors), and mRNA nuclear export pathway.
In one embodiment of the method according to the invention, said RNA molecule can encode a polypeptide of therapeutic interest.
In another embodiment, said RNA molecule can be a non-coding RNA molecule selected in the group comprising siRNA, ribozyme, shRNA and antisense RNA. In particular, said DNA sequence can encode a RNA molecule selected in the group consisting of mRNA, non-coding RNA, particularly siRNA, ribozyme, shRNA and antisense RNA.
The invention also relates to the use of a chimeric enzyme according to the invention as a capping enzyme and preferably a pol(A) polymerase and a DNA-dependent RNA polymerase.
The invention also relates to a kit for the production of a RNA molecule with 5′-terminal cap, in particular 5′-terminal m7GpppN cap, comprising at least one chimeric enzyme according to the invention as defined above, and/or an isolated nucleic acid molecule and/or a group of nucleic acid molecule according to the invention as defined above, and/or a vector according to the invention as defined above, or
a chimeric enzyme, in particular a cytoplasmic chimeric enzyme comprising at least one catalytic domain of a RNA triphosphatase, at least one catalytic domain of a guanylyltransferase, at least one catalytic domain of a N7-guanine methyltransferase, and at least one catalytic domain of a DNA-dependent RNA polymerase and/or an isolated nucleic acid molecule and/or a group of isolated nucleic acid molecules encoding said chimeric enzyme and a poly(A) polymerase, in particular a cytoplasmic poly(A) polymerase, comprising at least one RNA-binding domain of a protein-RNA tethering system linked to at least one catalytic domain of said poly(A) polymerase and/or an isolated nucleic acid molecule encoding said poly(A) polymerase;
and optionally a DNA sequence encoded said RNA molecule, which is covalently linked to at least one sequence encoding the RNA element of said protein-RNA tethering system, which specifically binds to said RNA-binding domain.
Particularly, said kit for the production of an RNA molecule with a 5′-terminal cap, comprises a DNA sequence encoded said RNA molecule, which is operatively linked to the promoter for a bacteriophage DNA-dependant RNA polymerase or to the promoter for said DNA-dependent RNA polymerase of the chimeric enzyme of the invention.
In particular, said kit for the production of an RNA molecule with a 5′-terminal cap, comprises at least one chimeric enzyme according to the invention, and/or an isolated nucleic acid molecule and/or a group of isolated nucleic acid molecules according to the invention, and/or a vector according to the invention and optionally a DNA sequence encoded said RNA molecule, which is covalently linked to at least one sequence encoding the element which specifically binds to said RNA-binding domain and particularly which is operatively linked to the promoter for a bacteriophage DNA-dependant RNA polymerase or to the promoter for said DNA-dependent RNA polymerase of the chimeric enzyme of the invention.
In particular, said kit for the production of an RNA molecule with a 5′-terminal cap, further comprises an isolated nucleic acid molecule encoding at least one catalytic domain of a DNA-dependent RNA polymerase, and/or at least one catalytic domain of a DNA-dependent RNA polymerase, in particular of a bacteriophage DNA-dependent RNA polymerase.
Particularly, said kit further comprises its instructions of use. The invention also relates to a composition (in particular a kit or a pharmaceutical composition) comprising:
In particular, said composition (in particular a kit or a pharmaceutical composition) comprising:
More particularly, said composition (in particular a kit or a pharmaceutical composition) comprising:
Advantageously, the kit or the compositions of the invention can be used as an orthogonal gene expression system. As used herein, the term “orthogonal” designate biological systems whose basic structures are independent and generally originates from different species.
The invention also relates to a chimeric enzyme according to the invention, an isolated nucleic acid molecule according to the invention, a group of nucleic acid molecule according to the invention or a vector according to the invention, for its use as a medicament, in particular for the prevention and/or treatment of human or animal pathologies, preferably by means of gene therapy.
The invention also relates to a pharmaceutical composition comprising a chimeric enzyme according to the invention, and/or an isolated nucleic acid molecule according to the invention and/or a group of nucleic acid molecule according to the invention, and/or a vector according to the invention. Preferably, said pharmaceutical composition according to the invention is formulated in a pharmaceutical acceptable carrier.
Pharmaceutical acceptable carriers are well known by one skilled in the art.
The pharmaceutical composition according to the invention can further comprise at least one DNA sequence of interest, wherein said DNA sequence is operatively linked to a promoter for said catalytic domain of a DNA-dependent RNA polymerase and covalently linked to at least one sequence encoding the element which specifically binds to said RNA-binding domain.
Such components (in particular selected in the group consisting of a chimeric enzyme according to the invention, an isolated nucleic acid molecule according to the invention, a vector according to the invention and at least one DNA sequence of interest) can be present in the pharmaceutical composition or medicament according to the invention in a therapeutically amount (active and non-toxic amount).
Such therapeutically amount can be determined by one skilled in the art by routine tests including assessment of the effect of administration of said components on the pathologies and/or disorders which are sought to be prevent and/or to be treated by the administration of said pharmaceutical composition or medicament according to the invention.
For example, such tests can be implemented by analyzing both quantitative and qualitative effect of the administration of different amounts of said aforementioned components (in particular selected in the group consisting of a chimeric enzyme according to the invention, an isolated nucleic acid molecule according to the invention, a vector according to the invention and at least one DNA sequence of interest) on a set of markers (biological and/or clinical) characteristics of said pathologies and/or of said disorders, in particular from a biological sample of a subject.
The invention also relates to a therapeutic method comprising the administration of a chimeric enzyme according to the invention, and/or an isolated nucleic acid molecule according to the invention, and/or a group of nucleic acid molecule according to the invention and/or a vector according to the invention in a therapeutically amount to a subject in need thereof. The therapeutic method according to the invention can further comprise the administration of at least one DNA sequence of interest, wherein said DNA sequence is operatively linked to a promoter for said catalytic domain of a DNA-dependent RNA polymerase and covalently linked to at least one sequence encoding the element which specifically binds to said RNA-binding domain, in a therapeutically amount to a subject in need thereof.
Said chimeric enzyme, nucleic acid molecule and/or said vector according to the invention can be administrated simultaneously, separately or sequentially of said DNA sequence of interest, in particular before said DNA sequence of interest.
The invention also relates to a pharmaceutical composition according to the invention for its use for the prevention and/or treatment of human or animal pathologies, in particular by means of gene therapy.
Said pathologies can be selected from the group consisting of pathologies, which can be improved by the administration of said at least one DNA sequence of interest.
The invention also relates to the use of a chimeric enzyme according to the invention, and/or an isolated nucleic acid molecule according to the invention, and/or a group of nucleic acid molecule according to the invention and/or a vector according to the invention, for the preparation of a medicament for the prevention and/or treatment of human or animal pathologies, in particular by means of gene therapy.
