Patent Application
20220204951
The present disclosure is in the field of enzyme catalysis. For example, the disclosure pertains to glucosyltransferase enzymes with modified amino acid sequences. Such modified enzymes synthesize products with decreased molecular weight.
The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named 20190306_CL6607USNP_SequenceListing.txt, created on Mar. 6, 2019, and having a size of about 315 kilobytes and is filed concurrently with the specification. The sequence listing contained in this ASCII-formatted document is part of the specification and is herein incorporated by reference in its entirety.
Driven by a desire to use polysaccharides in various applications, researchers have explored for polysaccharides that are biodegradable and that can be made economically from renewably sourced feedstocks. One such polysaccharide is alpha-1,3-glucan, an insoluble glucan polymer characterized by having alpha-1,3-glycosidic linkages. This polymer has been prepared, for example, using a glucosyltransferase enzyme isolated from Streptococcus salivarius (Simpson et al., Microbiology 141:1451-1460, 1995). Also for example, U.S. Pat. No. 7,000,000 disclosed the preparation of a spun fiber from enzymatically produced alpha-1,3-glucan. Various other glucan materials have also been studied for developing new or enhanced applications. For example, U.S. Patent Appl. Publ. No. 2015/0232819 discloses enzymatic synthesis of several insoluble glucans having mixed alpha-1,3 and -1,6 linkages.
While these and other advances have been made in producing insoluble glucan polymers using glucosyltransferase enzymes, less attention appears to have been drawn to modulating the molecular weight of insoluble glucan products synthesized by such enzymes. Addressing this technological gap, disclosed herein are glucosyltransferases with modified amino acid sequences that produce lower molecular weight insoluble glucan products.
In one embodiment, the present disclosure concerns a non-native glucosyltransferase comprising at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, wherein the non-native glucosyltransferase synthesizes insoluble alpha-glucan comprising 1,3-glycosidic linkages, and the molecular weight of the insoluble alpha-glucan is lower than the molecular weight of insoluble alpha-glucan synthesized by a second glucosyltransferase that only differs from the non-native glucosyltransferase at the substitution position(s).
In another embodiment, the present disclosure concerns a polynucleotide comprising a nucleotide sequence encoding a non-native glucosyltransferase as disclosed herein, optionally wherein one or more regulatory sequences are operably linked to the nucleotide sequence, and preferably wherein the one or more regulatory sequences include a promoter sequence.
In another embodiment, the present disclosure concerns a reaction composition comprising water, sucrose, and a non-native glucosyltransferase as disclosed herein.
In another embodiment, the present disclosure concerns a method of producing insoluble alpha-glucan comprising 1,3-glycosidic linkages, the method comprising: (a) contacting at least water, sucrose, and a non-native glucosyltransferase enzyme as disclosed herein, whereby insoluble alpha-glucan comprising 1,3-glycosidic linkages is produced; and (b) optionally, isolating the insoluble alpha-glucan produced in step (a).
In another embodiment, the present disclosure concerns a method of preparing a polynucleotide sequence encoding a non-native glucosyltransferase as disclosed herein, the method comprising: (a) identifying a polynucleotide sequence encoding a parent glucosyltransferase that (i) comprises an amino acid sequence that is at least about 40% identical to SEQ ID NO:4 or SEQ ID NO:66 (positions 55-960 of SEQ ID NO:4), and (ii) synthesizes insoluble alpha-glucan comprising 1,3-glycosidic linkages; and (b) modifying the polynucleotide sequence identified in step (a) to substitute at least one amino acid of the parent glucosyltransferase at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, thereby providing a polynucleotide sequence encoding a non-native glucosyltransferase that synthesizes insoluble alpha-glucan comprising 1,3-glycosidic linkages, wherein the molecular weight of the insoluble alpha-glucan is lower than the molecular weight of insoluble alpha-glucan synthesized by the parent glucosyltransferase.
salivarius K12.
salivarius SK126.
salivarius PS4.
Streptococcus sp. C150.
a This DNA coding sequence is codon-optimized for expression in E. coli, and is merely disclosed as an example of a suitable coding sequence.
bSEQ ID NOs: 21-24, 31, 32 and 35-58 are intentionally not included in this table and merely serve as placeholders.
The disclosures of all cited patent and non-patent literature are incorporated herein by reference in their entirety.
Unless otherwise disclosed, the terms “a” and “an” as used herein are intended to encompass one or more (i.e., at least one) of a referenced feature.
Where present, all ranges are inclusive and combinable, except as otherwise noted. For example, when a range of “1 to 5” (i.e., 1-5) is recited, the recited range should be construed as including ranges “1 to 4”, “1 to 3”, “1-2”, “1-2 & 4-5”, “1-3 & 5”, and the like.
The terms “alpha-glucan”, “alpha-glucan polymer” and the like are used interchangeably herein. An alpha-glucan is a polymer comprising glucose monomeric units linked together by alpha-glycosidic linkages. In typical embodiments, an alpha-glucan herein comprises 100% alpha-glycosidic linkages, or at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% alpha-glycosidic linkages. Examples of alpha-glucan polymers herein include alpha-1,3-glucan.
The terms “poly alpha-1,3-glucan”, “alpha-1,3-glucan”, “alpha-1,3-glucan polymer” and the like are used interchangeably herein. Alpha-1,3-glucan is a polymer comprising glucose monomeric units linked together by glycosidic linkages, wherein at least about 50% of the glycosidic linkages are alpha-1,3. Alpha-1,3-glucan in certain embodiments comprises at least 90% or 95% alpha-1,3 glycosidic linkages. Most or all of the other linkages in alpha-1,3-glucan herein typically are alpha-1,6, though some linkages may also be alpha-1,2 and/or alpha-1,4.
The terms “glycosidic linkage”, “glycosidic bond”, “linkage” and the like are used interchangeably herein and refer to the covalent bonds connecting the sugar monomers within a saccharide compound (oligosaccharides and/or polysaccharides). The term “alpha-1,3-glycosidic linkage” as used herein refers to the type of covalent bond that joins alpha-D-glucose molecules to each other through carbons 1 and 3 on adjacent alpha-D-glucose rings. The term “alpha-1,6-glycosidic linkage” as used herein refers to the covalent bond that joins alpha-D-glucose molecules to each other through carbons 1 and 6 on adjacent alpha-D-glucose rings. The glycosidic linkages of a glucan polymer herein can also be referred to as “glucosidic linkages”. Herein, “alpha-D-glucose” will be referred to as “glucose”.
The glycosidic linkage profile of an alpha-glucan herein can be determined using any method known in the art. For example, a linkage profile can be determined using methods using nuclear magnetic resonance (NMR) spectroscopy (e.g., 13C NMR and/or 1H NMR). These and other methods that can be used are disclosed in, for example, Food Carbohydrates: Chemistry, Physical Properties, and Applications (S. W. Cui, Ed., Chapter 3, S. W. Cui, Structural Analysis of Polysaccharides, Taylor & Francis Group LLC, Boca Raton, Fla., 2005), which is incorporated herein by reference.
The “molecular weight” of large alpha-glucan polymers herein can be represented as weight-average molecular weight (Mw) or number-average molecular weight (Mn), the units of which are in Daltons or grams/mole. Alternatively, the molecular weight of large alpha-glucan polymers can be represented as DPw (weight average degree of polymerization) or DPn (number average degree of polymerization). The molecular weight of smaller alpha-glucan polymers such as oligosaccharides typically can be provided as “DP” (degree of polymerization), which simply refers to the number of glucoses comprised within the alpha-glucan; “DP” can also characterize the molecular weight of a polymer on an individual molecule basis. Various means are known in the art for calculating these various molecular weight measurements such as with high-pressure liquid chromatography (HPLC), size exclusion chromatography (SEC), or gel permeation chromatography (GPC).
The term “sucrose” herein refers to a non-reducing disaccharide composed of an alpha-D-glucose molecule and a beta-D-fructose molecule linked by an alpha-1,2-glycosidic bond. Sucrose is known commonly as table sugar. Sucrose can alternatively be referred to as “alpha-D-glucopyranosyl-(1→2)-beta-D-fructofuranoside”. “Alpha-D-glucopyranosyl” and “glucosyl” are used interchangeably herein.
The terms “glucosyltransferase”, “glucosyltransferase enzyme”, “GTF”, “glucansucrase” and the like are used interchangeably herein. The activity of a glucosyltransferase herein catalyzes the reaction of the substrate sucrose to make the products alpha-glucan and fructose. Other products (by-products) of a GTF reaction can include glucose, various soluble gluco-oligosaccharides, and leucrose. Wild type forms of glucosyltransferase enzymes generally contain (in the N-terminal to C-terminal direction) a signal peptide (which is typically removed by cleavage processes), a variable domain, a catalytic domain, and a glucan-binding domain. A glucosyltransferase herein is classified under the glycoside hydrolase family 70 (GH70) according to the CAZy (Carbohydrate-Active EnZymes) database (Cantarel et al., Nucleic Acids Res. 37:D233-238, 2009).
The term “glucosyltransferase catalytic domain” herein refers to the domain of a glucosyltransferase enzyme that provides alpha-glucan-synthesizing activity to a glucosyltransferase enzyme. A glucosyltransferase catalytic domain typically does not require the presence of any other domains to have this activity.
The terms “enzymatic reaction”, “glucosyltransferase reaction”, “glucan synthesis reaction”, “reaction composition”, “reaction formulation” and the like are used interchangeably herein and generally refer to a reaction that initially comprises water, sucrose, at least one active glucosyltransferase enzyme, and optionally other components. Components that can be further present in a glucosyltransferase reaction typically after it has commenced include fructose, glucose, leucrose, soluble gluco-oligosaccharides (e.g., DP2-DP7) (such may be considered as products or by-products, depending on the glucosyltransferase used), and/or insoluble alpha-glucan product(s) of DP8 or higher (e.g., DP100 and higher). It would be understood that certain glucan products, such as alpha-1,3-glucan with a degree of polymerization (DP) of at least 8 or 9, are water-insoluble and thus not dissolved in a glucan synthesis reaction, but rather may be present out of solution (e.g., by virtue of having precipitated from the reaction). It is in a glucan synthesis reaction where the step of contacting water, sucrose and a glucosyltransferase enzyme is performed. The term “under suitable reaction conditions” as used herein refers to reaction conditions that support conversion of sucrose to alpha-glucan product(s) via glucosyltransferase enzyme activity.
The terms “percent by volume”, “volume percent”, “vol %”, “v/v %” and the like are used interchangeably herein. The percent by volume of a solute in a solution can be determined using the formula: [(volume of solute)/(volume of solution)]×100%.
