Patent Application
20170096656
Macroalgae (seaweeds) are used for various industrial applications and are currently produced on large scale in various parts of the world. The biomass production per area of macroalgae has been estimated to be up to 2.8 times higher than of sugarcane [1]. This production is likely to increase in the future, since their growth rate also increases with higher CO2 concentration and global warming. Macroalgae are therefore also a promising non-food feedstock for bioconversion into 2nd generation biofuels.
Brown algae (Phaeophyceae) are very promising biorefinery feedstock species because of the potential high bulk biomass production. The major constituent carbohydrates of Brown algae, i.e. alginate, laminarin and mannitol, amount up to 60% of dry weight in common Brown algae such as Laminaria. Alginate constitutes more than ⅓ of the carbohydrates and needs to be utilized to ensure cost effective production of biofuels and/or platform chemicals (such as organic acids and diols) from macroalgal biomass by microbial fermentation. Efficient conversion of alginate to fermentable (unsaturated) monosaccharides is therefore essential. As an example with alginate utilization included, the total ethanol yields per biomass dry weight of Brown algae will be significantly higher for seaweed than for lignocellulose [2].
Alginate (alginic acid) is a major constituent of the algal cell wall and intracellular material. It is a linear polymer comprised of blocks of (1→4)-linked β-D-mannuronate (M) and its (1→4)-linked C-5 epimer α-L-guluronate (G) residues. The residues are arranged in homopolymeric blocks of consecutive M- or G-residues, or heteropolymeric blocks of alternating M and G-residues [reviewed in 3]. Two genera of bacteria, Pseudomonas and Azotobacter, are known to produce alginate as exopolysaccharide [4, 5]. Alginate occurs as a Ca2+-alginate gel in the seaweed. Aqueous alginate solutions are therefore highly viscous and the polysaccharides are not easily accessible for enzymatic degradation. Replacement of Ca2+ with Na+, e.g. by adding large excess of Na+, will dissolve alginate and metal chelators (e.g. EDTA) that will bind Ca2+ have been applied for cell wall degradation in combination with enzymatic disruption/eliminative cleavage by alginate lyases [6]. However, this is not economically feasible on an industrial scale.
Alginate is an important industrial polysaccharide and has a wide variety of uses in the food sector for its dehydrating, gelling, stabilizing and thickening properties [reviewed in 7], as well as in various biotechnological and medical applications [reviewed in 3, 8]. The degradation of alginate to oligosaccharides and further to (unsaturated) mono-uronates is a challenging task on an industrial scale. Alginate is very resistant to acid hydrolysis and chemicals in the quantities needed for efficient industrial hydrolysis and their subsequent removal are costly.
Enzymatic degradation of alginate can be either selective or complete depending on the choice of enzymes. Enzymatic degradation is inherently a more economical process and environmentally more benign than chemical hydrolysis. Provided that substrate specificity demands are met by the enzymes, the technological set up would be simpler as chemical processes would need additional steps of neutralization and removal of chemicals. More robust thermostable enzymes, as described in this invention, may be used directly in crude feedstock slurries, and high process temperature would be advantageous leading to greater solubilisation of alginate, reduce viscosity and correspondingly facilitate enzymatic access to the polysaccharide chain.
For efficient degradation of alginate, enzymes of different specificities with respect to MM, GG and MG/GM blocks are needed. Alginate degrading enzymes have been identified from various organisms, including alginate utilizing bacteria. Alginate lyases catalyse β-elimination of the 4-O glycosidic bond between monomers, forming a double bond between the C4 and C5 carbons. Classification is based on their substrate specificity towards cleavage of M-rich blocks (polyM lyases), G-rich blocks (polyG lyases), or heteropolymeric MG blocks (polyMG lyases). The enzymes therefore typically have high specific activity towards one type of bond, with much lower, or no activity toward the other bond types, whereby also the specific microenvironment plays a role. Therefore no single alginate lyase enzyme is known to show high enough cleavage activity on all bond types, in order to give substantially complete degradation of alginate, with high conversion into (unsaturated) mono-uronates. In the present invention, we describe how near complete degradation of alginate with the production of (unsaturated) monosaccharides (mono-uronates) can be achieved with the use of a composition containing two, three or four different alginate lyase enzymes.
Several bacterial alginate lyase genes have been identified, cloned and sequenced. Both native and recombinantly expressed enzymes have been characterized, giving insight into alginate lyase structure and function [9-13]. In the Carbohydrate-Active Enzymes (CAZY) database (http://www.cazy.org/), alginate lyases are assigned to different polysaccharide lyase (PL) families based on amino acid sequence similarities. PL enzyme families may have other substrates specificities than alginate lyase activity and sequence identities between known alginate lyases can be low within a particular family. Alginate lyase activity is therefore non-obvious from primary sequence comparisons alone. As an example, AlyRm3 has seven homologues with amino acid sequence identity 22-39% with 60-90% sequence coverage (designated for clarification as the AlyRm3-group in this description). There is also a partial identity with the C-terminal region of sequences in families PL15 and PL17 (sequence coverage of around 30%) representing a Heparinase II/III-like protein domain (pfam07940 is a member of the superfamily cl15421). The apparent identity of AlyRm3 is to conserved sequence motives of the heparinase domain (see alignment in
According to the comprehensive CAZY database, genes encoding polysaccharide lyases are in general rare in thermophilic bacteria, missing in most species and representative genes encoding enzymes annotated as having activity on polysaccharides containing galacturonic acid (including pectate lyases and rhamnogalacturonan lyases). Furthermore, functional annotation is often based on only few characterized enzymes in each family.