The invention also relates to a first combination product, which comprises as active ingredients:
The invention also relates to a second combination product, which comprises as active ingredients:
for its use as a medicament, wherein said active ingredients are formulated for separate, simultaneous or sequential administration.
Said DNA sequence of interest can be an anti-oncogene (a tumor suppressor gene).
Said DNA sequence of interest can encode a polypeptide of therapeutic interest or a non-coding RNA selected in the group comprising siRNA, ribozyme, shRNA and antisense RNA.
Said polypeptide of therapeutic interest can be selected from, a monoclonal antibody or its fragments, a growth factor, a cytokine, a cell or nuclear receptor, a ligand, a coagulation factor, the CFTR protein, insulin, dystrophin, a hormone, an enzyme, an enzyme inhibitor, a polypeptide which has an antineoplastic effect, a polypeptide which is capable of inhibiting a bacterial, parasitic or viral, in particular HIV, infection, an antibody, a toxin, an immunotoxin.
Preferably, the combination product according to the invention can be formulated in a pharmaceutical acceptable carrier.
In one embodiment of the combination product according to the invention, said vector is administrated before said DNA sequence of interest.
The invention also relates to a combination product according to the invention for its use as a medicament in the prevention and/or treatment of human or animal pathologies, particularly by means of gene therapy.
Said pathologies can be selected from the group consisting of pathologies, which can be improved by the administration of at least one DNA sequence of interest, as described above.
For example, said pathologies, as well as their clinical, biological or genetic subtypes, can be selected from the group comprising liver disorders (e.g. acute liver failure due to acetaminophen intoxication or other causes, prevention of liver failure post-hepatectomy, liver primary cancers including hepatoma or cholangiocarcinoma, nonalcoholic steatohepatitis, as well as liver monogenic disorders such as hemochromatosis, ornithine transarbamylase deficiency, argininosuccinatelyase deficiency, argininosuccinate synthetase 1, hemochromatosis or Wilson's disease), disorders due or associated to deficiencies of secreted proteins (e.g. lysosomal storage diseases such as Gaucher's disease, Niemann-Pick disease, Tay-Sacks or Sandhoff disease, Hunter syndrome, or Hurler disease; deficiencies of coagulation factors including factors VIIIc, IX, Von Willebrand, fibrinogen or other coagulation proteins, as well as colony stimulating factors including erythropoietin, granulocyte colony stimulating factor and thrombopoietin), cancers and their predisposition (e.g. breast, colorectal, pancreas, gastric, esophageal and lung cancers, as well as melanoma), malignant hemopathies (e.g. leukemias, Hodgkin's and non-Hodgkin's lymphomas, myeloma), hemoglobinopathies (e.g. sickle cell anemia, glucose-6-phosphate dehydrogenase deficiency) and thalassemias, autoimmune disorders (e.g. systemic lupus erythematosus, scleroderma, autoimmune hepatitis), cardiovascular disorders (e.g. cardiac rhythm and conduction disorders, hypertrophic cardiomyopathy, cardiovascular disease, or chronic cardiac failure), metabolic disorders (e.g. type I and type II diabetes mellitus and their complications, dyslipidemia, atherosclerosis and their complications), infectious disorders (e.g. AIDS, viral hepatitis B, viral hepatitis C, influenza flu, Zika, Ebola and other viral diseases; botulism, tetanus and other bacterial disorders; malaria and other parasitic disorders), muscular disorders (e.g. Duchenne muscular dystrophy and Steinert myotonic muscular dystrophy), respiratory diseases (e.g. cystic fibrosis, alpha-1 antitrypsin deficiency, acute respiratory distress syndrome, pulmonary arterial hypertension, pulmonary veno-occlusive disease), renal diseases (e.g. polycystic kidney disease, glomerulopathy), colorectal disorders (e.g. Crohn's disease and ulcerative colitis), ocular disorders especially retinal diseases (e.g. Leber's amaurosis, retinitis pigmentosa, age related macular degeneration), central nervous system disorders (e.g. Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, multiple sclerosis, Huntington's disease, neurofibromatosis, adrenoleukodystrophy, bipolar disease, schizophrenia and autism), bone and joint disorders (e.g. rheumatoid arthritis, ankylosing spondylitis, osteoarthritis) and skin and connective tissue disorders (e.g. neurofibromatosis and psoriasis).
In one embodiment, the combination product of the invention comprises:
The invention also relates to a method for producing the chimeric enzyme according to the invention comprising the step of expressing in at least one host cell said nucleic acid molecule or said group of nucleic acid molecules encoding the chimeric enzyme of the invention in conditions allowing the expression of said nucleic acid molecule(s) in said host cell.
The invention also relates to a method for producing the chimeric enzyme according to the invention comprising the steps of:
The present invention will be explained in detail with examples in the following, but the technical scope of the present invention is not limited to these examples.
1. Objectives
The objective of this experiment was to determine if the heterodimeric vaccinia virus capping enzyme appropriately tethered to Firefly Luciferase reporter mRNA synthesized in cellulo increases its expression.
The vaccinia virus capping enzyme consist of two subunits, which form a heterodimer: (i) a 95 kDa subunit encoded by the vaccinia virus D1R gene (genomic sequence AY243312.1; UniProtKB/Swiss-Prot accession number P04298), designated hereafter as D1R, which has RNA-triphosphatase, RNA guanylyltransferase and RNA N7-guanine methyltransferase enzymatic activities (Cong and Shuman 1993, Niles and Christen 1993, Higman and Niles 1994, Mao and Shuman 1994, Gong and Shuman 2003), (ii) and a 31-kDa subunit encoded by the vaccinia virus D12L gene (genomic sequence AY243312.1; UniProtKB/Swiss-Prot accession number P04318), designated hereafter as D12L, which has no intrinsic enzymatic activity, but enhances the RNA N7-guanine methyltransferase activity of the D1R subunit (Higman, Bourgeois et al. 1992, Higman, Christen et al. 1994, Mao and Shuman 1994). Cotransfection of plasmids encoding these two subunits therefore generate in cellulo the heterodimer D1R/D12L capping enzyme, which can eventually fused to a protein tethering domain.
2. Methods
a. Plasmids
The coding sequences of the following plasmids were optimized for expression in human cells with respect to codon adaptation index using the GeneOptimizer algorithm (Raab, Graf et al. 2010). All gene sequences were artificially synthesized and assembled from stepwise PCR using oligonucleotides, cloned and fully sequenced.