The terms “percent by weight”, “weight percentage (wt %)”, “weight-weight percentage (% w/w)” and the like are used interchangeably herein. Percent by weight refers to the percentage of a material on a mass basis as it is comprised in a composition, mixture, or solution.
The terms “aqueous conditions”, “aqueous reaction conditions”, “aqueous setting”, “aqueous system” and the like are used interchangeably herein. Aqueous conditions herein refer to a solution or mixture in which the solvent is at least about 60 wt % water, for example. A glucosyltransferase reaction herein is performed under aqueous conditions.
A glucan that is “insoluble”, “aqueous-insoluble”, “water-insoluble” (and like terms) (e.g., alpha-1,3-glucan with a DP of 8 or higher) does not dissolve (or does not appreciably dissolve) in water or other aqueous conditions, optionally where the aqueous conditions are further characterized to have a pH of 4-9 (e.g., pH 6-8) and/or temperature of about 1 to 85° C. (e.g., 20-25° C.). In contrast, glucans such as certain oligosaccharides herein that are “soluble”, “aqueous-soluble”, “water-soluble” and the like (e.g., alpha-1,3-glucan with a DP less than 8) appreciably dissolve under these conditions.
The terms “polynucleotide”, “polynucleotide sequence”, “nucleic acid molecule” and the like are used interchangeably herein. These terms encompass nucleotide sequences and the like. A polynucleotide may be a polymer of DNA or RNA that is single- or double-stranded, that optionally contains synthetic, non-natural or altered nucleotide bases. A polynucleotide may be comprised of one or more segments of cDNA, genomic DNA, synthetic DNA, or mixtures thereof.
The term “gene” as used herein refers to a DNA polynucleotide sequence that expresses an RNA (RNA is transcribed from the DNA polynucleotide sequence) from a coding region, which RNA can be a messenger RNA (encoding a protein) or a non-protein-coding RNA. A gene may refer to the coding region alone, or may include regulatory sequences upstream and/or downstream to the coding region (e.g., promoters, 5′-untranslated regions, 3′-transcription terminator regions). A coding region encoding a protein can alternatively be referred to herein as an “open reading frame” (ORF). A gene that is “native” or “endogenous” refers to a gene as found in nature with its own regulatory sequences; such a gene is located in its natural location in the genome of a host cell. A “chimeric” gene refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature (i.e., the regulatory and coding regions are heterologous with each other). Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. A “foreign” or “heterologous” gene can refer to a gene that is introduced into the host organism by gene transfer. Foreign/heterologous genes can comprise native genes inserted into a non-native organism, native genes introduced into a new location within the native host, or chimeric genes. Polynucleotide sequences in certain embodiments disclosed herein are heterologous. A “transgene” is a gene that has been introduced into the genome by a gene delivery procedure (e.g., transformation). A “codon-optimized” open reading frame has its frequency of codon usage designed to mimic the frequency of preferred codon usage of the host cell.
As used herein, the term “polypeptide” is defined as a chain of amino acid residues, usually having a defined sequence. As used herein the term polypeptide is interchangeable with the terms “peptides” and “proteins”. Typical amino acids contained in polypeptides herein include (respective three- and one-letter codes shown parenthetically): alanine (Ala, A), arginine (Arg, R), asparagine (Asn, N), aspartic acid (Asp, D), cysteine (Cys, C), glutamic acid (Glu, E), glutamine (Gln, Q), glycine (Gly, G), histidine (His, H), isoleucine (Ile, I), leucine (Leu, L), lysine (Lys, K), methionine (Met, M), phenylalanine (Phe, F), proline (Pro, P), serine (Ser, S), threonine (Thr, T), tryptophan (Trp, W), tyrosine (Tyr, Y), valine (Val, V).
The term “heterologous” means not naturally found in the location of interest. For example, a heterologous gene can be one that is not naturally found in a host organism, but that is introduced into the host organism by gene transfer. As another example, a nucleic acid molecule that is present in a chimeric gene can be characterized as being heterologous, as such a nucleic acid molecule is not naturally associated with the other segments of the chimeric gene (e.g., a promoter can be heterologous to a coding sequence).
A “non-native” amino acid sequence or polynucleotide sequence comprised in a cell or organism herein does not occur in a native (natural) counterpart of such cell or organism. Such an amino acid sequence or polynucleotide sequence can also be referred to as being heterologous to the cell or organism. “Regulatory sequences” as used herein refer to nucleotide sequences located upstream of a gene's transcription start site (e.g., promoter), 5′ untranslated regions, introns, and 3′ non-coding regions, and which may influence the transcription, processing or stability, and/or translation of an RNA transcribed from the gene. Regulatory sequences herein may include promoters, enhancers, silencers, 5′ untranslated leader sequences, introns, polyadenylation recognition sequences, RNA processing sites, effector binding sites, stem-loop structures, and other elements involved in regulation of gene expression. One or more regulatory elements herein may be heterologous to a coding region herein.
A “promoter” as used herein refers to a DNA sequence capable of controlling the transcription of RNA from a gene. In general, a promoter sequence is upstream of the transcription start site of a gene. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. Promoters that cause a gene to be expressed in a cell at most times under all circumstances are commonly referred to as “constitutive promoters”. A promoter may alternatively be inducible. One or more promoters herein may be heterologous to a coding region herein.
A “strong promoter” as used herein refers to a promoter that can direct a relatively large number of productive initiations per unit time, and/or is a promoter driving a higher level of gene transcription than the average transcription level of the genes in a cell.
The terms “3′ non-coding sequence”, “transcription terminator”, “terminator” and the like as used herein refer to DNA sequences located downstream of a coding sequence. This includes polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression.
As used herein, a first nucleic acid sequence is “hybridizable” to a second nucleic acid sequence when a single-stranded form of the first nucleic acid sequence can anneal to the second nucleic acid sequence under suitable annealing conditions (e.g., temperature, solution ionic strength). Hybridization and washing conditions are well known and exemplified in Sambrook J, Fritsch E F and Maniatis T, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989), which is incorporated herein by reference, particularly Chapter 11 and Table 11.1.
The term “DNA manipulation technique” refers to any technique in which the sequence of a DNA polynucleotide sequence is modified. Although the DNA polynucleotide sequence being modified can be used as a substrate itself for modification, it does not have to be physically in hand for certain techniques (e.g., a sequence stored in a computer can be used as the basis for the manipulation technique). A DNA manipulation technique can be used to delete and/or mutate one or more DNA sequences in a longer sequence. Examples of a DNA manipulation technique include recombinant DNA techniques (restriction and ligation, molecular cloning), polymerase chain reaction (PCR), and synthetic DNA methods (e.g., oligonucleotide synthesis and ligation). Regarding synthetic DNA techniques, a DNA manipulation technique can entail observing a DNA polynucleotide in silico, determining desired modifications (e.g., one or more deletions) of the DNA polynucleotide, and synthesizing a DNA polynucleotide that contains the desired modifications.
The term “in silico” herein means in or on an information storage and/or processing device such as a computer; done or produced using computer software or simulation, i.e., virtual reality.
The terms “upstream” and “downstream” as used herein with respect to polynucleotides refer to “5′ of” and “3′ of”, respectively.
The term “expression” as used herein refers to (i) transcription of RNA (e.g., mRNA or a non-protein-coding RNA) from a coding region, and/or (ii) translation of a polypeptide from mRNA. Expression of a coding region of a polynucleotide sequence can be up-regulated or down-regulated in certain embodiments.
The term “operably linked” as used herein refers to the association of two or more nucleic acid sequences such that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence. That is, the coding sequence is under the transcriptional control of the promoter. A coding sequence can be operably linked to one (e.g., promoter) or more (e.g., promoter and terminator) regulatory sequences, for example.
The term “recombinant” when used herein to characterize a DNA sequence such as a plasmid, vector, or construct refers to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis and/or by manipulation of isolated segments of nucleic acids by genetic engineering techniques.
The term “transformation” as used herein refers to the transfer of a nucleic acid molecule into a host organism or host cell by any method. A nucleic acid molecule that has been transformed into an organism/cell may be one that replicates autonomously in the organism/cell, or that integrates into the genome of the organism/cell, or that exists transiently in the cell without replicating or integrating. Non-limiting examples of nucleic acid molecules suitable for transformation are disclosed herein, such as plasmids and linear DNA molecules. Host organisms/cells herein containing a transforming nucleic acid sequence can be referred to as “transgenic”, “recombinant”, “transformed”, “engineered”, as a “transformant”, and/or as being “modified for exogenous gene expression”, for example.
The terms “sequence identity”, “identity” and the like as used herein with respect to polynucleotide or polypeptide sequences refer to the nucleic acid residues or amino acid residues in two sequences that are the same when aligned for maximum correspondence over a specified comparison window. Thus, “percentage of sequence identity”, “percent identity” and the like refer to the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the results by 100 to yield the percentage of sequence identity. It would be understood that, when calculating sequence identity between a DNA sequence and an RNA sequence, T residues of the DNA sequence align with, and can be considered “identical” with, U residues of the RNA sequence. For purposes of determining “percent complementarity” of first and second polynucleotides, one can obtain this by determining (i) the percent identity between the first polynucleotide and the complement sequence of the second polynucleotide (or vice versa), for example, and/or (ii) the percentage of bases between the first and second polynucleotides that would create canonical Watson and Crick base pairs.
Percent identity can be readily determined by any known method, including but not limited to those described in: 1) Computational Molecular Biology (Lesk, A. M., Ed.) Oxford University: NY (1988); 2) Biocomputing: Informatics and Genome Projects (Smith, D. W., Ed.) Academic: NY (1993); 3) Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., Eds.) Humana: NJ (1994); 4) Sequence Analysis in Molecular Biology (von Heinje, G., Ed.) Academic (1987); and 5) Sequence Analysis Primer (Gribskov, M. and Devereux, J., Eds.) Stockton: NY (1991), all of which are incorporated herein by reference.
Preferred methods for determining percent identity are designed to give the best match between the sequences tested. Methods of determining identity and similarity are codified in publicly available computer programs, for example. Sequence alignments and percent identity calculations can be performed using the MEGALIGN program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wisc.), for example. Multiple alignment of sequences can be performed, for example, using the Clustal method of alignment which encompasses several varieties of the algorithm including the Clustal V method of alignment (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci., 8:189-191 (1992)) and found in the MEGALIGN v8.0 program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). For multiple alignments, the default values can correspond to GAP PENALTY=10 and GAP LENGTH PENALTY=10. Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal method can be KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids, these parameters can be KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4. Additionally, the Clustal W method of alignment can be used (described by Higgins and Sharp, CABIOS. 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci. 8:189-191(1992); Thompson, J. D. et al, Nucleic Acids Research, 22 (22): 4673-4680, 1994) and found in the MEGALIGN v8.0 program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). Default parameters for multiple alignment (protein/nucleic acid) can be: GAP PENALTY=10/15, GAP LENGTH PENALTY=0.2/6.66, Delay Divergent Seqs(%)=30/30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Matrix=IUB.