Polysaccharide lyases are classified into families (PL families) based on the similarities of their primary structure, and activity on alginate is ascribed to sequences in seven PL families, PL5, PL6, PL7, PL14, PL15, PL17, and PL18 (of 22). Representatives of these families have only been detected in genomes of four thermophilic species, in Rhodothermus marinus (PL6, PL17), Spirochaeta thermophila (PL7, PL17), Merioribacter roseus (PL6, PL17) and one particular Paenibacillus strain Y412MC10 (PL7, PL15, PL17). Four non-classified polysaccharide lyases (with unknown activity) have also been annotated as such in genomes of three thermophiles, in Caldicellulosiruptor saccharolyticus (one gene), in Meiothermus ruber (two genes) and in Thermobispora bispora (one gene). Of the four unclassified polysaccharide lyases in the CAZY database, the putative polysaccharide lyase from C. saccharolyticus has the heparinase II/III-like protein domain observed in AlyRm3 and PL15 and PL17 sequences.
A thermostable alginate lyase has been isolated and characterized from Bacillus stearothermophilus. It has optimum activity at 50° C. and is stable for 4 h at 60° C. [14]. However, it is not known to which PL family it belongs and none of the sequenced Geobacillus genomes to date (Geobacillus is the revised genus name for Bacillus stearothermophilus) harbour any identified polysaccharide lyase genes. No other thermostable alginate lyases with optimum activity higher than 60° C. have been reported so far and no such enzymes with optimum activity at 70° C. or 80° C. or higher, have been described until now. The present invention is therefore the first known discovery of such highly thermostable alginate lyases.
The four alginate lyases, AlyRm1, AlyRm2, AlyRm3 and AlyRm4, described in this invention are from Rhodothermus marinus str. 378. Two of these, AlyRm1 and AlyRm2, belong to family PL6. The three characterized enzymes to date in this family have activity on chondroitin sulfate or alginate. Two other sequences originating from a thermophile, M. roseus, are found in this family. The AlyRm1 and AlyRm2 sequences are strain specific as homologues are found in the genome of R. marinus DSM 4252 but not in the R. marinus strain SG0.5JP17-172. AlyRm4 belongs to family PL17 which contains alginate and oligoalginate lyases. It is also strain specific as homologues are only found in the R. marinus DSM 4252 genome. Other thermophilic strains containing a PL17 sequence putatively encoding alginate lyases are S. thermophila, M. roseus and the Paenibacillus strain Y412MC10. The AlyRm3 alginate lyase apparently belongs to a hitherto unknown PL family. No homologues have been detected in other thermophilic species. It is only found in R. marinus strain 378 and R. marinus DSM 4252, but not in R. marinus strain SG0.5JP17-172. Alginate lyases have valuable properties applicable for biotechnological utilisation. They have been used to determine the fine structure of alginate, for production of defined alginate oligomers, and for protoplasting seaweed [reviewed in 7]. Their application for degradation of alginate polymers produced by Pseudomonas aeruginosa in cystic fibrosis patients has been described [14] and studied [15, 16]. Alginate lyases may also be used for degradation of alginate in the production of biofuels or renewable commodity compounds from algal biomass [17, 18]. For utilization in those various industrial processes, robust alginate lyases which can function at extreme circumstances, such as elevated temperatures, may be of great value and have many uses.
The present invention relates to a new set of enzymes that extends the current scientific knowledge of alginate lyases. The present application describes the first thermophilic alginate lyases with optimum activity higher than 60° C. The genes encoding the enzymes were identified in Rhodothermus marinus str. 378, a Gram-negative, aerobic, thermophile. The bacterium, which has been isolated from marine habitats around the world in proximity to hot spring vents, is a known producer of various robust enzymes [19]. The thermophilic R. marinus alginate lyases expand the previously described activity range of alginate lyases. Higher processing temperatures are possible, which is advantageous as solubility of alginate increases and viscosity is reduced. Consequently this facilitates enzymatic access resulting in a more efficient degradation of alginate. Thermophilic enzymes also simplify integration of degradation processes with prior pre-treatment of seaweeds which is optimally carried out at elevated temperatures. Thermophilic and thermostable enzymes reduce the need for cooling from often high pre-processing temperatures of algal biomass that would be required for mesophilic enzymatic alginate degrading processes, and the associated higher costs are therefore avoided. High temperature also prevents contamination by spoilage bacteria. A further advantage of thermophilic alginate lyases is that such enzymes expressed heterologously in a mesophilic host can be purified substantially by simple and relatively inexpensive heat precipitation of the host's proteins.