For all the following examples, the conditions tested consist of a variable combination of several plasmids. In the present example, the pK1ERNAP/pT3RNAP plasmids together with Firefly luciferase reporter plasmids were used to generate in cellulo the Firefly Luciferase mRNA with or without tethering domain, which then can be specifically modified by enzyme produced by the test plasmid appropriately tethered to the Firefly Luciferase mRNA.
The expression plasmids consisted of the phage T3 and K1E RNA polymerase open reading-frames (ORFs), which were subcloned in the pCMVScript plasmid backbone (Stratagene, La Jolla, Calif.), following the removal of the T7 φ10 promoter sequence. These corresponding plasmids, designated as p-followed by the name of the ORF, have the following design (i.e. pK1ERNAP or pT3RNAP;
The test plasmids contained the coding sequence of the capping enzymes under investigation with (
The Firefly Luciferase reporter plasmids containing the Firefly Luciferase gene under control of the K1E or T3 RNA polymerase promoters, contained a 5′-UTR sequence, Kozak consensus sequence followed by the ORF of Luciferase gene from Photinus pyralis and stop codon, RNA tethering domain consisting of four BoxBr in tandem from λ virus (optional, lacking in the untethered version; nucleotides 38312-38298 of genomic sequence of Enterobacteria phage lambda KT232076.1; SEQ ID No 7 corresponding to the nucleotide sequence of the BoxBr RNA stem-loops from A bacteriophage), poly(A) track of 40 adenosine residues, followed by a self-cleaving RNA sequence from the genomic ribozyme of the hepatitis D virus, and terminated by the bacteriophage T7 φ10 transcription stop. These plasmids were designated either pK1Ep-Luciferase/pT3p-Luciferase in their untethered versions (
b. Cell Culture and Transfection
For standard experiments, the Human Embryonic Kidney 293 (HEK-293, ATCC CRL 1573) were routinely grown at 37° C. in 5% CO2 atmosphere at 100% relative humidity. Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 4 mM L-alanyl-L-glutamine, 10% fetal bovine serum (FBS), 1% non-essential amino-acids, 1% sodium pyruvate, 1% penicillin and streptomycin, and 0.25% fungizone.
Cells were routinely plated in 24-well plates at 1×105 cells per well the day before transfection and transfected at 80% cell confluence. Transient transfection was performed with Lipofectamine 2000 reagent (Invitrogen, Carlsbad, Calif.) according to manufacturer's recommendations. Except otherwise stated, cells were transfected with 2 μl of Lipofectamine 2000 and 0.8 μg of total plasmid DNA. For standard luciferase and hSEAP gene reporter expression assays, cells were analyzed 48 hours after transfection, except otherwise stated.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Luciferase luminescence was assayed by the Luciferase Assay System (Promega, Madison, Wis.) according to the manufacturer's recommendations. In brief, cells were lysed in Cell Culture Lysis Reagent buffer (CLR), and then centrifuged at 12,000×g for two minutes at 4° C. Luciferase Assay Reagent (Promega; 100 μl/well) diluted at 1:10 was added to supernatant (20 μl/well). Luminescence readout was taken on a Tristar 2 microplate reader (Berthold, Bad Wildbad, Germany) with a read time of one second per well.
In order to normalize for transfection efficacy, cells were transfected with the pORF-eSEAP plasmid (InvivoGen, San Diego, Calif.), which encodes for the human secreted embryonic alkaline phosphatase (hSEAP) driven by the EF-1α/HTLV composite promoter. Enzymatic activity was assayed in cell culture medium using the Quanti-Blue colorimetric enzyme assay kit (InvivoGen). Gene reporter expression was expressed as the ratio of luciferase luminescence (RLU, relative light units) to eSEAP absorbance (OD, optic density).
d. Statistical Analysis
Statistical analyses were performed with paired two-tailed Student's t-test. Results are means (n≥4)±standard deviation. P-value<0.05 was considered statistically significant.
3. Results
In this set of experiments, the Firefly Luciferase mRNA was produced by the phage K1E or T3 RNA polymerases by cotransfection of pK1ERNAP/pT3RNAP and pK1Ep-Luciferase-4xλBoxBr/pT3p-Luciferase-4xλBoxBr for the tethered version of the Firefly Luciferase reporter plasmids or pK1Ep-Luciferase-4xλBoxBr/pT3p-Luciferase-4xλBoxBr for their untethered version. The test plasmids contain the coding sequence of the D1R/D12L vaccinia virus with or without tethering domain were co-transfected. The translatability of the resulting transcripts, which is expected to increase in case of proficient capping, is measured by the Firefly Luciferase assay. A general depiction of the assay is shown
Results of the first set of experiments with the K1E-driven system are shown in the table below:
As expected when capping is lacking, Firefly Luciferase mRNA generated by pK1Ep-Luciferase and pK1Ep-Luciferase-4xλBoxBr cotransfected with the K1ERNAP plasmid alone (designated pK1ERNAP) was poorly expressed (row 1 and 2). Cotransfection of the untethered D1R plasmid (designated pD1R) together with pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr increased the expression by approximately 9-fold in comparison to cotransfection of pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr plasmids only (row 3 vs. 1 or 2, p<0.05, two-way Student t-test), whereas the transfection of the untethered pD12L plasmid with pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr had virtually no effect on Firefly Luciferase expression (row 4 vs. 1 or 2, p=NS, two-way Student t-test). The cotransfection of the untethered pD12L and pD1R plasmids together with pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr, which result in the vaccinia virus D1R/D12L capping enzyme heterodimer without tethering domain, significantly increased the expression of Firefly Luciferase in comparison to previous conditions, therefore confirming that mRNA capping is requested for mRNA translation (row 5 vs. 1 to 4, p=NS, two-way Student t-test p<0.05, two-way Student t-test). Finally, cotransfection of the tethered D12L plasmid (pNλ-D12L) and D1R together with pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr, which produces the tethering vaccinia virus capping enzyme D1R/Nλ-D12L, increased drastically the expression of the Luciferase mRNA by 63.3 (row 6 vs. 2) and 2.6-fold (row 6 vs. 5) in comparison to no vaccinia virus capping enzyme (pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr alone), or untethering vaccinia virus capping enzyme (pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr/pD1R/pD12L), respectively.