Various polypeptide amino acid sequences and polynucleotide sequences are disclosed herein as features of certain embodiments. Variants of these sequences that are at least about 70-85%, 85-90%, or 90%-95% identical to the sequences disclosed herein can be used or referenced. Alternatively, a variant amino acid sequence or polynucleotide sequence can have at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity with a sequence disclosed herein. A variant amino acid sequence or polynucleotide sequence herein has the same function/activity of the disclosed sequence, or at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the function/activity of the disclosed sequence. Any polypeptide amino acid sequence disclosed herein not beginning with a methionine can typically further comprise at least a start-methionine at the N-terminus of the amino acid sequence. In contrast, any polypeptide amino acid sequence disclosed herein beginning with a methionine can optionally lack such a methionine residue.
The terms “aligns with”, “corresponds with”, and the like can be used interchangeably herein. Some embodiments herein relate to a glucosyltransferase comprising at least one amino acid substitution at a position corresponding with at least one particular amino acid residue of SEQ ID NO:62. An amino acid position of a glucosyltransferase or subsequence thereof (e.g., catalytic domain or catalytic domain plus glucan-binding domains) (can refer to such an amino acid position or sequence as a “query” position or sequence) can be characterized to correspond with a particular amino acid residue of SEQ ID NO:62 (can refer to such an amino acid position or sequence as a “subject” position or sequence) if (1) the query sequence can be aligned with the subject sequence (e.g., where an alignment indicates that the query sequence and the subject sequence [or a subsequence of the subject sequence] are at least about 30%, 40%, 50%, 60%, 70%, 80%, or 90% identical), and (2) if the query amino acid position directly aligns with (directly lines up against) the subject amino acid position in the alignment of (1). In general, one can align a query amino acid sequence with a subject sequence (SEQ ID NO:62 or a subsequence of SEQ ID NO:62) using any alignment algorithm, tool and/or software described disclosed herein (e.g., BLASTP, ClustalW, ClustalV, Clustal-Omega, EMBOSS) to determine percent identity. Just for further example, one can align a query sequence with a subject sequence herein using the Needleman-Wunsch algorithm (Needleman and Wunsch, J. Mol. Biol. 48:443-453, 1970) as implemented in the Needle program of the European Molecular Biology Open Software Suite (EMBOSS [e.g., version 5.0.0 or later], Rice et al., Trends Genet. 16:276-277, 2000). The parameters of such an EMBOSS alignment can comprise, for example: gap open penalty of 10, gap extension penalty of 0.5, EBLOSUM62 (EMBOSS version of BLOSUM62) substitution matrix.
The numbering of particular amino acid residues of SEQ ID NO:62 herein (e.g., Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, Gln-616) is with respect to the full-length amino acid sequence of SEQ ID NO:62. The first amino acid (i.e., position 1, Met-1) of SEQ ID NO:62 is at the start of the signal peptide. Unless otherwise disclosed, substitutions herein are with respect to the full-length amino acid sequence of SEQ ID NO:62.
A “non-native glucosyltransferase” herein (“mutant”, “variant”, “modified” and like terms can likewise be used to describe such a glucosyltransferase) has at least one amino acid substitution at a position corresponding with a particular amino acid residue of SEQ ID NO:62. Such at least one amino acid substitution typically is in place of the amino acid residue(s) that normally (natively) occurs at the same position in the native counterpart (parent) of the non-native glucosyltransferase (i.e., although SEQ ID NO:62 is used as a reference for position, an amino acid substitution herein is with respect to the native counterpart of a non-native glucosyltransferase) (considered another way, when aligning the sequence of a non-native glucosyltransferase with SEQ ID NO:62, determining whether a substitution exists at a particular position does not depend in-and-of-itself on the respective amino acid residue in SEQ ID NO:62, but rather depends on what amino acid exists at the subject position within the native counterpart of the non-native glucosyltransferase). The amino acid normally occurring at the relevant site in the native counterpart glucosyltransferase often (but not always) is the same as (or conserved with) the particular amino acid residue of SEQ ID NO:62 for which the alignment is made. A non-native glucosyltransferase optionally can have other amino acid changes (mutations, deletions, and/or insertions) relative to its native counterpart sequence.
It may be instructive to illustrate a substitution/alignment herein. SEQ ID NO:12 (GTF 0544) is a truncated form of a Streptococcus sobrinus glucosyltransferase. It is noted that Leu-193 of SEQ ID NO:12 corresponds with Leu-373 of SEQ ID NO:62 (alignment not shown). If SEQ ID NO:12 is mutated at position 193 to substitute the Leu residue with a different residue (e.g., Gln), then it can be stated that the position 193-mutated version of SEQ ID NO:12 represents a non-native glucosyltransferase having an amino acid substitution at a position corresponding with Leu-373 of SEQ ID NO:62, for example.
The term “isolated” means a substance (or process) in a form or environment that does not occur in nature. Non-limiting examples of isolated substances include (1) any non-naturally occurring substance (e.g., a non-native glucosyltransferase herein), (2) any substance including, but not limited to, any host cell, enzyme, variant, nucleic acid, protein, peptide, cofactor, or carbohydrate/saccharide that is at least partially removed from one or more or all of the naturally occurring constituents with which it is associated in nature; (3) any substance modified by the hand of man relative to that substance found in nature (e.g., a non-native glucosyltransferase herein); or (4) any substance modified by increasing the amount of the substance relative to other components with which it is naturally associated. It is believed that the embodiments (e.g., enzymes and reaction compositions) disclosed herein are synthetic/man-made (could not have been made except for human intervention/involvement), and/or have properties that are not naturally occurring.
The term “increased” as used herein can refer to a quantity or activity that is at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 50%, 100%, or 200% more than the quantity or activity for which the increased quantity or activity is being compared. The terms “increased”, “elevated”, “enhanced”, “greater than”, “improved” and the like are used interchangeably herein. These terms can be used to characterize the “over-expression” or “up-regulation” of a polynucleotide encoding a protein, for example.
While advances have been made in producing insoluble glucan polymers using glucosyltransferase enzymes, less attention appears to have been drawn to modulating the molecular weight of insoluble glucan products synthesized by such enzymes. Addressing this technological gap, disclosed herein are glucosyltransferases with modified amino acid sequences that produce lower molecular weight insoluble glucan products.
Certain embodiments of the present disclosure concern a non-native glucosyltransferase comprising at least one amino acid substitution at a position corresponding with amino acid residue(s) Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, wherein the non-native glucosyltransferase synthesizes insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages, and the molecular weight of the insoluble alpha-glucan is lower than the molecular weight of insoluble alpha-glucan synthesized by a second glucosyltransferase that only differs from the non-native glucosyltransferase at the substitution position(s). Thus, in general, mutant glucosyltransferase enzymes are disclosed herein that can synthesize lower molecular weight insoluble alpha-glucan having alpha-1,3 glycosidic linkages.
A non-native glucosyltransferase herein synthesizes insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages. In some aspects, at least about 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 69%, 70%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% of the glycosidic linkages of such an alpha-glucan can be alpha-1,3 linkages. The linkage profile of an insoluble alpha-glucan can optionally be characterized as having a range between any two of these values. The other linkages in any of these aspects having 30%-99.5% alpha-1,3 linkages can be alpha-1,6, and/or not include any alpha-1,4 or alpha-1,2 linkages, for example.
Insoluble alpha-glucan in some aspects can have, for example, less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or 0.5% of alpha-1,2 or alpha-1,4 glycosidic linkages. In another embodiment, an insoluble alpha-glucan only has alpha-1,3 and optionally alpha-1,6 linkages (i.e., no alpha-1,2 or alpha-1,4 linkages). In aspects in which insoluble alpha-glucan comprises 50% alpha-1,3 glycosidic linkages, such glucan typically does not comprise alternan (alternating alpha-1,3 and -1,6 linkages).
Insoluble alpha-glucan in some aspects can be linear/unbranched (no branch points). Alternatively, there can be branches in an insoluble alpha-glucan herein. For example, an insoluble alpha-glucan can have less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or 0.5% branch points as a percent of the linkages in the polymer.
In certain aspects, an insoluble alpha-glucan can have a molecular weight in DPw or DPn of less than about 300. For example, the DPw or DPn can be about, or less than about, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, or 11. The molecular weight of an insoluble alpha-glucan can optionally be expressed as a range between any two of these values (e.g., 11-25, 12-25, 11-22, 12-22, 11-20, 12-20, 20-300, 20-200, 20-150, 20-100, 20-75, 30-300, 30-200, 30-150, 30-100, 30-75, 50-300, 50-200, 50-150, 50-100, 50-75, 75-300, 75-200, 75-150, 75-100, 100-300, 100-200, 100-150, 150-300, 150-200, 200-300). Molecular weight herein can be measured following any suitable method, including those methods disclosed in the present Examples (below) or as disclosed in U.S. Pat. Appl. Publ. Nos. 2017/0002335, 2015/0064748, or 2015/0232819, for example.
Alpha-glucan herein is insoluble in non-caustic aqueous systems, such as those conditions of a glucosyltransferase reaction herein (e.g., pH 4-8, see below). In general, the solubility of a glucan polymer in aqueous settings herein is related to its linkage profile, molecular weight, and/or degree of branching. For example, alpha-1,3-glucan with ≥95% 1,3 linkages is generally insoluble at a DPw of 8 and above in aqueous conditions at 20° C. In general, as molecular weight increases, the percentage of alpha-1,3 linkages required for alpha-1,3-glucan insolubility decreases.
Any of the foregoing linkage profiles and/or molecular weight profiles, for example, can be combined herein to appropriately characterize an insoluble alpha-glucan product of a non-native glucosyltransferase of the present disclosure.
A non-native glucosyltransferase, for example, can comprise the amino acid sequence of any glucosyltransferase disclosed in the following publications that is capable of producing insoluble alpha-glucan as presently disclosed, but with the exception that the non-native glucosyltransferase comprises at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62: U.S. Patent Nos. 7000000 and 8871474; and U.S. Patent Appl. Publ. Nos. 2015/0232819 and 2017/0002335, all of which are incorporated herein by reference. In some aspects, such a non-native glucosyltransferase (i) has at least one of the foregoing substitutions, and (ii) comprises an amino acid sequence that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to the amino acid sequence of the respective counterpart/parent glucosyltransferase not having the at least one substitution.