The thermophilic R. marinus alginate lyases differ in activity, but together they cover a wide activity range. This allows preparation of enzyme compositions containing one, or two, or three or four such enzymes for highly selective as well for more indiscriminate degradation of alginate with regard to glycosidic bond type. Such enzyme mixtures can be used to partially degrade alginate to yield oligosaccharides composed of alginate segments consisting essentially of D-mannuronic acid residues, or segments consisting essentially of L-guluronic acid residues, and also segments consisting essentially of alternating D-mannuronic acid and L-guluronic acid residues. By controlling the composition of the enzymes also a near complete degradation of alginate to yield fermentable monomers is possible. The (unsaturated) mono-uronates can alternatively be used as substrate in chemical syntheses. Such controlled degradation to different degrees of polymerization will give products that have valuable industrial application properties.
The present invention relates to the identification, production, and use of thermostable alginate lyase enzymes, the proteins themselves and polynucleotides encoding these, which enzymes together comprise the near complete range of specificities with regard to the glycosidic bond types in GG, MM and MG/GM disaccharide units for controlled and directed degradation of alginate. They can be used according to the invention in mixtures of different compositions and proportions with regard to enzyme types and specificities. These mixtures can be optimized for either partial degradation of alginate to yield oligosaccharides of specific monomer composition or alternatively for near complete degradation to (unsaturated) monomers. The mixtures can also be optimized in enzyme composition and proportions with regard to the fractional content of different uronate blocks in respective alginate substrates which may be species dependent.
As such, the invention provides in one embodiment a recombinant construct comprising a DNA sequence comprising a coding region for alginate lyase enzyme from thermophilic bacteria, or coding for an alginate lyase active domain, as further defined herein. The presence of alginate lyases is strain specific and suitable organisms for the isolation of thermostable alginate lyase enzymes include strains belonging to the genera Alicyclobacterium, Ammonifex, Anerocellum, Anaerolinea, Anaerophaga, Anoxybacillus, Caldicellulosiruptor, Clostridium, Caldilinea, Caldisericum, Calditerrivibrio, Caloramator, Chloroacidobacterium, Carboxydothermus, Chloroflexus, Clostridium, Desulfotomaculum, Dictyoglomus, Exiguobacterium, Fervidobacterium, Geobacillus, Marinithermus, Marinitoga, Meiothermus, Oceanithermus, Paenibacillus, Petrotoga, Rhodothermus, Roseiflexus, Spirochaeta, Syntrophothermus, Thermacetogenium, Thermaerobacter, Thermanaerovibrio, Therminicola, Thermoanaerobacter, Thermoanaerobacterium, Thermobacillus, Thermobaculum, Thermobifida, Thermobispora, Thermodesulfatator, Thermodesulfobacterium, Thermodesulfobium, Thermodesulfovibrio, Thermomicrobium, Thermomonospora, Thermosediminibacter, Thermosipho, Thermosynecchococcus, Thermotoga, Thermovibrio, Thermovirga, Thermus and other thermophilic organisms.
The thermostable alginate lyase enzymes can be from R. marinus, Melioribacter roseus, Spirochaeta thermophila, Caldicellulosiruptor saccharolyticus, Meiothermus ruber, Thermobiospora biospora, Paenibacillus spp., among other organisms.
The thermostable alginate lyase enzymes can be coded by genes identical or similar to alyRm1, alyRm2, alyRm3 and alyRm4, which are disclosed herein, among other genes. The sequences of the alyRm1, alyRm2, alyRm3 and alyRm4 and useful active variants thereof genes are shown herein as SEQ ID NO:7-12, respectively.
In certain embodiments the thermostable alginate lyase enzymes can be a fusion protein that includes His-tag (His6) or other suitable additions.
In certain embodiments the thermostable alginate lyase enzyme is modified, such that the amino acid sequence can have a number of amino acids deletions, amino acid modifications or amino acid additions.
In certain embodiments the thermostable alginate lyase enzymes can be expressed from bacteria such as E. coli. Methods to isolate and purify the enzyme from such production system are well known to the skilled person.
In certain embodiments the thermostable alginate lyase enzymes can be expressed from eukaryotic organisms such as yeasts or fungi. The invention also encompasses certain recombinant constructs and vectors for carrying the coding sequences of the thermostable alginate lyase enzymes.
In certain embodiments a composition for use in a method of the invention comprises at least one thermostable alginate lyase enzyme, although typically a composition will comprise more enzymes, for example, two, three, four or more.
Thus, in one aspect a composition for use in the invention may comprise thermostable alginate lyase enzymes with different specificities. A composition for use in the invention may comprise more than one enzyme activity in one or more of the classes active on M-rich blocks (polyM lyases), G-rich blocks (polyG lyases), or heteropolymeric MG blocks (polyMG lyases).
In another aspect of the invention, such a composition may comprise an auxiliary enzyme activity, such as β-glucanase enzymes.
The invention also contemplates certain methods for carrying out degradation of alginate from different macroalgae, such as from Microcystis, Ascophyllum, Laminaria, Ecklonia and Sargassum, by adding an enzyme composition of the invention to solutions of the alginate and incubating the mixture at suitable temperature and pH for a suitable length of time.
In one embodiment, the alginate can be from bacteria, such as Pseudomonas and Azotobacter.