In a second set of experiments, the Firefly Luciferase mRNA was produced by the phage T3 RNA polymerase and tethered to the vaccinia virus capping enzyme. Results of the second set of experiments with the T3-driven system are shown in the table below:
This second set of experiments gave very similar results with cotransfection results in the following order: RNA with no 4xλBoxBr and no capping enzyme (row 1, pT3RNAP/pT3p-Luciferase) 4xλBoxBr-RNA and no capping enzyme (row 2, pT3RNAP/pT3p-Luciferase-4xλBoxBr) 4xλBoxBr-RNA with D12L subunit alone (row 4, pT3RNAP/pD12L/pT3p-Luciferase-4xλBoxBr)<4xλBoxBr-RNA with D1R (row 3, pT3RNAP/pD1R/pT3p-Luciferase-4xλBoxBr)<4xλBoxBr-RNA with untethered D1R/D12L capping enzyme (row 5, pT3RNAP/pD1R/pD12L/UpT3p-Luciferase-4xλBoxBr)<<4xλBoxBr-RNA with tethered D1R/D12L capping enzyme (row 6, pT3RNAP/pD1R/pNλ-D12L/UpT3p-Luciferase-4xλBoxBr). The expression levels of this latter condition was statistically greater than all other conditions, especially 3.2 fold higher than with the untethered D1R/D12L capping enzyme, therefore demonstrating the importance of guiding the D1R/D12L capping enzyme to the target reporter mRNA by tethering domain (p<0.05, two-way Student t-test).
4. Conclusions
These experiments show that the vaccinia virus capping enzyme, which contains no known or demonstrated binding domain for a specific RNA sequence, drastically increases gene Firefly Luciferase reporter expression when appropriately tethered to uncapped and polyadenylated Firefly Luciferase reporter mRNA by the Nλ-BoxBr tethering system.
1. Objectives
The objective of this set of experiments was to demonstrate if NP868R, the African swine fever virus capping enzyme, appropriately tethered to polyadenylated Firefly Luciferase reporter mRNA increases its expression in cellulo. NP868R (also named G4R) is a single-unit 868 amino-acids protein, which all enzymatic activities required for cap-0 formation demonstrated in vitro, i.e. RNA-triphosphatase, RNA guanylyltransferase and RNA N7-guanine methyltransferase (Pena, Yanez et al. 1993, Jais 2011, Dixon, Chapman et al. 2013, Jais, Decroly et al. 2018).
2. Methods
a. Plasmids
The expression (pK1ERNAP or pT3RNAP), as well as the Firefly Luciferase reporter plasmids in their tethered versions (pK1Ep-Luciferase and pT3p-Luciferase) or untethered versions (pK1Ep-Luciferase-4xλBoxBr and pT3p-Luciferase-4xλBoxBr) were the same as described above.
The test plasmid consisted of the coding sequence from the African swine fever virus NP868R capping enzyme (NCBI ASFV genomic sequence strain BA71V NC_001659; UniProtKB/Swiss-Prot accession number P32094; SEQ ID No 8 and SEQ ID No 9 corresponding to the nucleotide and amino acid sequences of African swine fever virus NP868R capping enzyme, respectively) with (pNλ-NP868R) or without the NA tethering domain (pNP868R) subcloned in the pCMVScript plasmid backbone as described above.
b. Cell Culture and Transfection
Same as described in Example 1.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Same as described in Example 1.
d. Statistical Analysis
Same as described in Example 1.
3. Results
The design of the assay was very similar to Example 1, except that the single subunit capping enzyme NP868R was used instead of the heterodimeric D1R/D12L capping enzyme. In brief, uncapped but polyadenylated Firefly Luciferase mRNA was synthesized in cellulo by the phage K1E or T3 RNA polymerases and its expression in presence of NP868R was assayed (
Results of the first set of experiment with the K1E-driven system are shown in the table below:
In this first set of experiments, cells were cotransfected with pK1ERNAP/pK1Ep-Luciferase or pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr plasmids, showed low levels of Firefly Luciferase reporter expression (row 1 and 2). Cotransfection of the pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr with the untethered pNP868R plasmid (pNP868R) increased the expression by approximately 29-fold in comparison to pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr alone (row 3 vs. 1 or 2 respectively, p<0.05, two-way Student t-test), therefore confirming that mRNA capping is requested for mRNA translation. Finally, cotransfection of pK1ERNAP/pK1Ep-Luciferase-4xλBoxBr with tethered NP868R (pNλ-NP868R) even increased by 2.1-fold the expression of Firefly Luciferase in comparison to untethered NP868R condition, demonstrating the importance of guiding the enzyme to the target mRNA by tethering domains for proficient mRNA capping (raw 4 vs. 3, p<0.05, two-way Student t-test).
Results of the second set of experiments with the T3-driven system are shown in the table below:
In this second set of experiments, the Firefly Luciferase mRNA was produced by the phage T3 RNA polymerase and tethered to the African swine fever virus capping enzyme. This second set of experiments gave very similar results with cotransfection results in the following order: RNA with no 4xλBoxBr and no capping enzyme (row 1, pT3RNAP/pT3p-Luciferase) 4xλBoxBr-RNA without capping enzyme (row 2, pT3RNAP/pT3p-Luciferase-4xλBoxBr)<4xλBoxBr-RNA with untethered NP868R capping enzyme (row 3, pT3RNAP/pNP868R/pT3p-Luciferase-4xλBoxBr)<<4xλBoxBr-RNA with tethered NP868R capping enzyme (row 4, pT3RNAP/pNλ-NP868R/pT3p-Luciferase-4xλBoxBr). The expression levels of this last condition was statistically greater than all other conditions, especially 2.9 fold higher than with the untethered NP868R capping enzyme, therefore demonstrating the importance of tethering NP868R to the target mRNA by tethering domains for proficient mRNA capping (row 4 vs.3, p<0.05, two-way Student t-test).
4. Conclusions
These experiments show that another capping enzyme, NP868R from the African swine fever virus, which contains no known or predicted binding domain for a specific RNA sequence, increases Firefly Luciferase reporter expression when appropriately tethered to uncapped and polyadenylated reporter mRNA by the Nλ-BoxBr tethering system.
1. Objectives
The objectives of the present experiments were to investigate if other protein:RNA tethering systems than the Nλ-4xBoxBr system can guide the African swine fever virus capping enzyme NP868R in order to increase the expression of appropriately tethered Luciferase reporter mRNA produced by the phage K1E RNA polymerase.
The following tethering systems were presently tested: i) MS2 protein and the RNA stem loop tethered sequence from MS2 virus (Valegard, Murray et al. 1994, Valegard, Murray et al. 1997), ii) NA peptide from the lambda virus and its BoxBl RNA tethered sequence (Das 1993, Greenblatt, Nodwell et al. 1993, Friedman and Court 1995), iii) NA peptide from the P22 lamboid virus and its BoxBr RNA tethered sequences (Das 1993, Greenblatt, Nodwell et al. 1993, Friedman and Court 1995), iv) NA peptide from the ϕ21 lamboid virus and its BoxBr RNA tethered sequence (Das 1993, Greenblatt, Nodwell et al. 1993, Friedman and Court 1995), v) TAT binding domain from the Human immunodeficiency virus-1 (HIV-1), which contains a biologically validated nuclear localization signal (Duconge and Toulme 1999), and TAR RNA tethered sequence (Dingwall, Ernberg et al. 1990, Weeks, Ampe et al. 1990, Karn, Dingwall et al. 1991, Puglisi, Tan et al. 1992, Frankel and Young 1998), and vi) the human small nuclear ribonucleoprotein U1 subunit 70 (SNRNP70) protein tethering sequence (Romac, Graff et al. 1994), which contains a biologically validated nuclear localization signal (Keene, Query et al. 1999), and its U1snRNA-stem loop tethered sequence.