In some aspects, a non-native glucosyltransferase (i) comprises at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, and (ii) comprises, or consists of, an amino acid sequence that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO:2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 26, 28, 30, 34, or 59. Certain information regarding insoluble alpha-glucan products of glucosyltransferases with most of these amino acid sequences is provided in Table 2.
aGTF reactions and product analyses were performed as follows. Reactions were prepared comprising sucrose (50 g/L), potassium phosphate buffer (pH 6.5, 20 mM) and a GTF enzyme (2.5% bacterial cell extract by volume; extracts prepared according to U.S. Appl. Publ. No. 2017/0002335, in a manner similar to procedure disclosed in U.S. Pat. No. 8,871,474). After 24-30 hours at 22-25° C., insoluble product was harvested by centrifugation, washed three times with water, washed once with ethanol, and dried at 50° C. for 24-30 hours. Approximate linkages and DPn are shown for each insoluble product. Linkages and DPn were determined by 13C NMR and SEC, respectively.
In some aspects, a non-native glucosyltransferase (i) comprises at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, and (ii) comprises, or consists, of a glucosyltransferase catalytic domain that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO:66 (amino acid residues 55-960 of SEQ ID NO:4), residues 54-957 of SEQ ID NO:65, residues 55-960 of SEQ ID NO:30, residues 55-960 of SEQ ID NO:28, or residues 55-960 of SEQ ID NO:20. Such a non-native glucosyltransferase, for instance, is believed to be able to produce alpha-glucan that is water-insoluble and comprise at least about 50% (e.g., ≥90% or ≥95%) alpha-1,3 linkages. It is noted that a glucosyltransferase with amino acid positions 54-957 of SEQ ID NO:65 can produce alpha-1,3-glucan with 100% alpha-1,3 linkages (data not shown, refer to Table 6 of U.S. Pat. Appl. Publ. No. 2017/0002335, which is incorporated herein by reference), for example. It is further noted that SEQ ID NOs:65 (GTF 7527), 30 (GTF 2678), 4 (GTF 6855), 28 (GTF 2919), and 20 (GTF 2765) each represent a glucosyltransferase that, compared to its respective wild type counterpart, lacks the signal peptide domain and all or a substantial portion of the variable domain. Thus, each of these glucosyltransferase enzymes has a catalytic domain followed by a glucan-binding domain. The approximate location of catalytic domain sequences in these enzymes is as follows: 7527 (residues 54-957 of SEQ ID NO:65), 2678 (residues 55-960 of SEQ ID NO:30), 6855 (SEQ ID NO:66, which is residues 55-960 of SEQ ID NO:4), 2919 (residues 55-960 of SEQ ID NO:28), 2765 (residues 55-960 of SEQ ID NO:20). The amino acid sequences of the catalytic domains (approx.) of GTFs 2678, 6855, 2919 and 2765 have about 94.9%, 99.0%, 95.5% and 96.4% identity, respectively, with the approximate catalytic domain sequence of GTF 7527 (i.e., amino acids 54-957 of SEQ ID NO:65). Each of these particular glucosyltransferases (GTFs 2678, 6855, 2919 and 2765) can produce alpha-1,3-glucan with 100% alpha-1,3 linkages and a DPw of at least 400 (data not shown, refer to Table 4 of U.S. Pat. Appl. Publ. No. 2017/0002335). Based on this activity, and the relatedness (high percent identity) of the foregoing catalytic domains, it is contemplated that a non-native glucosyltransferase herein having one of the foregoing catalytic domains further with at least one amino acid substitution as presently disclosed can produce lower molecular weight insoluble alpha-glucan comprising at least about 50% (e.g., 90% or 95%) alpha-1,3 linkages.
In some aspects, a non-native glucosyltransferase (i) comprises at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, and (ii) comprises or consists of an amino acid sequence that is at least about 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 69%, 70%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO:62 or a subsequence thereof such as SEQ ID NO:4 (without start methionine thereof) or SEQ ID NO:66 (positions 55-960 of SEQ ID NO:4, approximate catalytic domain).
Although it is believed that a non-native glucosyltransferase in certain aspects need only have a catalytic domain, the non-native glucosyltransferase can be comprised within a larger amino acid sequence. For example, a catalytic domain may be linked at its C-terminus to a glucan-binding domain, and/or linked at its N-terminus to a variable domain and/or signal peptide.
Although amino acid substitutions in a non-native glucosyltransferase are generally disclosed herein with respect to the corresponding positions in SEQ ID NO:62, such substitutions can alternatively be stated simply with respect to its position number in the sequence of the non-native glucosyltransferase itself, as convenience may dictate.
Still further examples of non-native glucosyltransferases can be any as disclosed herein and that include 1-300 (or any integer there between [e.g., 10, 15, 20, 25, 30, 35, 40, 45, or 50]) residues on the N-terminus and/or C-terminus. Such additional residues may be from a corresponding wild type sequence from which the glucosyltransferase enzyme is derived, or may be a heterologous sequence such as an epitope tag (at either N- or C-terminus) or a heterologous signal peptide (at N-terminus), for example. A non-native glucosyltransferase herein typically lacks an N-terminal signal peptide; such an enzyme can optionally be characterized as being mature if its signal peptide was removed during a secretion process.
A non-native glucosyltransferase herein can be derived from any microbial source, for example, such as bacteria. Examples of bacterial glucosyltransferases are those derived from a Streptococcus species, Leuconostoc species, or Lactobacillus species. Examples of Streptococcus species include S. salivarius, S. sobrinus, S. dentirousetti, S. downei, S. mutans, S. oralis, S. gallolyticus and S. sanguinis. Examples of Leuconostoc species include L. mesenteroides, L. amelibiosum, L. argentinum, L. carnosum, L. citreum, L. cremoris, L. dextranicum and L. fructosum. Examples of Lactobacillus species include L. acidophilus, L. delbrueckii, L. helveticus, L. salivarius, L. casei, L. curvatus, L. plantarum, L. sakei, L. brevis, L. buchneri, L. fermentum and L. reuteri.
A non-native glucosyltransferase herein can be prepared by fermentation of an appropriately engineered microbial strain, for example. Recombinant enzyme production by fermentation is well known in the art using microbial species such as E. coli, Bacillus strains (e.g., B. subtilis), Ralstonia eutropha, Pseudomonas fluorescens, Saccharomyces cerevisiae, Pichia pastoris, Hansenula polymorpha, and species of Aspergillus (e.g., A. awamori) and Trichoderma (e.g., T. reesei) (e.g., see Adrio and Demain, Biomolecules 4:117-139, 2014, which is incorporated herein by reference). A nucleotide sequence encoding a non-native glucosyltransferase amino acid sequence is typically linked to a heterologous promoter sequence to create an expression cassette for the enzyme, and/or is codon-optimized accordingly. Such an expression cassette may be incorporated in a suitable plasmid or integrated into the microbial host chromosome, using methods well known in the art. The expression cassette may include a transcriptional terminator nucleotide sequence following the amino acid coding sequence. The expression cassette may also include, between the promoter sequence and glucosyltransferase amino acid coding sequence, a nucleotide sequence encoding a signal peptide (e.g., heterologous signal peptide) that is designed for direct secretion of the glucosyltransferase enzyme. At the end of fermentation, cells may be ruptured accordingly (generally when a signal peptide for secretion is not employed) and the glucosyltransferase enzyme can be isolated using methods such as precipitation, filtration, and/or concentration. Alternatively, a lysate or extract comprising a glucosyltransferase can be used without further isolation. If the glucosyltransferase was secreted (i.e., it is present in the fermentation broth), it can optionally be used as isolated from, or as comprised in, the fermentation broth. The activity of a glucosyltransferase enzyme can be confirmed by biochemical assay, such as measuring its conversion of sucrose to glucan polymer.
A non-native glucosyltransferase herein can comprise at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62. In some aspects, a non-native glucosyltransferase comprises at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Ser-553, Asn-573, Asp-575, Lys-578, or Gln-616 of SEQ ID NO:62. In some aspects, the amino acid substitution at a position corresponding with amino acid residue Leu-513 of SEQ ID NO:62 can be with an Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, or Tyr residue. In some aspects, the amino acid substitution at a position corresponding with amino acid residue Pro-550 of SEQ ID NO:62 can be with a Leu, Val, or Ile residue (e.g., Leu or Val). In some aspects, the amino acid substitution at a position corresponding with amino acid residue Ser-553 of SEQ ID NO:62 can be with an Ala, Cys, Glu, Phe, His, Ile, Met, Asn, Arg, Thr, Val, or Tyr residue. In some aspects, the amino acid substitution at a position corresponding with amino acid residue Asn-557 of SEQ ID NO:62 can be with a Glu, Gln, Ile, Thr, Asp, Asn, Leu, Val, or Ser residue (e.g., Glu, Gln, Ile, or Thr). In some aspects, the amino acid substitution at a position corresponding with amino acid residue Asn-558 of SEQ ID NO:62 can be with an Asp or Glu residue (e.g., Asp). In some aspects, the amino acid substitution at a position corresponding with amino acid residue Trp-571 of SEQ ID NO:62 can be with a Val, Asp, Cys, Ile, Leu, Glu, or Ser residue (e.g., Val, Asp, or Cys). In some aspects, the amino acid substitution at a position corresponding with amino acid residue Asn-573 of SEQ ID NO:62 can be with an Ala, Asp, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Thr, Val, or Trp residue. In some aspects, the amino acid substitution at a position corresponding with amino acid residue Asp-575 of SEQ ID NO:62 can be with a Ala, Cys, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Arg, Ser, Val, Trp, or Tyr residue. In some aspects, the amino acid substitution at a position corresponding with amino acid residue Lys-578 of SEQ ID NO:62 can be with an Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, or Tyr residue. In some aspects, the amino acid substitution at a position corresponding with amino acid residue Asn-581 of SEQ ID NO:62 can be with a Pro or Gly residue (e.g., Pro). In some aspects, the amino acid substitution at a position corresponding with amino acid residue Thr-585 of SEQ ID NO:62 can be with Pro or Gly residue (e.g., Pro). In some aspects, the amino acid substitution at a position corresponding with amino acid residue Gln-616 of SEQ ID NO:62 can be with an Ala, Cys, Asp, Glu, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Arg, Ser, Thr, Val, Trp, or Tyr residue.
Suitable substitution sites, and examples of particular substitutions at these sites, can include those as listed in Table 3 in Example 1 (below) that are associated with a decrease in the molecular weight (DPw) of insoluble alpha-1,3-glucan product by about, or at least about, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, or 85%, for example. The foregoing substitutions as listed in Table 3 are as they correspond with the listed residue position number in SEQ ID NO:62.