In certain methods the alginate substrates in the reaction mixture can be oligosaccharides or polysaccharides and the like or their mixtures.
In one aspect, the enzyme or enzymes in a composition for use in the invention may be derived from Rhodothermus marinus. In the invention, it is anticipated that a core set of alginate degrading enzyme activities may be derived from R. marinus. That activity can then be supplemented with additional enzyme activities from other sources. Such additional activities may be derived from classical sources and/or produced by a genetically modified organism.
In one aspect, the enzyme in a composition for use in the invention is thermostable. Herein, this means that the enzyme has a temperature optimum of 60° C. or higher, for example about 70° C. or higher, such as about 75° C. or higher, for example about 80° C. or higher, such as about 85° C. or higher. Activities in a composition for use in the invention will typically not have the same temperature optima, but preferably will, nevertheless, be thermostable.
In addition, enzyme activities in a composition for use in the invention may be able to work at neutral pH between 5 and 9. For the purposes of this invention, neutral pH indicates a pH of about 4.5 to 9.5, about 5 to 9, about 5.5 to 8.5, about 5.5 to 8, about 5.5 to 7.5, about 5.5 to 7, about 5 to 6.5, about 5 to 6, about 5.5 to 6.
Enzyme activities in a composition for use in the invention may be defined by a combination of any of the above temperature optima and pH values.
In one embodiment of the invention, different enzymes or combinations of enzymes can be used to obtain different degree of hydrolysis of alginate to unsaturated monomers.
In one embodiment of the invention, enzymes or combinations of enzymes may be immobilised, such as on a surface or in a matrix of some sort, such as in a column, in order to increase durability and reuse of the enzyme(s) during the process of alginate degradation. Immobilisation of enzymes may be one aspect of process development and may include additional aspects of enzyme manipulation for improved process design.
In one aspect, this means that by using a single alginate lyase of the invention such as AlyRm3 can give about 50% conversion into unsaturated monomers or by using an enzyme such as AlyRm4 can give about 70% conversion into unsaturated monomers.
In another aspect, this means by using a mixture of two or more enzymes of the invention, about 85% conversion into unsaturated monomers can be obtained, or such as by using a mixture of AlyRM3 and AlyRm4 together, about 99% conversion into unsaturated monomers can be obtained.
A further aspect of the invention provides an isolated polynucleotide comprising a sequence coding for a thermostable alginate lyase selected from the group consisting of AlyRm1 depicted in SEQ ID NO:1, or SEQ ID NO: 2, AlyRm2 depicted in SEQ ID NO:3, or SEQ ID NO:4, AlyRm3 depicted in SEQ ID NO:5, and AlyRm4 depicted in SEQ ID NO: 6. In certain embodiments the isolated polynucleotide comprises a sequence selected from SEQ ID NO:7,
SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO: 12, or a nucleotide sequence coding for the same amino acid sequence as any of these. In another embodiment, the invention provides complimentary DNA (cDNA) that codes for any of the protein(s) of the invention, such as amino acid sequences comprising the above mentioned sequences.
Additional features and advantages of the present invention are described in, and will be apparent from, the following Detailed Description of the Invention and the figures.
Bioinformatic analysis of DNA sequence databases was used to identify the predicted open reading frame (ORF) of four alginate lyases in the genome of R. marinus isolate MAT378, termed alyRm1 to alyRm4. The enzyme domains were isolated, cloned, and expressed in soluble form in E. coli to investigate their activity. The enzymes were classified according to their domain structure. The current invention relates to thermostable/thermophilic alginate lyase enzymes from thermophilic bacteria. The recombinant enzymes were produced with polyhistidine tags that aid their purification. The enzymes were purified and their activity in degrading alginate and oligosaccharides made from β-D-mannuronic acid (M-block), or from α-L-guluronic acid (G-block) was assayed. Various assay methods were used for studying these activities and characterizing the enzymes.
In useful embodiments of the invention the lyase enzyme(s) of the invention and which are used in the methods of the invention comprise an alginate lyase domain, but parts of other sections of the full length protein as expressed native may be truncated. As described in more detail in the Examples, certain domains in the specific illustrated embodiments herein are contemplated to be lyase activity domains. Thus, the lyase domain of AlyRm1 protein can be seen as the section 20-490 aa of the full length native protein. N-terminally of this sequence is a signal peptide. In some embodiments of the invention an N-terminal signal peptide is not part of the lyase enzyme. C-terminally of the lyase domain of AlyRm1 is a section termed herein as a C-terminal attachment domain. (C-terminal part of SEQ ID:2 but not part of SEQ ID NO:1). As seen in Example X, this domain has certain effects on the activity and functional characteristics of the protein, but both variants, with and without the C-terminal domain, are active and thermophilic (with optimal activity at or above 60° C.). Accordingly, in embodiments of the invention, a lyase protein may used without such C-terminal domain, in full or in part. Thus, all methods, proteins, nucleotides and constructs disclosed and claimed herein, may in some embodiments refer to proteins and corresponding coding sequences comprising such lyase activity domain but without in full or in part such C-terminal domain and/or sequences which are natively N-terminally of the lyase activity domains such as but not limited to signal peptide sequences.