2. Methods
a. Plasmids
The pK1ERNAP expression plasmid was described in Example 1.
The test plasmids consisted of the coding sequence of the African swine fever virus NP868R capping enzyme fused at its amino-terminal end to: i) bacteriophage N-antitermination protein the N-terminus of the entire MS2 protein (pMS2-NP868R, NCBI accession number NC_001417.2, UniProtKB/Swiss-Prot P03612; SEQ ID No 36 and SEQ ID No 37 corresponding to the nucleotide and amino-acid sequences, respectively), ii) N-terminal peptide from lambda bacteriophage previously described, iii)N-terminal peptide from P22 bacteriophage N-antitermination protein (pP22N-NP868R, UniProtKB/Swiss-Prot P04891), iv)N-terminal peptide from ϕ21 bacteriophage N-antitermination protein (pNϕ21-NP868R, UniProtKB/Swiss-Prot P07243), v) the TAT protein binding domain from HIV-1 isolate HXB2 (pTAT-NP868R, NCBI reference sequence: AAB50256.1), and vi) human small nuclear ribonucleoprotein U1 subunit 70 (SNRNP70) RNA-binding protein sequence (pSNRNP70-NP868R, amino-acid 92-202, NCBI accession number NM_003089.5).
The RNA tethering domains of the Firefly Luciferase reporter plasmids substituted by four tandem repeats of: i) MS2 RNA stem-loops (pK1Ep-Luciferase-4xMS2sl plasmid; nucleotides 1748-766 from Enterobacteriophage MS2 isolate DL52, NCBI accession number J0966307.1; SEQ ID No 38), ii) BoxBl RNA sequence from A virus (pK1Ep-Luciferase-4xABoxBl; NCBI accession number J02459.1 nucleotides 35518-35534), iii) λBoxBr RNA sequence from P22 lamboid virus (pK1Ep-Luciferase-4xP22BoxBr; NCBI accession number NC_002371.2, nucleotides 31,953-31,971), iv) λBoxBr RNA sequence from ϕ21 lamboid virus (pK1Ep-Luciferase-4xϕ21BoxBr; NCBI accession number AH007390.1, nucleotides 866-883), v) TAR RNA sequence from Human immunodeficiency virus type 1, isolate HXB2 (pK1Ep-Luciferase-4xTAR; NCBI accession number K03455.1, nucleotides 471-497) and vi) U1snRNA RNA stem-loop (pK1Ep-Luciferase-4xU1snRNA; NCBI accession number M28013.1, nucleotides 123-155).
b. Cell Culture and Transfection
Same as described in Example 1.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Same as described in Example 1.
d. Statistical Analysis
Same as described in Example 1.
3. Results
The design of the assay was very similar to Example 2, except that various protein:RNA tethering systems were tested in replacement to the Nλ:BoxBr system. In brief, uncapped Firefly Luciferase mRNA with a short polyadenylation tail of 40 adenosine residues was synthesized in cellulo by the phage K1E RNA polymerase and its expression in presence of NP868R tethered by various systems was assayed (
Results of these experiments are shown in the table below:
The cotransfection of pK1ERNAP with plasmids having only one component of the tethering system, i.e. the protein domains fused to the NP868R capping enzyme of the test plasmid or Firefly Luciferase reporter plasmids with four tandem RNA tethered repeats introduced in their 3′UTR, had no significant effects on the expression of the Firefly Luciferase reporter mRNA with any system when compared to no tethering system (row 2 or 3 vs. 1; p=NS for all comparisons, two-way Student t-test). The cotransfection of pK1ERNAP with plasmids encoding for the components of the MS2-4xMS2sl (i.e. pMS2-NP868R/pK1Ep-Luciferase-4xMS2sl), Nλ-NP868R-4xABoxBl (i.e. pNλ-NP868R/pK1Ep-Luciferase-4xλBoxBl), NP22-NP868R-4xP22BoxBr (i.e. pNP22-NP868R/pK1Ep-Luciferase-4xP22BoxBr), Nϕ21-4xϕ21BoxBr (i.e. pNϕ21-NP868R/pK1Ep-Luciferase-4xϕ21BoxBr), tethering system increased significantly by 3.8- to 4.6-fold the expression levels of firefly luciferase reporter in comparison to conditions with the untethering capping enzyme and/or untethered Firefly Luciferase plasmids (row 4 vs. 1-3; p<0.05 for all comparisons, two-way Student t-test). In contrast, the cotransfection of pK1ERNAP with either the TAT/4xTAR tethering system (i.e. pTAT-NP868R/pK1Ep-Luciferase-4xTAR) or the SNRNP70/4xU1snRNA tethering system (i.e. pSNRNP70-NP868R/pK1Ep-Luciferase-4xU1snRNA) shows very low change of Firefly Luciferase in comparison to conditions with the untethering capping enzyme and/or untethered Firefly Luciferase plasmids (row 4 vs. 1-3; p=NS for all comparisons, two-way Student t-test).
In conclusion, the best performances were obtained with the Nλ-4xλBoxBl tethering expression system (i.e. pNλ-NP868R/pK1Ep-Luciferase-4xλBoxBl), with performances of other tethering systems ranging in the following order (i.e. ratio of condition 4 vs.1): Nλ-4xλBoxBl>MS2-4xMS2sl>Nϕ21-4xϕ21BoxBr>NP22-4xP22BoxBr>>TAT-4xTAR>SNRNP70-4xU1snRNA.
4. Conclusions
The present experiments show that the African swine fever virus capping enzyme NP868R can increase the expression of Firefly Luciferase mRNA produced by the K1E phage RNA polymerase when appropriately tethered to the mRNA by bacteriophage protein-RNA tethering systems.
1. Objectives
The objectives of the present experiments were to investigate if other protein:RNA tethering systems than the Nλ-4xBoxBr system can be used to guide the heterodimeric capping enzyme from the vaccinia virus to the a target mRNA, and thereby increase its expression.
The protein:RNA tethering systems tested hereinafter are the same as described in the previous example.
2. Methods
a. Plasmids
The pK1ERNAP expression plasmid was described in Example 1.