A non-native glucosyltransferase herein can comprise one, two, three, four, five, six, seven, or more of the presently disclosed amino acid substitutions, for instance. For example, a non-native glucosyltransferase with two or more of the presently disclosed amino acid substitutions can comprise at least one amino acid substitution at a position corresponding with (i) amino acid residue Pro-550, Asn-557, Asn-558, Asn-581, or Thr-585 of SEQ ID NO:62, and/or (ii) amino acid residue Leu-513, Ser-553, Asn-573, Asp-575, Lys-578, or Gln-616 of SEQ ID NO:62. Examples of substitution positions are at P550(L) and N557(I), P550(L) and N581(P), N557(I) and N581(P), 5553(C) and N558(D), 5553(C) and D575(V), S553(C) and T585(P), N558(D) and T585(P), D575(V) and T585(P), N558(D) and D575(V), P550(V) and S553(R), P550(V) and N581(P), P550(V) and T585(P), S553(R) and N581(P), S553(R) and T585(P), N581(P) and T585(P), P550(L) and S553(F), P550(L) and N581(P), S553(F) and N581(P), P550(V) and N557(E), P550(V) and T585(P) N557(E) and T585(P), where substituting amino acid residues are listed parenthetically as examples; one or more substitutions in addition to any at the foregoing position pairs can optionally be at position P550(L, V), N557(I, E), N581(P), 5553(any herein such as C, R, F), N558(D), D575(any herein such as V, A), T585(P), L513(any herein), N573(any herein such as I, V, P), K578(any herein such as N, D, R), Q616(any herein), W571(V, D, C), and/or any other position herein accordingly, where substituting amino acid residues are listed parenthetically as examples.
Simply for illustration purposes, a non-native glucosyltransferase herein can comprise a combination of amino acid substitutions at positions as shown in Table A (i-lxiii), where each substitution position corresponds with the respective amino acid position number in SEQ ID NO:62. The substituting amino acid residues in Table A are listed parenthetically as examples. In some aspects, a non-native glucosyltransferase can comprise a combination of amino acid substitutions as shown in Table A, where the substituting amino acids are those shown parenthetically in Table A.
aAmino acid residues listed parenthetically are examples of substituting amino acid residues.
A non-native glucosyltransferase with one or more amino acid substitutions herein can be based on any of a variety of glucosyltransferase amino acid sequences as presently disclosed, for example. Simply for illustration purposes, examples of such a non-native glucosyltransferase include those with a single amino acid substitution (e.g., at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62) or a combination of amino acid substitutions (e.g., any of embodiments i-lxiii of Table A) and that comprise or consist of an amino acid sequence that is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO:65 (optionally without the start methionine of SEQ ID NO:65) or residues 54-957 of SEQ ID NO:65, SEQ ID NO:30 (optionally without the start methionine of SEQ ID NO:30) or residues 55-960 of SEQ ID NO:30, SEQ ID NO:4 (optionally without the start methionine of SEQ ID NO:4) or SEQ ID NO:66 (residues 55-960 of SEQ ID NO:4), SEQ ID NO:28 (optionally without the start methionine of SEQ ID NO:28) or residues 55-960 of SEQ ID NO:28, or SEQ ID NO:20 (optionally without the start methionine of SEQ ID NO:20) or residues 55-960 of SEQ ID NO:20.
In some aspects, one or more substitutions are conserved or non-conserved substitutions; such conservation (or not) can be, for instance, with respect to the amino acid that occurs in the native glucosyltransferase from which the non-native glucosyltransferase is derived.
A non-native glucosyltransferase herein can synthesize insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages with a molecular weight lower than the molecular weight of insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages synthesized by a second glucosyltransferase (or, simply, “another” glucosyltransferase) (e.g., parent glucosyltransferase) that only differs from the non-native glucosyltransferase at the substitution position(s). A second glucosyltransferase herein, for example, can be comprised of all of, or mostly, native amino acid sequence. Thus, while a second glucosyltransferase herein can be a native glucosyltransferase in some aspects, it can be a prior-modified glucosyltransferase in other aspects (e.g., a glucosyltransferase with one or more other amino acid substitutions differing from the substitution[s] of the present disclosure). In some embodiments, a second glucosyltransferase to which a non-native glucosyltransferase is compared has a native amino acid residue(s) at the substitution position(s). Determining whether an amino acid residue is native can be done by comparing the second glucosyltransferase amino acid sequence to the native/wild type glucosyltransferase amino acid sequence from which the second glucosyltransferase is derived.
In some aspects, a non-native glucosyltransferase herein can synthesize insoluble alpha-glucan with a molecular weight that is about, or at least about, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% lower than the molecular weight of insoluble alpha-glucan synthesized by a second glucosyltransferase. Such a determination can be made with respect to any glucan synthesis reaction/process as disclosed herein (e.g., taking into account initial sucrose conc., temperature, pH, and/or reaction time), and using any suitable measurement technique (e.g., SEC). Typically, a comparison between non-native and second glucosyltransferases herein can be made under identical or similar reaction conditions. The molecular weight of insoluble alpha-glucan can be expressed as DPw, for example. Molecular weight can optionally be expressed as DP in embodiments regarding insoluble glucan with 20 or less monomeric units, for example.
Some embodiments disclosed herein concern a polynucleotide comprising a nucleotide sequence that encodes a non-native glucosyltransferase as presently disclosed (e.g., a non-native glucosyltransferase comprising at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62). Optionally, one or more regulatory sequences are operably linked to the nucleotide sequence, and preferably a promoter sequence is included as a regulatory sequence.
A polynucleotide comprising a nucleotide sequence encoding a non-native glucosyltransferase herein can be a vector or construct useful for transferring a nucleotide sequence into a cell, for example. Examples of a suitable vector/construct can be selected from a plasmid, yeast artificial chromosome (YAC), cosmid, phagemid, bacterial artificial chromosome (BAC), virus, or linear DNA (e.g., linear PCR product). A polynucleotide sequence in some aspects can be capable of existing transiently (i.e., not integrated into the genome) or stably (i.e., integrated into the genome) in a cell. A polynucleotide sequence in some aspects can comprise, or lack, one or more suitable marker sequences (e.g., selection or phenotype marker).
A polynucleotide sequence in certain embodiments can comprise one or more regulatory sequences operably linked to the nucleotide sequence encoding a non-native glucosyltransferase. For example, a nucleotide sequence encoding a non-native glucosyltransferase may be in operable linkage with a promoter sequence (e.g., a heterologous promoter). A promoter sequence can be suitable for expression in a cell (e.g., bacterial cell such as E. coli or Bacillus; eukaryotic cell such as a fungus, yeast, insect, or mammalian cell) or in an in vitro protein expression system, for example. Examples of other suitable regulatory sequences include transcription terminator sequences.
Some aspects herein are drawn to a cell comprising a polynucleotide sequence as presently disclosed; such a cell can be any type disclosed herein (e.g., bacterial cell such as E. coli or Bacillus; eukaryotic cell such as a fungus, yeast, insect, or mammalian cell). A cell can optionally express a non-native glucosyltransferase encoded by the polynucleotide sequence. In some aspects, the polynucleotide sequence exists transiently (i.e., not integrated into the genome) or stably (i.e., integrated into the genome) in the cell.
Some embodiments disclosed herein concern a reaction composition comprising water, sucrose, and one or more non-native glucosyltransferases herein (e.g., a non-native glucosyltransferase comprising at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62). Such a reaction composition produces, at least, insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages as disclosed.
The temperature of a reaction composition herein can be controlled, if desired, and can be about 5-50° C., 20-40° C., 30-40° C., 20-30° C., 20-25° C., 20° C., 25° C., 30° C., 35° C., or 40° C., for example.
The initial concentration of sucrose in a reaction composition herein can be about 20-400 g/L, 75-175 g/L, or 50-150 g/L, for example. In some aspects, the initial sucrose concentration is about, or at least about, 50, 75, 100, 150 or 200 g/L, or is about 50-600 g/L, 100-500 g/L, 50-100 g/L, 100-200 g/L, 150-450 g/L, 200-450 g/L, or 250-600 g/L. “Initial concentration of sucrose” refers to the sucrose concentration in a reaction composition just after all the reaction components have been added/combined (e.g., at least water, sucrose, non-native glucosyltransferase enzyme).
The pH of a reaction composition in certain embodiments can be about 4.0-9.0, 4.0-8.5, 4.0-8.0, 5.0-8.0, 5.5-7.5, or 5.5-6.5. In some aspects, the pH can be about 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, or 8.0. The pH can be adjusted or controlled by the addition or incorporation of a suitable buffer, including but not limited to: phosphate, tris, citrate, or a combination thereof. The buffer concentration in a reaction composition herein can be about 0.1-300 mM, 0.1-100 mM, 10-100 mM, 10 mM, 20 mM, or 50 mM, for example.
A reaction composition can be contained within any vessel (e.g., an inert vessel/container) suitable for applying one or more of the reaction conditions disclosed herein. An inert vessel in some aspects can be of stainless steel, plastic, or glass (or comprise two or more of these components) and be of a size suitable to contain a particular reaction. For example, the volume/capacity of an inert vessel (and/or the volume of a reaction composition herein), can be about, or at least about, 1, 10, 50, 100, 500, 1000, 2500, 5000, 10000, 12500, 15000, or 20000 liters. An inert vessel can optionally be equipped with a stirring device. Any of the foregoing features, for example, can be used to characterize an isolated reaction herein.
A reaction composition herein can contain one, two, or more different glucosyltransferase enzymes, for example, just as long that at least one of the enzymes is a non-native glucosyltransferase as presently disclosed. In some embodiments, only one or two glucosyltransferase enzymes is/are comprised in a reaction composition. A glucosyltransferase reaction herein can be, and typically is, cell-free (e.g., no whole cells present).
Any of the features disclosed herein (e.g., above and in the below Examples) regarding a reaction composition can characterize appropriate aspects of a glucan production method herein, and vice versa.
The present disclosure also concerns a method for producing insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages, the method comprising: (a) contacting at least water, sucrose, and at least one non-native glucosyltransferase as disclosed herein that produces insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages, whereby insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages is produced; and b) optionally, isolating the insoluble alpha-glucan produced in step (a). Conducting such a method, which can optionally be characterized as a glucan synthesis method, is typically also performed when conducting a reaction composition herein.
