# Patent

## Title
Enzymic production of neoagarobiose

## Abstract

The present invention is directed to methods and systems of producing neoagarobiose, useful in whitening melanoma cells and in cosmetics, using polypeptides having neoagarobiosebiohydralase activity, including Aga86E from Saccharophagus degradans. The reaction can be enhanced by including other agarases, including Aga16B, also from S. degradans.

## Background
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
The subject matter of this application was in part funded by the National Science Foundation (DEB0109869) and from Maryland Sea Grant. The government has certain rights in this invention.


CROSS-REFERENCE TO RELATED APPLICATION
The present application claims priority to U.S. Provisional Application Ser. No. 60/914,791, ENZYMIC PRODUCTION OF NEOAGAROBIOSE, filed on Apr. 30, 2007 and is hereby incorporated in its entirety by reference.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ON A COMPACT DISC
Not applicable.
FIELD OF THE INVENTION
The invention is directed to compositions and methods for the production of degradation products of agar, agarose, and derivatives thereof, including the production of neoagarobiose.
BACKGROUND OF THE INVENTION
Saccharophagus degradans 2-40 (formerly Microbulbifer degradans 2-40) is a rod-shaped, aerobic, marine bacterium isolated from the surface of decomposing saltwater cord grass, Spartina alterniflora, in the lower Chesapeake Bay (Andrykovitch and Marx, 1988). S. degradans 2-40 is related to a group of marine γ-subgroup proteobacteria capable of degrading complex polysaccharides (CPs) (Ekborg et al., 2005; Gonzalez and Weiner, 2000), a critical function in the marine food web. S. degradans 2-40 is unique among these bacteria due to its ability to utilize CPs of algal, higher plant, fungal, and animal origins, such as agar, alginate, cellulose, chitin, β-glucan, laminarin, pectin, pullulan, starch, and xylan, as sole carbon and energy sources (Andrykovitch and Marx, 1988; Ensor et al., 1999; Howard et al., 2003; Kelly et al., 1990). The mechanism by which this bacterium degrades these normally recalcitrant substrates has been established only for the chitinolytic system (Howard et al., 2003).
Agar, a cell wall constituent of many red algae (Rhodophytd), exists in nature as a mixture of unsubstituted and substituted agarose polymers that form an agarocolloid gel (Craigie, 1990; Duckworth and Yaphe, 1970). Agarose is composed of repeating neoagarobiose units (3-6-anhydro-L-galactose-α1-3-D-galactose) joined by β1-4 bonds that form a helix in aqueous environments. The galactose moieties of the repeating neoagarobiose units can be methylated, pyruvated, sulfonated, or glycosylated to form various substituted derivatives with different gelling and solubility characteristics. Up to 70% of the algal cell wall can be agar polymers. The remaining material consists of other galactans and embedded xylan and cellulose microfibrils.
Agarolytic organisms are common, but comparatively few agarase systems have been characterized. Agar-degrading organisms were first reported by Gran in 1902 (Swartz and Gordon, 1959). Since then, at least 30 bacteria with this capacity have been identified. The vast majority of these bacteria are marine isolates belonging to the following genera: Agarivorans (Ohta et al., 2005), Alterococcus (Shieh and Jean, 1998), Alteromonas (Potin et al., 1993), Cytophaga (Turvey and Christison, 1967; Van der Meulen and Harder, 1975), Microbulbifer (Ohta et al., 2004a; Ohta et al., 2004b), Microscilla (Zhong et al., 2001), Pseudoalteromonas (Belas, 1989; Morrice et al., 1983a; Morrice et al., 1983b; Schroeder et al., 2003), Pseudomonas (Ha et al., 1997; Kang et al., 2003), Vibrio (Aoki et al., 1990; Araki et al., 1998; Sugano et al., 1994a; Sugano et al., 1993; Sugano et al., 1994b), and Zobellia (Allouch et al., 2003; Barbeyron et al., 2001). Agarase activity has also been observed in bacteria isolated from terrestrial environments, such as Paenibacillus spp. (Hosoda et al., 2003; Uetanabaro et al., 2003) and Streptomyces coelicolor (Bibb et al., 1987).