The test plasmid consisted of the coding sequence of the D12L subunit from the vaccinia virus capping enzyme fused at its amino-terminal end with the tethering protein sequences described above. The D1R plasmid was the same as previously described.
The Firefly Luciferase reporter plasmids containing the various tethered RNA sequences were the same as described in the previous example.
b. Cell Culture and Transfection
Same as described in Example 1.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Same as described in Example 1.
d. Statistical Analysis
Same as described in Example 1.
3. Results
The design of the assay was very similar to Example 1, except that various protein:RNA tethering systems were tested in replacement to the Nλ:BoxBr system (
Results of these experiments are shown in the table below:
The cotransfection of pK1ERNAP with plasmids having only one out of the two components of the tethering system, i.e. the protein domains fused to the D12L subunit of the vaccinia virus capping of the test plasmid or the Firefly Luciferase reporter plasmids with four tandem RNA tethered repeats introduced in their 3′UTR, had no significant effects on the expression of the Firefly Luciferase reporter mRNA with any system when compared to no tethering system (row 2 or 3 vs. 1; p=NS for all comparisons, two-way Student t-test). Similarly to previous findings, the cotransfection of pK1ERNAP with plasmids with all the components of the MS2-4xMS2sl and D1R subunit of the vaccinia virus capping enzyme (i.e. pMS2-D12L/pD1R/pK1Ep-Luciferase-4xMS2sl), Nλ-D12L-4xABoxBl (i.e. pNλ-D12L/pD1R/pK1Ep-Luciferase-4xABoxBl), NP22-D12L-4xP22BoxBr (i.e. pNP22-D12L/pD1R/pK1Ep-Luciferase-4xP22BoxBr), Nϕ21-4xϕ21BoxBr (i.e. pNϕ21-D12L/pD1R/pK1Ep-Luciferase-4xϕ21BoxBr), tethering system increased significantly by 2- to 2.5-fold the expression levels of firefly luciferase reporter in comparison to conditions with the untethering capping enzyme and/or untethered Firefly Luciferase plasmids (row 4 vs. 1-3; p<0.05 for all comparisons, two-way Student t-test). In contrast, the cotransfection of pK1ERNAP with either the TAT/4xTAR tethering system (i.e. pTAT-D12L/pD1R/pK1Ep-Luciferase-4xTAR) or the SNRNP70/4xU1snRNA tethering system (i.e. pSNRNP70-D12L/pD1R/pK1Ep-Luciferase-4xU1snRNA) shows very low change of Firefly Luciferase in comparison to conditions with the untethering capping enzyme and/or untethered Firefly Luciferase plasmids (p=NS for all comparisons, two-way Student t-test).
Finally, the performances of the tethering systems ranged in a different order than in the previous example (i.e. ratio of condition 4 vs.1): Nϕ21-4xϕ21BoxBr>NP22-4xP22BoxBr>Nλ-4xλBoxBl>MS2-4xMS2sl>>TAT-4xTAR>SNRNP70-4xU1snRNA.
4. Conclusions
The present experiments show that the heterodimeric D1R/D12L capping enzyme from the vaccinia virus can also increase the expression of Firefly Luciferase mRNA produced by the K1E phage RNA polymerase when appropriately tethered to the mRNA by bacteriophage RNA-binding domain of a bacteriophage protein-RNA tethering system.
1. Objectives
The present experiments aimed to determine if poly(A) polymerases fused to NP868R African Swine Fever virus capping enzyme can increase the expression of Firefly Luciferase reporter mRNA produced by the K1E phage RNA polymerase when appropriately tethered to the target transcript by the Nλ-BoxBl the thering system.
2. Methods
a. Plasmids
The ORFs of the following poly(A) polymerases were synthesized: i) PAP1 poly(A) polymerase from Saccharomyces cerevisiae sorted to the cytoplasm by deletion of the 42 carboxyl-terminal amino-acids that contains a nuclear localization signal (Zhelkovsky, Helmling et al. 1998) (NCBI accession number: P29468); the vaccinia virus VP55 poly(A) polymerase (UniProtKB/Swiss-Prot accession number P23371 corresponding to the nucleotide and amino-acid sequences, respectively), the viral R341 poly(A) polymerase from Acanthamoeba polyphaga mimivirus (UniProtKB/Swiss-Prot accession number: E3VZZ8), iv) the viral MG561 poly(A) polymerase from Megavirus chilensis (NCBI Accession number: YP_004894612), v) the viral C475L poly(A) polymerase from the African swine fever virus (UniProtKB/Swiss-Prot accession number: A0A0A1E081), vi) mutant PAPOLA (K656R-K657R mutation of the human PAPOLA, UniProtKB/Swiss-Prot accession number P51003) mutated at its the nuclear localization signal (Raabe, Murthy et al. 1994, Vethantham, Rao et al. 2008), vii) the wild-type canonical Mus musculus testis specific PAPOLB (UniProtKB/Swiss-Prot Q9WVP6).
Four types of test plasmids were generated by in-frame subcloning of the poly(A) polymerases ORFs: i) in the pCMV-Script backbone only (e.g. pPAP1), ii) downstream to the NA tethering domain (e.g. pNλ-PAP1), iii) downstream to the Nλ-NP868R protein through a G4 flexible linker (e.g. pNλ-NP868R-G4-PAP1) resulting in the expression of monomeric protein, or iv) between the N protein tethering domain from the lambda bacteriophage and NP868R through a G4 flexible linker (e.g. pNλ-PAP1-G4-NP868R) also resulting in the expression of monomeric protein. The design of these two latter constructions is shown
The Firefly Luciferase reporter plasmids in their untethered (pK1Ep-Luciferase) or tethered version (pK1Ep-Luciferase-4xλBoxBl) were the same as described above.
b. Cell Culture and Transfection
Same as described in Example 1.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Same as described in Example 1.
d. Statistical Analysis
Same as described in Example 1.
3. Results
The design of the assay was very similar to Example 2, except that the poly(A) polymerases were fused to African Swine Fever virus NP868R capping enzyme (
Results of these experiments are shown in the table below:
In the absence of mRNA capping provided by pNλ-NP868R, non-statistically significant increase of Firefly Luciferase mRNA expression of ˜1.5-fold and 2.5-fold was observed when untethered (row 2 vs. 1) or tethered poly(A) polymerase plasmids (row 3 vs. 1) were transfected, respectively (p=NS, two-way Student t-test). When the Firefly Luciferase mRNA was capped by co-transfection of pNλ-NP868R, a statistically significant increase of expression of ˜1.5-fold (row 5 vs. 4) and ˜2-fold (row 6 vs. 4) was observed when the untethered or tethered poly(A) polymerases plasmids were cotransfected, respectively (p<0.05 for all untethered poly(A) polymerases vs. no poly(A) polymerases, two-way Student t-test).