A glucan synthesis method as presently disclosed comprises contacting at least water, sucrose, and a non-native glucosyltransferase herein that produces insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages. These and optionally other reagents can be added altogether or in any order as discussed below. This step can optionally be characterized as providing a reaction composition comprising water, sucrose and a non-native glucosyltransferase enzyme that synthesizes insoluble alpha-glucan comprising alpha-1,3-linkages. The contacting step herein can be performed in any number of ways. For example, the desired amount of sucrose can first be dissolved in water (optionally, other components may also be added at this stage of preparation, such as buffer components), followed by addition of glucosyltransferase enzyme. The solution may be kept still, or agitated via stirring or orbital shaking, for example. A glucan synthesis method can be performed by batch, fed-batch, continuous mode, or by any variation of these modes.
Completion of a reaction in certain embodiments can be determined visually (e.g., no more accumulation of insoluble glucan), and/or by measuring the amount of sucrose left in the solution (residual sucrose), where a percent sucrose consumption of at least about 90%, 95%, or 99% can indicate reaction completion. A reaction of the disclosed process can be conducted for about 1 hour to about, or at least about, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 36, 48, 60, 72, 96, 120, 144, or 168 hours, for example.
The molecular weight of insoluble alpha-glucan produced in some aspects of a glucan synthesis method herein can be about, or at least about, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% lower than the molecular weight of insoluble alpha-glucan synthesized by a second glucosyltransferase.
Such molecular weight down-modulation in some aspects is achieved in a reaction conducted for about 36-60 hours (e.g., ˜48 hours).
Insoluble alpha-glucan comprising alpha-1,3-linkages produced in a method herein can optionally be isolated. In certain embodiments, isolating insoluble alpha-glucan can include at least conducting a step of centrifugation and/or filtration. Isolation can optionally further comprise washing insoluble alpha-glucan one, two, or more times with water or other aqueous liquid, and/or drying the insoluble alpha-glucan product.
Any of the disclosed conditions for synthesizing insoluble alpha-glucan, such as the foregoing or those described in the below Examples, can be applied to practicing a reaction composition as presently disclosed (and vice versa), and/or used to characterize features/activity of a non-native glucosyltransferase, accordingly.
In some aspects, an insoluble alpha-glucan product that has been isolated (optionally characterized as “purified”) can be present in a composition at a wt % (dry weight basis) of at least about 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 98.5%, 99%, 99.5%, 99.8%, or 99.9%. Such isolated polymer can be used as an ingredient/component in a product/application, for example.
The present disclosure also concerns a method of preparing a polynucleotide sequence encoding a non-native glucosyltransferase herein. This method comprises:
(a) identifying a polynucleotide sequence encoding a parent glucosyltransferase that (i) comprises an amino acid sequence that is at least about 40% identical to SEQ ID NO:4 or SEQ ID NO:66 (positions 55-960 of SEQ ID NO:4), and (ii) synthesizes insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages; and
(b) modifying the polynucleotide sequence identified in step (a) to substitute at least one amino acid of the parent glucosyltransferase at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, thereby providing a polynucleotide sequence encoding a non-native glucosyltransferase that synthesizes insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages and having a molecular weight that is lower than the molecular weight of insoluble alpha-glucan synthesized by the parent glucosyltransferase.
Such a method can optionally further comprise using a polynucleotide prepared in this manner in a method of expressing the non-native glucosyltransferase encoded by the polynucleotide. Such an expression method can follow any heterologous protein expression method as known in the art, for example. The present method of preparing a polynucleotide can optionally alternatively be characterized as a method of decreasing the product molecular weight of a glucosyltransferase.
A parent glucosyltransferase enzyme herein can comprise an amino acid sequence that is at least about 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 69%, 70%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO:4 (optionally without start methionine thereof) or SEQ ID NO:66 (positions 55-960 of SEQ ID NO:4, approximate catalytic domain), for example. It is noted simply for reference purposes that SEQ ID NO:4 without its start methionine is a subsequence of SEQ ID NO:62.
Identification step (a) herein can, in some instances, comprise identifying an amino acid sequence of a parent glucosyltransferase enzyme. A polynucleotide sequence can be determined from this amino acid sequence according to the genetic code (codons), such as the genetic code used in the species from which the parent glucosyltransferase was identified.
Identifying a polynucleotide encoding a parent glucosyltransferase herein can be performed (a) in silico, (b) with a method comprising a nucleic acid hybridization step, (c) with a method comprising a protein sequencing step, and/or (d) with a method comprising a protein binding step, for example.
Regarding in silico detection, the amino acid sequences of candidate parent glucosyltransferase enzymes (and/or nucleotide sequences encoding such glucosyltransferase enzymes) stored in a computer or database (e.g., public databases such as GENBANK, EMBL, REFSEQ, GENEPEPT, SWISS-PROT, PIR, PDB) can be reviewed in silico to identify a glucosyltransferase enzyme comprising an amino acid sequence with a percent sequence identity as described above for a parent glucosyltransferase. Such review could comprise using any means known in the art such as through use of an alignment algorithm or software as described above (e.g., BLASTN, BLASTP, ClustalW, ClustalV, Clustal-Omega, EMBOSS).
Identifying a parent glucosyltransferase as disclosed above can optionally be performed via a method comprising a nucleic acid hybridization step. Such a method can comprise using DNA hybridization (e.g., Southern blot, dot blot), RNA hybridization (e.g., northern blot), or any other method that has a nucleic acid hybridization step (e.g., DNA sequencing, PCR, RT-PCR, all of which may comprise hybridization of an oligonucleotide), for example. A polynucleotide sequence encoding SEQ ID NO:4 or a subsequence thereof (e.g., SEQ ID NO:66, which is positions 55-960 of SEQ ID NO:4) can be used as a probe, for example, in such a hybridization. Conditions and parameters for carrying out hybridization methods in general are well known and disclosed, for example, in Sambrook J, Fritsch E F and Maniatis T, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989); Silhavy T J, Bennan M L and Enquist L W, Experiments with Gene Fusions, Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1984); Ausubel F M et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience, Hoboken, N.J. (1987); and Innis M A, Gelfand D H, Sninsky J J and White T J (Editors), PCR Protocols: A Guide to Methods and Applications, Academic Press, Inc., San Diego, Calif. (1990).
Identifying a parent glucosyltransferase as disclosed above can optionally be performed via a method comprising a protein sequencing step. Such a protein sequencing step can comprise one or more procedures such as N-terminal amino acid analysis, C-terminal amino acid analysis, Edman degradation, or mass spectrometry, for example.
Identifying a parent glucosyltransferase as disclosed above can optionally be performed via a method comprising a protein binding step. Such a protein binding step can be performed using an antibody that binds to a motif or epitope within SEQ ID NO:4 (e.g., within SEQ ID NO:66, which is positions 55-960 of SEQ ID NO:4), for example.
A polynucleotide identified in step (a) (i.e., before its modification in step [b]) can, in some aspects, encode a glucosyltransferase comprising an amino acid sequence that is identical to, or at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to, the amino acid sequence of any glucosyltransferase disclosed in Table 1. An alpha-glucan as produced by such a glucosyltransferase can be as disclosed herein, for example.
A method of preparing a polynucleotide sequence encoding a non-native glucosyltransferase herein comprises step (b) of modifying the polynucleotide sequence (encoding a parent glucosyltransferase) identified in step (a). Such modification substitutes at least one amino acid of the parent glucosyltransferase at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62. The non-native glucosyltransferase (encoded by the modified polynucleotide sequence) resulting from such one or more substitutions can be optionally be characterized as a “child glucosyltransferase” herein.
A suitable modification of a polynucleotide in step (b) can be made following any DNA manipulation technique known in the art. Modifying step (b) can optionally be performed in silico, followed by synthesis of the polynucleotide sequence encoding a non-native glucosyltransferase. For example, a polynucleotide sequence identified in step (a) can be manipulated in silico using a suitable sequence manipulation program/software (e.g., VECTOR NTI, Life Technologies, Carlsbad, Calif.; DNAStrider; DNASTAR, Madison, Wisc.). Following such virtual manipulation, the modified polynucleotide sequence can be artificially synthesized by any suitable technique (e.g., annealing-based connection of oligonucleotides, or any technique disclosed in Hughes et al., Methods Enzymol. 498:277-309, which is incorporated herein by reference). It should be appreciated that the foregoing methodology is not believed to necessarily rely on having a pre-existing polynucleotide (encoding a parent glucosyltransferase) in hand.
Modifying step (b) can optionally be performed using a physical copy of a polynucleotide sequence identified in step (a) encoding a parent glucosyltransferase. As an example, such a polynucleotide can serve as a template for amplification using primers designed in a manner such that the amplified product encodes a non-native glucosyltransferase herein (e.g., refer to Innis et al., ibid.).
The amino acid substitutions in this method can be any of those one or more substitutions as disclosed herein. Essentially any non-native glucosyltransferase as presently disclosed can be encoded by a polynucleotide as prepared by this method, for instance.
Non-limiting examples of compositions and methods disclosed herein include:
1. A non-native glucosyltransferase comprising at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, wherein the non-native glucosyltransferase synthesizes insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages , and the molecular weight of the insoluble alpha-glucan is lower than the molecular weight of insoluble alpha-glucan synthesized by a second glucosyltransferase that only differs from the non-native glucosyltransferase at the substitution position(s).
2. The non-native glucosyltransferase of embodiment 1, comprising at least one amino acid substitution at a position corresponding with amino acid residue Leu-513, Ser-553, Asn-573, Asp-575, Lys-578, or Gln-616 of SEQ ID NO:62.
3. The non-native glucosyltransferase of embodiment 1 or 2, wherein: (i) the amino acid substitution at the position corresponding with amino acid residue Leu-513 is with an Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, or Tyr residue; (ii) the amino acid substitution at the position corresponding with amino acid residue Pro-550 is with a Leu, Val, or Ile residue; (iii) the amino acid substitution at the position corresponding with amino acid residue Ser-553 is with an Ala, Cys, Glu, Phe, His, Ile, Met, Asn, Arg, Thr, Val, or Tyr residue; (iv) the amino acid substitution at the position corresponding with amino acid residue Asn-557 is with a Glu, Gln, Ile, Thr, Asp, Asn, Leu, Val, or Ser residue; (v) the amino acid substitution at the position corresponding with amino acid residue Asn-558 is with an Asp or Glu residue; (vi) the amino acid substitution at the position corresponding with amino acid residue Trp-571 is with a Val, Asp, Cys, Ile, Leu, Glu, or Ser residue; (vii) the amino acid substitution at the position corresponding with amino acid residue Asn-573 is with an Ala, Asp, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Thr, Val, or Trp residue; (viii) the amino acid substitution at the position corresponding with amino acid residue Asp-575 is with an Ala, Cys, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Arg, Ser, Val, Trp, or Tyr residue; (ix) the amino acid substitution at the position corresponding with amino acid residue Lys-578 is with an Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, or Tyr residue; (x) the amino acid substitution at the position corresponding with amino acid residue Asn-581 is with a Pro or Gly residue; (xi) the amino acid substitution at the position corresponding with amino acid residue Thr-585 is with a Pro or Gly residue; and/or (xii) the amino acid substitution at the position corresponding with amino acid residue Gln-616 is with an Ala, Cys, Asp, Glu, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Arg, Ser, Thr, Val, Trp, or Tyr residue.