In the AlyRm2 protein, a corresponding C-terminal portion can be defined, and a protein of the invention and used in the methods of the invention may be without such C-terminal section, in full or in part. The same applies to other lyases of the invention.
In some embodiments of the invention the alginate lyase of the invention comprises a sequence selected from any of the SEQ ID NO:1, SEQ IDNO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6. In other embodiments the alginate lyase comprises a substantially similar sequence to any of those, which retains the thermophilic alginate lyase activity. Thus, N- and/or C-terminal domains and portions may be truncated, and/or non-critical amino acids may be altered, to improve characteristics of the protein.
In general, when the description refers to herein without further specifying an ‘alginate lyase’, this term includes an alginate lyase active domain, with or without N- and/or C-terminal protein domains and sequences, that are not crucial for the lyase activity.
As illustrated in the Examples and Figures, the proteins in the exemplified embodiments of the invention have varying optimal lyase activity, ranging from about 65° C. to about 90° C. Thus in embodiments of the invention, the alginate lyase used has optimum activity at about 60° C. or higher, such as at about 65° C. or higher, and more preferably at about 70° C. or higher, or about 75° C. or higher, and more preferably at about 80° C. or higher, such as at about 85° C. or higher.
In preferred embodiments of the proteins and methods of the invention, the alginate lyase of the invention has thermostable alginate lyase activity on alginate oligo/polysaccharides such that it preferentially cleaves M-G bonds and less preferentially G-G or M-M or G-M bonds. However, in certain other embodiments, the lyase thermostable alginate lyase activity on alginate oligo/polysaccharides such that it preferentially cleaves M-G or G-G bonds and less preferentially M-M or G-M bonds. In yet further embodiments, the lyase has thermostable alginate lyase activity on alginate oligo/polysaccharides such that it preferentially cleaves M-G or G-G or M-M or G-M bonds in a random fashion. In another embodiment, the lyase thermostable alginate lyase activity on alginate oligo/polysaccharides such that it preferentially cleaves M-M in an Exo-fashion and yielding preferentially monosugars.
In other embodiments, more than one or more than two or more than three different lyases are used in a composition, wherein such multiple lyases may have different activities, such as but not limited to those activity characteristics as described in the preceding paragraph, and thus by choosing different lyases and ratios of these, a customized activity profile of a lyase mixture can be attained, as desired for various applications.
It follows that in some very useful embodiments of the invention, lyase(s) of the invention are used to degrade certain substrates of interest. In some embodiments the substrate which is degraded with the invention comprises a first segment consisting essentially of D-mannuronic acid residues (M), a second segment consisting essentially of L-guluronic acid residues (G), and a third segment consisting essentially of alternating D-mannuronic acid and L-guluronic acid residues (GM or MG).
In certain embodiments the substrate is an alginate oligosaccharide. In other embodiments the substrate is an alginate polysaccharide, which may or may not be derived from macroalgae. In other embodiments, the substrate comprises a mixture of alginate oligosaccharide and alginate polysaccharide. The invention provides useful in particular embodiments wherein the substrate comprises polysaccharide derived from macroalgae from the genera of Microcystis, Ascophyllum, Laminaria, Ecklonia or Sargassum.
The invention is herein below described with certain illustrative non-limiting examples.
This example demonstrates how putative alginate lyase encoding genes were identified by sequence similarity analysis using the NCBI BLAST program (non-redundant protein sequences database). Sequence Alignments were performed using the EBI ClustalW2-Multiple Sequence Alignment tool (http://www.ebi.ac.uk/). Molecular weight (MW) and isoelectric points (pI) were computed using the Compute pI/Mw tool (ExPASy). Protein sequence analysis was performed using InterPro (EMBL-EBI) and SMART (EMBL) databases. Signal peptides were predicted using the SignalP-4.0 Server (CBS).
The alyRm1, 2 and 4 genes were identified through sequence similarities with previously annotated alginate lyase genes (>40% aa identity). The alyRm3 gene was detected through non-obvious similarities following psi-BLAST where 23% aa identity was found with about 300 nt gene fragment encoding a partial alginate lyase protein from Yersinia pestis (WP_002427804.1) containing a heparinase II/III-like domain.