Poly(A) polymerases were fused to NP868R African Swine Fever virus capping enzyme, together with the Nλ-protein tethering domain. Two types of fusion were tested with poly(A) polymerases subcloned either downstream to Nλ-NP868R through a G4 flexible linker or between the N protein tethering domain from the lambda bacteriophage and NP868R through a Ga flexible linker. All tethered fusions genes of both types increased the expression of Firefly Luciferase mRNA in comparison to non-linked enzymes (row 7 and 8 vs. 6; p<0.05 for all comparisons, two-way Student t-test). Activity of the fusion proteins ranged as follows: Nλ-NP868R-G4-C475L<Nλ-NP868R-G4-R341<Nλ-MG561-G4-NP868R<Nλ-VP55-G4-NP868R<Nλ-C475L-G4-NP868R<Nλ-R341-G4-NP868R<Nλ-NP868R-G4-MG561<Nλ-PAPOLB-G4-NP868R<Nλ-NP868R-G4-PAPOLB<Nλ-NP868R-G4-VP55<Nλ-PAP1-G4-NP868R<Nλ-NP868R-G4-PAPOLA<Nλ-PAPOLA-G4-NP868R<Nλ-NP868R-G4-PAP1
4. Conclusions
The present experiments show that various poly(A) polymerases including mammalian, yeast, viral and bacterial enzymes fused to the African Swine Fever virus NP868R capping enzyme increase the expression of transcripts produced by phage RNA polymerase, when appropriately tethered with the Nλ-4xBoxBl system. Surprisingly, the fusion between various poly(A) polymerases and NP868R capping enzymes, which are not physically linked in the nature and contain no RNA-binding domain, can act synergistically and this effect is even greater when these fusion proteins are appropriately tethered (rows 7 and 8 in the above Table). These results are really surprising and one skilled in the art could have expected to obtain the same expression rate since the components are the same.
1. Objectives
The present experiments aim to determine if fusions of poly(A) polymerases with D12 subunit of the heterodimeric vaccinia virus capping enzyme can increase the expression of transcripts produced by phage RNA polymerase, when appropriately tethered with the Nλ-4xBoxBl system.
2. Methods
a. Plasmids
The pK1ERNAP expression plasmid was described in Example 1.
The poly(A) polymerases tested were described in previous example and subcloned in-frame (
The Firefly Luciferase reporter plasmids in their untethered (pK1Ep-Luciferase) or tethered version (pK1Ep-Luciferase-4xλBoxBl) were the same as described above.
b. Cell Culture and Transfection
Same as described in Example 1.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Same as described in Example 1.
d. Statistical Analysis
Same as described in Example 1.
3. Results
The design of the experiment was similar to previous example, except that the capping enzyme consisted of the vaccinia virus heterodimer D1R/D12 (
Results of these experiments are shown in the table below:
In the absence of mRNA capping provided by pNλ-D12L/D1R, non-statistically significant change of Firefly Luciferase mRNA expression of ˜1.5-fold and 2-fold was observed when untethered (row 2 vs. 1) or tethered poly(A) polymerase plasmids (row 3 vs. 1) were transfected, respectively (p=NS, two-way Student t-test). Similarly to previous findings, when the Firefly Luciferase mRNA was capped by co-transfection of pNλ-D12L/D1R, a statistically significant increase of expression of ˜1.5-fold (row 5 vs. 4) and ˜2-fold (row 6 vs. 4) was observed when the untethered or tethered poly(A) polymerases plasmids were cotransfected, respectively (p<0.05 for all untethered poly(A) polymerases vs. no poly(A) polymerases, two-way Student t-test).
Poly(A) polymerases were fused to the D12 subunit of the heterodimeric vaccinia virus capping enzyme, together with the Nλ-protein domain as described above. All tethered fusions genes of both types increased the expression of Firefly Luciferase mRNA in comparison to non-linked enzymes (row 7 and 8 vs. 6; p<0.05 for all comparisons, two-way Student t-test). Activity of the fusion complexes ranged as follows: Nλ-D12L/D1R-G4-C475L<Nλ-C475L-G4-D12L/D1R<Nλ-D12L/D1R-G4-MG561<Nλ-PAPOLB-G4-D12L/D1R<Nλ-VP55-G4-D12L/D1R<Nλ-D12L/D1R-G4-R341<Nλ-D12L/D1R-G4-VP55<Nλ-MG561-G4-D12L/D1R<Nλ-D12L/D1R-G4-PAPOLB<Nλ-PAPOLA-G4-D12L/D1R<Nλ-D12L/D1R-G4-PAP1<Nλ-R341-G4-D12L/D1R<Nλ-D12L/D1R-G4-PAPOLA<Nλ-PAP1-G4-D12L/D1R.
4. Conclusions
The present experiments that various poly(A) polymerases fused to the D12 subunit of the heterodimeric vaccinia virus capping enzyme together with D1R subunit, which are not physically linked in the nature and contain no RNA-binding domain, can act synergistically and this effect is even greater when these fusion proteins appropriately tethered.
1. Objectives
The objectives of this set of experiments were to determine if non-covalent coupling between the R341 poly(A) polymerase and NP868R capping enzyme also results in an active expression system able to enhance the expression of uncapped Firefly Luciferase reporter mRNA when appropriately tethered. In the present experiments, the non-covalent coupling was generated using complementary leucine zippers that form heterodimers.
2. Methods
a. Plasmids
The pK1ERNAP expression and Firefly Luciferase reporter plasmids in their untethered (pK1Ep-Luciferase) or tethered version (pK1Ep-Luciferase-4xλBoxBr) were the same as described above.
Non-covalent coupling between the Acanthamoeba polyphaga mimivirus R341 poly(A) polymerase and the African swine fever virus NP868R capping enzyme was induced by the EE1234L and RR1234L complementary leucine-zippers (SEQ ID No 28 and SEQ ID No 29 corresponding to the nucleotide and amino-acid sequences of G4-EE1234L leucine-zipper, respectively; SEQ ID No 30 and SEQ ID No 31 corresponding to the nucleotide and amino-acid sequences of RR1234L-G4 leucine-zipper, respectively). These amphipathic α-helices form an antiparallel heterodimer with dissociation affinity of ˜10−15M (Moll, Ruvinov et al. 2001). Two non-covalent heterodimeric complexes were generated between NP868R capping enzyme and R341 RNA polymerase (
b. Cell Culture and Transfection
Same as described in Example 1.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Same as described in Example 1.
d. Statistical Analysis
Same as described in Example 1.