4. The non-native glucosyltransferase of embodiment 1, 2, or 3, comprising two or more amino acid substitutions, wherein at least one of the substitutions is at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62.
5. The non-native glucosyltransferase of embodiment 4, comprising at least one amino acid substitution at a position corresponding with amino acid residue Pro-550, Asn-557, Asn-558, Asn-581, or Thr-585 of SEQ ID NO:62; optionally wherein: (i) the amino acid substitution at the position corresponding with amino acid residue Pro-550 is with a Leu, Val, or Ile residue; (ii) the amino acid substitution at the position corresponding with amino acid residue Asn-557 is with a Glu, Gln, Ile, Thr, Asp, Asn, Leu, Val, or Ser residue; (iii) the amino acid substitution at the position corresponding with amino acid residue Asn-558 is with an Asp or Glu residue; (iv) the amino acid substitution at the position corresponding with amino acid residue Asn-581 is with a Pro or Gly residue; and/or (v) the amino acid substitution at the position corresponding with amino acid residue Thr-585 is with a Pro or Gly residue.
6. The non-native glucosyltransferase of embodiment 1, 2, 3, 4, or 5, wherein the insoluble alpha-glucan comprises at least about 50% alpha-1,3 glycosidic linkages.
7. The non-native glucosyltransferase of embodiment 6, wherein the insoluble alpha-glucan comprises at least about 90% alpha-1,3 glycosidic linkages.
8. The non-native glucosyltransferase of embodiment 1, 2, 3, 4, 5, 6, or 7, wherein the insoluble alpha-glucan has a weight average degree of polymerization (DPw) of less than about 300.
9. The non-native glucosyltransferase of embodiment 8, wherein the insoluble alpha-glucan has a DPw of less than about 150.
10. The non-native glucosyltransferase of embodiment 9, wherein the insoluble alpha-glucan has a DPw of less than about 75.
11. The non-native glucosyltransferase of embodiment 6, 7, 8, 9, or 10, comprising a catalytic domain that is at least about 90% identical to SEQ ID NO:66 (residues 55-960 of SEQ ID NO:4), residues 54-957 of SEQ ID NO:65, residues 55-960 of SEQ ID NO:30, residues 55-960 of SEQ ID NO:28, or residues 55-960 of SEQ ID NO:20.
12. The non-native glucosyltransferase of embodiment 11, comprising an amino acid sequence that is at least about 90% identical to SEQ ID NO:4, SEQ ID NO:65, SEQ ID NO:30, SEQ ID NO:28, or SEQ ID NO:20.
13. The non-native glucosyltransferase of embodiment 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12, wherein the molecular weight of the insoluble alpha-glucan is at least about 10% lower than the molecular weight of insoluble alpha-glucan synthesized by the second glucosyltransferase.
14. A polynucleotide comprising a nucleotide sequence encoding a non-native glucosyltransferase according to any one of embodiments 1-13, optionally wherein one or more regulatory sequences are operably linked to the nucleotide sequence, and preferably wherein the one or more regulatory sequences include a promoter sequence.
15. A reaction composition comprising water, sucrose, and a non-native glucosyltransferase according to any one of embodiments 1-13.
16. A method of producing insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages, the method comprising: (a) contacting at least water, sucrose, and a non-native glucosyltransferase enzyme according to any one of embodiments 1-13, whereby insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages is produced; and (b) optionally, isolating the insoluble alpha-glucan produced in step (a).
17. A method of preparing a polynucleotide sequence encoding a non-native glucosyltransferase (e.g., of any one of embodiments 1-13), the method comprising: (a) identifying a polynucleotide sequence encoding a parent glucosyltransferase that (i) comprises an amino acid sequence that is at least about 40% identical to SEQ ID NO:4 or SEQ ID NO:66 (positions 55-960 of SEQ ID NO:4), and (ii) synthesizes insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages; and (b) modifying the polynucleotide sequence identified in step (a) to substitute at least one amino acid of the parent glucosyltransferase at a position corresponding with amino acid residue Leu-513, Pro-550, Ser-553, Asn-557, Asn-558, Trp-571, Asn-573, Asp-575, Lys-578, Asn-581, Thr-585, or Gln-616 of SEQ ID NO:62, thereby providing a polynucleotide sequence encoding a non-native glucosyltransferase that synthesizes insoluble alpha-glucan comprising alpha-1,3-glycosidic linkages, wherein the molecular weight of the insoluble alpha-glucan is lower than the molecular weight of insoluble alpha-glucan synthesized by the parent glucosyltransferase.
18. The method of embodiment 17, wherein the identifying step is performed: (a) in silico, (b) with a method comprising a nucleic acid hybridization step, (c) with a method comprising a protein sequencing step, and/or (d) with a method comprising a protein binding step; and/or wherein the modifying step is performed: (e) in silico, followed by synthesis of the polynucleotide sequence encoding the non-native glucosyltransferase enzyme, or (f) using a physical copy of the polynucleotide sequence encoding the parent glucosyltransferase.
The present disclosure is further exemplified in the following Examples. It should be understood that these Examples, while indicating certain preferred aspects herein, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of the disclosed embodiments, and without departing from the spirit and scope thereof, can make various changes and modifications to adapt the disclosed embodiments to various uses and conditions.
This Example describes screening for glucosyltransferase variants that produce alpha-glucan with decreased molecular weight.
The amino acid sequence of the glucosyltransferase used to prepare amino acid substitutions in this Example was SEQ ID NO:4 (GTF 6855), which essentially is an N-terminally truncated (signal peptide and variable region removed) version of the full-length wild type glucosyltransferase (represented by SEQ ID NO:62) from Streptococcus salivarius SK126 (see Table 1). Substitutions made in SEQ ID NO:4 can be characterized as substituting for native amino acid residues, as each amino acid residue/position of SEQ ID NO:4 (apart from the Met-1 residue of SEQ ID NO:4) corresponds accordingly with an amino acid residue/position within SEQ ID NO:62. In reactions comprising at least sucrose and water, the glucosyltransferase of SEQ ID NO:4 typically produces alpha-glucan having about 100% alpha-1,3 linkages and a weight-average degree of polymerization (DPw) of 400 or greater (e.g., refer to U.S. Patent Nos. 8871474 and 9169506, and U.S. Pat. Appl. Publ. No. 2017/0002336, which are incorporated herein by reference). This alpha-glucan product, which is insoluble, can be isolated following enzymatic synthesis via filtration, for example.
Single mutations were individually introduced into a DNA sequence encoding SEQ ID NO:4 using a PCR (polymerase chain reaction)-based mutagenesis protocol (QUIKCHANGE LIGHTNING site-directed mutagenesis kit, Agilent Technologies, Santa Clara, Calif.). For each mutation, a DNA sequence containing the mutation was produced using PCR with a SEQ ID NO:4-encoding DNA template, a forward primer encoding the mutation, and a shared reverse primer.
Plasmids (pBAD vector-based) for individually expressing various single amino acid-substituted variants of GTF 6855 (SEQ ID NO:4) were used to transform E. coli strain Bw25113 (ΔilvC), which is a derivative of the F−, λ−, E. coli K-12 strain BD792 (CGSC6159) with one additional knock-out (ΔilvC). LB agar plates with 100 mg/L ampicillin were used to select transformants. Plasmid DNA from the clones was individually sequenced to verify that each intended single substitution was present in a correct manner. To produce GTF 6855 (SEQ ID NO:4) and each single amino acid-substituted variant thereof, the above E. coli Bw25113 (ΔilvC) transformants were individually cultivated overnight at 30° C. in LB media containing 100 mg/L ampicillin and 0.025% L-arabinose. Cells were then harvested and lysed with BUGBUSTER (EMD Millipore; volume was 10% of culture volume) at room temperature for about 1 hour. Lysed cells were centrifuged to remove cell debris; each resulting supernatant, which contained GTF 6855 (SEQ ID NO:4) or a single amino acid-substituted variant thereof, was used for glucan polymerization reactions (below).
GTF 6855 (SEQ ID NO:4) and each single amino acid-substituted variant thereof were individually entered into glucan synthesis reactions with parameters that were the same as, or similar to, the following: vessel, 50-mL indented shake flask agitated at 75 rpm; initial pH, 5.7; reaction volume, 10 mL; sucrose, 400 g/L; GTF, 0.3 mL of culture supernatant (above); KH2PO4, 5 mM; temperature, 35° C.; time, about two days. The reactions were then heat de-activated at 80° C. for 30 minutes. Insoluble glucan polymers produced in the reactions were individually harvested, water-washed, and analyzed for molecular size via a standard size exclusion chromatography (SEC) approach. Table 3 (below) provides the DPw of each insoluble glucan product.
aGTF 6855, SEQ ID NO: 4. The DPw of insoluble alpha-1,3-glucan produced by GTF 6855 averaged at about 350.
bEach listed GTF with a substitution is a version of GTF 6855 comprising a substitution at a respective position, where the position number is in correspondence with the residue numbering of SEQ ID NO: 62. The wild type residue is listed first (before residue position number) and the substituting residue is listed second (after the residue position number) (this “wild type residue-position number-variant residue” annotation format applies throughout the present disclosure).
cInsoluble alpha-1,3-glucan not produced or detected.
Based on the data in Table 3, it is apparent that certain amino acid substitutions in GTF 6855 (SEQ ID NO:4) result in enzymes that produce insoluble alpha-1,3-glucan with decreased molecular weight, as compared to the molecular weight of insoluble alpha-1,3-glucan produced by unmodified GTF 6855 (SEQ ID NO:4). With regard to those enzymes in Table 3 that produced insoluble glucan, all but four amino acid substitutions resulted in decreases in molecular weight by at least about 23%; well over two-thirds of the amino acid substitutions listed in Table 3 resulted in molecular weight decreases of 50% or more. Decreases in molecular weight of up to about 86% (D575P, Q616E) were observed, for example.
One or more substitutions at any the foregoing sites in this Example (positions corresponding to Leu-513, Ser-553, Asn-573, Asp-575, Lys-578, or Gln-616 of SEQ ID NO:62) are expected to allow for production of insoluble alpha-1,3-glucan with a DPw significantly lower than the DPw of insoluble alpha-1,3-glucan produced by a parent non-substituted glucosyltransferase.