The alyRm1 was identified as a 1743 nt gene, encoding a 580 aa polypeptide with calculated MW of 63.683 and pI of 5.78. A putative signal sequence was predicted with cleavage site after Ala-19. The alyRm2 gene encodes a 2901 nt gene, encoding a 966 aa polypeptide with calculated MW of 107.238 and pI of 4.74. Both genes encode pectin lyase fold domains that contain parallel beta-helix repeats [20] often found in polysaccharide degrading enzymes. Based on their deduced aa sequences, both enzymes belong to family 6 of polysaccharide lyases. C-terminal domains of about 90 nt (10 kDa) are found in both genes. These domains show significant alignments with C-terminal modules predicted to mediate cell-attachment in members of the Bacteroides phylum [21]. A similar C-terminal region has been identified in a previously identified family 6 polysaccharide lyase from the thermophile Melioribacter roseus P3M (GenBank: AFN74606.1). The alyRm2 gene also contains a large N-terminal domain of about 1155 nt (43 kDa) of unknown function which contains no known motifs. Based on the above information the two R. marinus alginate lyases may be divided into the following regions: AlyRm1; signal peptide (aa 1-19), alginate lyase (aa 20-490) and C− terminal sorting/docking domain (aa 491-580) and AlyRm2; uncharacterized N-terminal domain, (aa 1-385), alginate lyase (aa 386-874) and C-terminal sorting/docking domain (aa 875-966) (see
The defined alginate lyase domains of AlyRm1 (aa 20-490) and AlyRm2 (aa 386-874) shared 36% aa identity. AlyRm1 showed 92% aa sequence identity (lyase domain showed 93% aa identity) with annotated polyM lyase of R. marinus strain DSM 4252 (GenBank: ACY48055.1) and the lyase domain showed 49% aa identity with a polyM lyase of M. roseus PM3 (GenBank: AFN74598.1). AlyRm2 was identical with a hypothetical protein from R. marinus DSM 4252 (GenBank: ACY48275.1) and the lyase domain showed 46% aa identity with a lyase precursor from M. roseus (GenBank: AFN74606.1).
1. AlyRm1 Rhodothermus marinus str. 378 with signal peptide sequence
2. AlyRm2 Rhodothermus marinus str. 378 without N-terminal sequence
3. gi|268316944|ref|YP_003290663.1| hypothetical protein Rmar_1386 [Rhodothermus marinus DSM 4252]
4. gi|379046722|gb|AFC88009.1| polyMG-specific alginate lyase [Stenotrophomonas maltophilia]
5. gi|515827351|ref|WP_017258104.1| hypothetical protein [Pedobacter arcticus]
6. gi|397690365|ref|YP_006527619.1| lyase precursor [Melioribacter roseus P3M-2]
7. gi|522162944|ref|WP_020674152.1| hypothetical protein [Amycolatopsis nigrescens]
8. gi|1002527|gb|AAC83384.1| chondroitinase B precursor [Pedobacter heparinus]
9. gi|216849|dbj|BAA01182.1| alginate lyase [Pseudomonas sp.]
10. gi|1397690357|ref|YP_006527611.1| poly(β-D-mannuronate) lyase [Melioribacter roseus P3M-2]
11. gi|518835313|ref|WP_019991221.1| hypothetical protein [Rudanella lutea]
The predicted ORF of alyRm3 was 2613 nt, encoding a 870 aa polypeptide, with calculated MW of 96.492 and pI 5.28. A signal sequence was predicted with cleavage site after Gln-17 and a heparinase II/III-like protein domain (aa 374-518) [22] was detected. The enzyme does not show high sequence similarity with previously described polysaccharide lyases and therefore cannot be assigned to a family. Highest sequence similarities were found with an annotated heparinase II/III family protein from R. marinus DSM 4252 (>99% aa identity, GenBank: ACY48059.1) and a heparinase II/III family protein from Rhodopirellula sp. SWK7 (39% aa identity, GenBank: ZP-23730810.1).
The gene encoding AlyRm4 consists of 2226 nt, which translate into a 742 aa polypeptide with MW of 83.561 and pI 6.11. A hydrophobic sequence was detected at the N-terminal end, indicating that the enzyme may be located in the periplasmic space. The enzyme contains both an alginate lyase domain (aa 26-309) and a heparinase II/III-like protein domain (aa 386-539). AlyRm4 belongs to family 17 of polysaccharide lyases and showed >99% aa identity with a heparinase II/III family protein from R. marinus DSM 4252 (GenBank: ACY48059.1) and 45% aa identity with a heparinase II/III family protein from M. roseus (GenBank: YP_006527616.1).
The sequences in
1. gi|511825188|ref|WP_016403995.1| poly(β-D-mannuronate) lyase [Agarivorans albus]
2. gi|397690362|ref|YP_006527616.1| Heparinase II/III family protein [Melioribacter roseus P3M-2]
3. AlyRm4 Rhodothermus marinus str. 378 without N-terminal signal peptide
4. gi|342674030|gb|AEL31264.1| oligoalginate lyase [Sphingomonas sp. MJ3]
5. gi|217228794|gb|ACK10579.1|Pseudomonas sp. OS-ALG-9 Sequence 50 from U.S. Pat. No. 7,439,034
6. gi|511825189|ref|WP_016403996.1| poly(β-D-mannuronate) lyase [Agarivorans albus]
7. gi|397690362|ref|YP_006527616.1| Heparinase II/III family protein [Melioribacter roseus P3M-2]
8. gi|410825542|gb|AFV91542.1| alginate lyase 2B [Flavobacterium sp. S20]
9. gi|90022924|ref|YP_528751.1| alginate lyase [Saccharophagus degradans 2-40]
10. AlyRm3 Rhodothermus marinus str. 378 without N-terminal signal peptide
11. gi|496390129|ref|WP_009099119.1| Heparinase II/III family protein [Rhodopirellula sp. SWK7]
12. gi|495374567|ref|WP_008099279.1| Heparinase II/III-like protein [Verrucomicrobiae bacterium DG1235]
13. gi|60115421|dbj|BAD90006.1| alginate lyase [Sphingomonas sp. A1]
14. gi|15891901|ref|NP_357573.1| oligo alginate lyase [Agrobacterium fabrum str. C58]
15. gi|261407486|ref|YP_003243727.1| Heparinase II/III family protein [Paenibacillus sp. Y412MC10]
16. gi|9501763|dbj|BAB03319.1| oligo alginate lyase [Sphingomonas sp.]