3. Results
Uncapped Firefly Luciferase reporter mRNA was generated by the K1E bacteriophage RNA polymerase, using the pK1Ep-Luciferase and pK1Ep-Luciferase-4xλBoxBr plasmids as previously described (
Results of these experiments are shown in the table below:
The Nλ-tethering of the Acanthamoeba polyphaga mimivirus R341 poly(A) polymerase with or without leucine zipper increased modestly the expression of uncapped 4xλBoxBr-Firefly Luciferase mRNA generated by the phage K1E RNA polymerase in comparison to untethered Acanthamoeba polyphaga mimivirus R341 poly(A) polymerase (row 1 or 3 vs. 2). The Nλ-tethering of the African Swine Fever Virus NP868R capping enzyme with or without leucine zipper increased frankly the expression of uncapped Firefly Luciferase 4xλBoxBr-mRNA generated by the phage K1E RNA polymerase in comparison to untethered NP868R capping enzyme or no capping enzyme (row 4 or 6 vs. 5).
The non-covalent coupling between the Acanthamoeba polyphaga mimivirus R341 poly(A) polymerase and the African swine fever virus NP868R capping enzyme was generated using the EE1234L and RR1234L complementary high-affinity leucine-zippers. This heterodimeric complex without the Nλ-tethering domain resulted in active complex that significantly increased the expression of uncapped Firefly Luciferase mRNA generated by the phage K1E RNA polymerase in comparison to conditions to either untethered R341 or NP868R with leucine zippers alone (row 7 vs. 2 or 5). Noticeably, the addition of Nλ-tethering at amino-terminal end of the Acanthamoeba polyphaga mimivirus R341 poly(A) polymerase or the African swine fever virus NP868R capping enzyme of this heterodimeric complex increased by 2.80- and 2.24-fold the expression of uncapped Firefly Luciferase mRNA in comparison to the untethered complex (row 8 or 9 vs. 7; p<0.05 for both comparisons, two-way Student t-test).
4. Conclusions
The present experiments show that the artificial coupling between the R341 poly(A) polymerase and the African swine fever virus NP868R capping enzyme, i.e. non-covalent through leucine zippers, also results in synergistically active heterodimers and this effect is even greater when these fusion proteins appropriately tethered.
1. Objectives
The objective of the following experiment was to determine if active complexes could be generated by assembling the Acanthamoeba polyphaga mimivirus poly(A) polymerase R341, the African swine fever virus NP868R capping enzyme and the phage K1E RNA polymerase when appropriately Nλ-tethered.
The assemblies tested hereinafter are designed according to the common Nλ-R341-[X1]-NP868R-[X2]-K1ERNAP protein scaffold, where [X1] and [X2] are variable.
The following open-reading-frames were generated to test this hypothesis (
2. Methods
a. Plasmids
The Firefly Luciferase reporter plasmids in their untethered (pK1Ep-Luciferase) or tethered version (pK1Ep-Luciferase-4xλBoxBl) were the same as described above.
The ORFs previously described were subcloned in the pCMVScript backbone, therefore resulting in the pNλ-R341-G4-NP868R-G4-K1ERNAP, pNλ-R341-G4-NP868R-F2A-K1ERNAP, pNλ-R341-F2A-NP868R-G4-K1ERNAP, and pNλ-R341-T2A-NP868R-G4-K1ERNAP plasmids.
b. Cell Culture and Transfection
Same as described in Example 1.
c. Firefly Luciferase Luminescence and SEAP Colorimetric Assays
Same as described in Example 1.
d. Statistical Analysis
Same as described in Example 1.
3. Results
A depiction of the assay is shown
Results of these experiments are shown in the table below:
The various fusion of K1ERNAP coding sequence with Nλ-R341-F2A-NP868R were compared with non-linked Nλ-R341-F2A-NP868R and K1ERNAP. All fusions constructions gave significantly greater expression levels than non-linked Nλ-R341-F2A-NP868R and K1ERNAP (row 2-to-5 vs. 1; p<0.05, two-way Student t-test for all comparisons). Best results were obtained with Nλ-R341-T2A-NP868R-G4-K1ERNAP and Nλ-R341-F2A-NP868R-G4-K1ERNAP fusions, with other conditions ranging in the following order: Nλ-R341-T2A-NP868R-G4-K1ERNAP Nλ-R341-F2A-NP868R-G4-K1ERNAP>>Nλ-R341-G4-NP868R-F2A-K1ERNAP>Nλ-R341-G4-NP868R-G4-K1ERNAP>pNλ-R341-G4-NP868R, pK1ERNAP.
4. Conclusions
The present experiments show that active tethered expression systems can be generated by assembling the poly(A) polymerase R341, African swine fever virus NP868R capping enzyme and phage K1E RNA polymerase under a Nλ-R341-[X1]-NP868R-[X2]-K1ERNAP scaffold, preferably where [X1]=T2A or F2A, and [X2]=G4. Unexpectedly, the construction Nλ-R341-F2A-NP868R-G4-K1ERNAP and Nλ-R341-T2A-NP868R-G4-K1ERNAP allow higher expression rate than the association of the constructions Nλ-R341 with NP868R-G4-K1ERNAP (row 4 and 5 vs. 1). These results are really surprising and one skilled in the art could have expected to obtain the same expression rate since the components are the same and are not physically linked in the nature and nor contain any RNA-binding domain.
Martinez-Costas, J., G. Sutton, N. Ramadevi and P. Roy (1998). “Guanylyltransferase and RNA 5′-triphosphatase activities of the purified expressed VP4 protein of bluetongue virus.” J Mol Biol 280(5): 859-866.
Marzluff, W. F., E. J. Wagner and R. J. Duronio (2008). “Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.” Nat Rev Genet 9(11): 843-854.
| Number | Date | Country | Kind |
|---|---|---|---|
| 17306006 | Jul 2017 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2018/070479 | 7/27/2018 | WO |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2019/020811 | 1/31/2019 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 5866680 | Keene et al. | Feb 1999 | A |
| Number | Date | Country |
|---|---|---|
| 2011128444 | Oct 2011 | WO |
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| Bharati, A.P., et al., “The mRNA capping enzyme of Saccharomyces cerevisiae has dual specificity to interact with CTD of RNA Polymerase II.” Scientific Reports, 2016, 6: 31294, pp. 1-12. |
| Ho, C.K., et al., “A Yeast-Based Genetic System for Functional Analysis of Viral mRNA Capping Enzymes.” Journal of Virology, Jun. 2000, 74(12): 5486-5494. |
| Wen, Y., et al., “Mammalian capping enzyme binds RNA and uses protein tyrosine phosphatase mechanism.” Proc. Natl. Acad. Sci. USA, Oct. 1998, 95: 12226-12231. |
| Number | Date | Country | |
|---|---|---|---|
| 20200165585 A1 | May 2020 | US |