This Example describes the effects of introducing multiple amino acid substitutions to a glucosyltransferase and determining their effect on its insoluble alpha-glucan synthesis function. This analysis indicates, for example, that amino acid substitutions identified above to decrease insoluble alpha-glucan product molecular weight can be included in substitution combinations that likewise impart this molecular weight effect.
Briefly, certain combinations of amino acid substitutions were made to SEQ ID NO:4 (GTF 6855, see Table 1 and Example 1 for description of this glucosyltransferase) by site-directed mutagenesis. For each combination, the QUIKCHANGE LIGHTNING site-directed mutagenesis kit was used in a successive manner to introduce each substitution to a SEQ ID NO:4-encoding sequence. Each combination of substitutions is listed in Table 4 below. The sequences encoding each modified glucosyltransferase were individually sequenced to confirm the intended changes. Each amino-acid-modified glucosyltransferase was then expressed and prepared according to Example 1.
Glucan synthesis reactions were conducted with each modified glucosyltransferase using parameters that were the same as, or similar to, the ones used in Example 1, followed by heat de-activation of each reaction at 80° C. for 30 minutes. Insoluble glucan polymers produced in the reactions were individually harvested, water-washed, and analyzed for molecular size via a standard SEC approach. Table 4 (below) provides the DPw of each insoluble alpha-1,3-glucan product.
aEach listed GTF is a version of GTF 6855 (SEQ ID NO: 4) comprising substitutions at respective positions, where each position number is in correspondence with the residue numbering of SEQ ID NO: 62.
Based on the data in Table 4, it is apparent that introduction of multiple amino acid substitutions to GTF 6855 (SEQ ID NO:4)—some combinations of which include substitutions shown in Example 1 to decrease molecular weight—can be employed in efforts to produce lower molecular weight insoluble alpha-1,3-glucan. For example, compare these DPw values (Table 4) to the ˜350 DPw of insoluble alpha-1,3-glucan produced by GTF 6855 (SEQ ID NO:4) without substitutions (Table 3).
It is apparent that a glucosyltransferase with multiple substitutions, including for example those at positions corresponding to (i) Pro-550, Asn-557, Asn-558, Asn-581, and/or Thr-585 of SEQ ID NO:62, and/or (ii) Leu-513, Ser-553, Asn-573, Asp-575, Lys-578, and/or Gln-616 of SEQ ID NO:62, can produce insoluble alpha-1,3-glucan with decreased molecular weight.
This Example describes synthesis of alpha-1,3-glucan in glucosyltransferase reactions containing a dextran primer that was previously modified to have 18.6% alpha-1,2 branches. The glucosyltransferase enzyme used in these reactions was modified (as disclosed in above Examples) to produce alpha-1,3-glucan of lower molecular weight compared to glucan product made by the enzyme's unmodified counterpart. Graft copolymers were synthesized comprising a dextran backbone and alpha-1,3-glucan arms.
Alpha-1,2-branched dextran was produced to prime glucosyltransferase reactions for alpha-1,3-glucan synthesis. Preparation of this primer was performed essentially as described in International Patent. Appl. Publ. No. WO2017/091533 and U.S. Patent Appl. Publ. No. 2018/0282385, which are both incorporated herein by reference. Briefly, linear dextran (i.e., polysaccharide with 100% alpha-1,6 glycosidic linkages) of molecular weight ˜14 kDa (DPw of ˜89) was produced using glucosyltransferase GTF8117. This dextran was then modified to have 18.6% alpha-1,2-branches using alpha-1,2-branching enzyme GTFJ18T1. The resulting dextran, which had a DPw of about 104 (˜17 kDa) and 18.6% alpha-1,2-branches, is referred to herein as P5 primer. P5 primer was then included in alpha-1,3-glucan synthesis reactions comprising a glucosyltransferase to produce graft copolymers comprising a dextran backbone and alpha-1,3-glucan arms. The glucosyltransferase used in these reactions is a non-native one as described in Example 2 above (Table 4). Enzyme preparation in the present Example was conducted as follows. Briefly, KOBW-3a cells heterologously expressing the glucosyltransferase were grown in LB medium containing 100 ng/mL ampicillin and 0.025% L-arabinose at 30° C. overnight. Cells were pelleted by centrifugation and then lysed with a 10% volume of BugBuster® Protein Extraction Reagent (EMD Millipore) at room temperature for at least 1 hour; cell debris was removed by centrifugation, after which clear cell lysate was collected for testing.
Thirteen separate 4.0-mL alpha-1,3-glucan synthesis reactions were performed in glass 50-mL indented flasks. Each reaction comprised water, sucrose (roughly 20, 50, or 200 g/L), phosphate buffer (5 mM, pH 5.7), optionally P5 primer (roughly 0.2, 1.0, or 5.0 g/L), and glucosyltransferase (above). The reactions were prepared by mixing an appropriate amount of P5 primer (using 50 g/L stock solution), 0.2 mL of cell lysate (containing the glucosyltransferase) and corresponding buffer. Each of these preparations and a sucrose stock solution (400 g/L) was warmed at 35° C. for at least 30 minutes. An appropriate volume of sucrose solution was then added to each preparation to initiate alpha-1,3-glucan synthesis. The reactions were carried out at 35° C. with shaking (10 rpm) for about 60 hours. Following this incubation, the entire contents of the reactions were individually transferred to 15-mL centrifuge tubes, which were placed in an 85° C. oven for about 30 minutes to deactivate the glucosyltransferase thereby terminating the reactions. Approximately 300-500 mg of wet cake produced in each reaction was analyzed by SEC to determine the molecular weight and DP of the insoluble polymer products. Table 5 provides the results of these analyses.
aPrimer P5 is DPw 104 (Mw = 16869 Da) (Mw/Mn = 1.48).
The size of individual alpha-1,3-glucan arms grafted onto primer in the glucan product of each primer-containing reaction is contemplated to be very similar to the size of alpha-1,3-glucan produced in control reactions that did not contain added primer; the control reaction products comprised alpha-1,3-glucan homopolymer. That said, it seems notable that, as the concentration of primer was increased in each set of reaction series (20, 50, or 200 g/L sucrose), graft copolymer product DPw decreased significantly.
Thus, graft copolymers were synthesized comprising a dextran backbone and alpha-1,3-glucan arms using a non-native glucosyltransferase of the instant disclosure. Primer was demonstrably consumed and incorporated into graft copolymer products. While alpha-1,2-branched dextran was used as primer in this Example, alpha-1,3-glucan synthesis was also observed when using dextran (as described above) that had not been modified with alpha-1,2 branches (data not shown).
This Example describes synthesis of alpha-1,3-glucan in glucosyltransferase reactions containing a dextran primer that was previously modified to have 9.7% alpha-1,2 branches. The glucosyltransferase enzyme used in these reactions was modified (as disclosed in above Examples) to produce alpha-1,3-glucan of lower molecular weight compared to glucan product made by the enzyme's unmodified counterpart. Graft copolymers were synthesized comprising a dextran backbone and alpha-1,3-glucan arms. Alpha-1,2-branched dextran was produced to prime glucosyltransferase reactions for alpha-1,3-glucan synthesis. Preparation of this primer was performed essentially as described in International Patent. Appl. Publ. No. WO2017/091533 and U.S. Patent Appl. Publ. No. 2018/0282385. Briefly, linear dextran (i.e., polysaccharide with 100% alpha-1,6 glycosidic linkages) of molecular weight ˜40 kDa (DPw of ˜250) was produced using glucosyltransferase GTF6831. This dextran was then modified to have 9.7% alpha-1,2-branches using alpha-1,2-branching enzyme GTFJ18T1. The resulting alpha-1,2-branched dextran, which had a DPw of about 271 (˜44 kDa), is referred to herein as P6 primer.
P6 primer was then included in alpha-1,3-glucan synthesis reactions comprising a glucosyltransferase to produce graft copolymers comprising a dextran backbone and alpha-1,3-glucan arms. The glucosyltransferase used in these reactions was the same as used and prepared in Example 3.
Thirteen separate 4.0-mL alpha-1,3-glucan synthesis reactions were performed in glass 50-mL indented flasks. Each reaction comprised water, sucrose (roughly 20, 50, or 200 g/L), phosphate buffer (5 mM, pH 5.7), optionally P6 primer (roughly 0.2, 1.0, or 5.0 g/L), and glucosyltransferase (above). The reactions were prepared by mixing an appropriate amount of P6 primer (using 50 g/L stock solution), 0.2 mL of cell lysate (containing the glucosyltransferase) and corresponding buffer. Each of these preparations and a sucrose stock solution (400 g/L) was warmed at 35° C. for at least 30 minutes. An appropriate volume of sucrose solution was then added to each preparation to initiate alpha-1,3-glucan synthesis. The reactions were carried out at 35° C. with shaking (10 rpm) for about 60 hours. Following this incubation, the entire contents of the reactions were individually transferred to 15-mL centrifuge tubes, which were placed in an 85° C. oven for about 30 minutes to deactivate the glucosyltransferase thereby terminating the reactions. Approximately 300-500 mg of wet cake produced in each reaction was analyzed by SEC to determine the molecular weight and DP of the insoluble polymer products. Table 6 provides the results of these analyses.
aPrimer P6 is DPw 271 (Mw = 43958 Da) (Mw/Mn = 1.19).
The size of individual alpha-1,3-glucan arms grafted onto primer in the glucan product of each primer-containing reaction is contemplated to be very similar to the size of alpha-1,3-glucan produced in control reactions that did not contain added primer; the control reaction products comprised alpha-1,3-glucan homopolymer. That said, it seems notable that generally, as the concentration of primer was increased in each set of reaction series (20, 50, or 200 g/L sucrose), graft copolymer product DPw decreased significantly. Thus, similarly to Example 3, graft copolymers were synthesized comprising a dextran backbone and alpha-1,3-glucan arms using a non-native glucosyltransferase of the instant disclosure. Primer was demonstrably consumed and incorporated into graft copolymer products.
This application is a continuation of application Ser. No. 16/295,423 (filed Mar. 7, 2019) (now Patent No. 11198853), which claims the benefit of U.S. Provisional Application Nos. 62/640,708 (filed Mar. 9, 2018) and 62/792,449 (filed Jan. 15, 2019), all of which prior applications are incorporated herein by reference in their entirety.
| Number | Date | Country | |
|---|---|---|---|
| 62792449 | Jan 2019 | US | |
| 62640708 | Mar 2018 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16295423 | Mar 2019 | US |
| Child | 17548677 | US |