17. gi|84376182|gb|EAP93067.1| hypothetical protein V12B01_24239 [Vibrio splendidus 12B01]
This example demonstrates the cloning of alginate lyase genes. The genes were amplified from the genome of R. marinus strain MAT378. The alyRm1 gene was amplified without the signal peptide sequence (without aa 1-17) and with and without the putative C-terminal cell-attachment domain (aa 491-580). They are designated AlyRm1 and AlyRm1ΔC, respectively. The alyRm2 gene was amplified without the N-terminal domain (aa 1-385) and with and without the putative C-terminal cell-attachment domain (aa 875-966). They are designated AlyRm2 and AlyRm2ΔC, respectively. The alyRm3 and alyRm4 genes were amplified without the predicted signal peptide sequences, AlyRM3 (without aa 1-17) and AlyRM4 (without aa 1-22) respectively. For heterologous expression in E. coli, all the alginate lyases genes were modified with an N-terminal hexa-histidine tag. Primers were designed as listed in Table 1 to amplify the coding regions of the respective genes and introducing the restriction sites BamHI or BglII at the 5′ ends and a HindIII site behind the stop codons. The amplifications were performed using standard PCR conditions and a proofreading polymerase, the fragments cut with the corresponding restriction enzymes and inserted into the L-rhamnose inducible expression vector pJOE5751. The vector contains a His6-eGFP fusion under control of the rhaPBAD promoter. The single BamHI and HindIII restriction sites in the vector allowed the replacement of the eGFP by the alginate lyase genes and fusion to the His6-tag. All genes, the corresponding primers and the resulting expression vectors are listed in Table 1.
This example demonstrates the expression of active enzymes in soluble form in E. coli, and purification to investigate their activity. An E. coli expression vector from Motejadded et al. [23] was used. E. coli JM109 carrying the respective recombinant plasmids were cultivated in LB medium (200 ml), containing 100 μg/ml ampicillin. For expression of the genes, cultures were grown at 37° C. till cell density reached OD600 of 0.3, then induced by adding 0.1% rhamnose and further grown for 4 h at 30° C. The cells were harvested by centrifugation at 4500×g for 20 min at 4° C., washed, resuspended in 10 mM potassium phosphate buffer pH 6.5 and disrupted by passing them twice through a French press cell. After centrifugation (13,000×g for 15 min at 4° C.), the supernatants of the crude cell extracts and the cell pellets were analysed by SDS-PAGE.
The purifications of recombinant alginate lyase proteins were performed by immobilized metal affinity chromatography (IMAC). The supernatant of the respective crude cell extract, containing approximately 25 mg E. coli protein, was applied onto 2 ml Talon® metal affinity resin (Clontech) in a column using gravity flow. The resin was washed with 10 ml of washing buffer (50 mM potassium phosphate, 300 mM NaCl, 5 mM imidazole pH 7.0). Bound protein was eluted with 3 ml of elution buffer (50 mM potassium phosphate, 300 mM NaCl, 150 mM imidazole pH 7.0. (His)6-alginase containing fractions were combined and applied onto an NAP10 column (GE Healthcare), equilibrated with 50 mM potassium phosphate, 300 mM NaCl pH 7.0 to remove imidazole and stored at 4° C.
Fractions containing purified samples were further analysed. Protein concentration was estimated using the method of Bradford [24] using Bradford reagent (Bio-Rad) and BSA standards for preparation of standard curves. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was performed using the method of Laemmli [25] using standard gels and a broad-range protein standard (Fermentas). Gels were stained using Coomassie Brilliant Blue R-250 (Sigma). Rhamnose induction of the E. coli JM109, harbouring the respective plasmids, resulted in the production of high amounts of the recombinant proteins as judged by SDS-PAGE (
This example demonstrates the activity of the alginate lyases on alginate from Macrocystis pyrifera (Kelp) (low viscosity, sodium salt alginate obtained from Sigma). Samples (10 μl) were incubated for 10 min with 1% alginate in 50 mM buffer (90 μl) (final concentrations) at different temperatures. Then, 100 μl of 3,5-dinitrosalicylic acid (DNS) were added to each sample and heated at 100° C. for 5 min. A 150 μl of each sample were diluted with 150 μl of water and optical density (OD) measured at 546 nm. One unit (U) of enzyme activity corresponds to the release of 1 μmol of reducing sugar equivalents (expressed as glucose) per minute. For enzyme characterization, the following buffers were used; sodium acetate (pH 4.5-5.5), potassium phosphate (pH 6.0-8.0), and Tris (pH 7.2-9.5). Tris buffers were specifically set to work at the appropriate incubation temperatures.
All six recombinant enzymes degraded alginate and their characteristics are summarized in Table 2.
The two AlyRm1 variants displayed somewhat different characteristics. The AlyRm1 variant containing the C-terminal docking domain (AlyRm1) had a higher optimum temperature, was more heat stable and less salt tolerant than the variant lacking the domain (AlyRm1ΔC), see
The two variants of AlyRm2 showed similar characteristics (
AlyRm3 was most active at around 75° C. and had a very narrow pH range around 5.5. The enzyme half-life was estimated around 8 h at 70° C. The enzyme was relatively stable at variable concentrations of NaCl (
The optimum temperature of AlyRm4 was 81° C. and the enzyme was heat stable at 70° C. for at least 16 h. The optimum pH was 6.5 and the enzyme was relatively stable at NaCl concentrations up to 1 M (
This example demonstrates the degradation of alginate following incubation with the recombinant enzymes and assayed using thin layer chromatography (TLC) at different reaction times. Reaction products were visualized on the TLC plate by developing with the solvent mixture n-butanol/acetic acid/water (2:1:1, by volume) and visualized using 2.5% sulfuric acid solution in 47.5% ethanol, followed by heating the TLC plate at 100° C. for 10 min.
The AlyRm1, AlyRm2 and AlyRm3 lyases produced different patterns of unidentified oligosaccharides, whereas AlyRm4 and a mix of all four enzymes seemed to produce mostly (unsaturated) mono-uronates, not detected by TLC (
None of the alginate lyase enzymes showed any activity on chondroitin sulfate.
This example demonstrates the degradation pattern of the four thermophilic alginate lyase enzymes when analyzed with TLC, MALDI-TOF-MS, HPAEC-PAD and 1D/2D 1H NMR. The methods used for the analysis have been previously described, i.e. in Hreggvidsson et al. [26] and in Jonsson [27]. Enzyme incubations were done as follows: Mixing 80 μl of 12.5 mg/ml of alginate (from Sigma), or G-block oligosaccharides, or M-block oligosaccharides (from Elicityl) into 10 μl of 0.5 M phosphate buffer pH 7 and 10 μl of 0.5 U/ml enzyme solution, followed by incubation at 65° C. for the appropriate time.
Degradation pattern of alginate, G-block and M-block by the thermostable alginate lyase, AlyRm1 is shown in
The data in
The same enzyme lacking the C-terminal domain (AlyRm1ΔC), however has major activity in cleaving G-G, M-G and/or G-M bonds but with minor activity on M-M bonds (results not shown): ( . . . M↓GMMM↓G↓GG↓GGG↓G↓G↓MMMMMMM↓GM↓GM↓GM↓GM↓MMMM).
Degradation pattern of alginate, G-block and M-block by the thermostable alginate lyase, AlyRm2ΔNC is shown in
The data in
The degradation pattern of alginate, G-block and M-block by the thermostable alginate lyase, AlyRm3 is shown in
The data in
The degradation pattern of alginate, G-block and M-block by the thermostable alginate lyase, AlyRm4 is shown in
The data in
The main characteristics of the thermostable alginate lyases from R. marinus are summarized in Table 2.
1Enzyme half-life estimated as 50% residual activity following incubation at 50, 60, 70 or 80° C. for up to 16 h. All enzymes were fully stable at 50° C. but none of them was stable following 30 min. incubation at 80° C. Assay performed at 60° C. (optimum pH).
2≧80% relative activity.
This example demonstrates the extent of degradation of alginate into (unsaturated) mono-uronates by the four thermophilic alginate lyase enzymes of the invention. A 4 ml reaction mixture composed of 1% alginate (10 mg/ml) in 50 mM acetate buffer (pH 5.5) and containing 0.6 U/ml of each enzyme (AlyRm1, AlyRm2, AlyRm3, AlyRm4) was incubated at 55° C. with shaking at 150 rpm for 24 h.
To a 0.8 ml sample of the above reaction mixture (or dilutions thereof) was then added the following: 25 μl of 25 mM HIO4 in 0.125M H2SO4 and kept at room temperature for 20 min.
Then 0.5 ml of 2% Sodium arsenite in 0.5M HCl and 2 ml of 0.3% TBA solution (2-Thiobarbituric Acid, pH 2) were added, stirred and incubated at 100° C. for 10 min. Then cooled and absorbance was measured at 548 nm. (The method is based upon the formation of β-formylpyruvate from periodate oxidation, where 0.01 μmol β-formylpyruvate gives optical density reading of 0.29 at 548 nm [ε=2.9×104 M−1 cm−1]. The standard curve made with 2-deoxy glucose (10 mg/ml) was linear up to 0.08 mg of 2-deoxy glucose in the above assay. Incubation with different combinations of the thermophilic alginate lyases were also in all cases linear up to 0.08 mg of alginate and therefore the extent of degradation into unsaturated monomers could be determined. The different enzyme combinations gave results as shown in Table 3.
The data presented in this example shows that different degree of conversion into unsaturated monomers can be obtained from around 50% to around 100%, by using different alginate lyases of the invention or mixtures thereof.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/IS2015/050001 | 1/12/2015 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 61926009 | Jan 2014 | US |