Each of these organisms is thought to degrade agar by using one of two biochemical pathways that employ a variety of secreted agarases. Most known agarolytic bacteria use secreted β-agarases to cleave agarose initially at the β1,4 linkages between neoagarobiose units. In this pathway, β-agarase I is thought to endolytically degrade agarose to neoagarooligosaccharides, with neoagarotetraose as the smallest product (Morrice et al., 1983a; Morrice et al., 1983b). These neoagarooligosaccharides appear to be degraded further by a β-agarase II to yield neoagarohexaose, neoagarotetraose, and neoagarobiose (Morrice et al., 1983a; Morrice et al., 1983b). This enzyme can have both endolytic and exolytic activities. A neoagarobiose hydrolase then cleaves neoagarobiose to its constituent monosaccharides. A few bacterial species employ an α-agarase pathway in which the α1,3 linkage within neoagarobiose units is cleaved initially. For example, Alteromonas agarlyticus secretes a depolymerizing agarase that yields agarotetraose (Potin et al., 1993). While the activities of these enzymes have been demonstrated and some have been purified, the nucleotide sequences of comparatively few agarase genes have been determined. GH16, GH50, and GH86 domains have been reported to be present in β-agarases and GH96 domains in α-agarases (see the Carbohydrate Active Enzymes (CAZY) database; (Coutinho and Henrissat, 1999a)). There is at least one report of a partial amino-terminal sequence of an α-neoagarooligosaccharide hydrolase (Sugano et al., 1994a).
S. degradans 2-40 is capable of rapid growth on agarose as the sole carbon source, degrading agar nearly twice as quickly as Pseudoalteromonas atlantica, and appears to produce multiple agarases (Whitehead et al., 2001). The mechanism by which S. degradans 2-40 degrades agar is thought to involve a β-agarase system (Whitehead et al., 2001). Recently, the genome sequence of S. degradans 2-40 was completed to enable the application of genomic approaches to the characterization of this agarolytic system.
There are numerous applications of agar and its enzymatically derived by-products. Neoagarobiose is highly sought for cosmetic applications, including moisturizers, and for its ability to whiten melanoma cells. Neoagarobiose is desirable for moisturizer formulations because it has a higher hygroscopic ability than glycerol or hyaluronic acid, typical moisturizing reagents. Besides being able to whiten melanoma cells, it also has low cytotoxicity (Kobayashi et al., 1997) and is hypoallergenic. Neoagarobiose is not readily available commercially, due to a challenges in its synthesis, and difficulty to produce from primary sources, such as agar.
Publications referred to throughout the specification are herein incorporated by reference in their entireties.
SUMMARY OF THE INVENTION
In a first aspect, the invention is drawn to methods of producing neoagarobiose, comprising: (a) providing a substrate selected from the group consisting of agar, agarose, neoagarotetraose, agarooligosaccharides, and derivatives thereof; (b) contacting the substrate with an Aga86E polypeptide, thereby creating a reaction mix; and (c) incubating the reaction mix under suitable conditions and sufficient time to produce neoagarobiose from the substrate. The Aga86E polypeptide can be provided on a solid support, and can be linked to the solid support chemically, by a protein, such as an antibody, or via streptavidin/avidin-biotin couplings, or even by plain adsorption, based on charge. Any solid support material can be used, such as polystyrene, cross-linked agarose, magnetic material, or polyacrylamide.7. The Aga86E polypeptide can be a polypeptide having an amino acid sequence with at least 70%, 80%, 90%, 95% and 100% sequence identity with an amino acid sequence of SEQ ID NO:3. Variants of Aga86E polypeptides can also be used that maintain Aga86E activity and which conserve the amino acid residues that are shown to be conserved in the polypeptides various domains as shown in FIGS. 4 and 5. The reaction mix can further comprises a buffer, the buffer selected from the group consisting of phosphate, Hank's Balanced Salt Solution (HBSS), N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-Tris), N-(2-hydroxyethyl)piperazine-N′3-propanesulfonic acid (EPPS or HEPPS), glyclclycine, N-2-hydroxyehtylpiperazine-N′-2-ethanesulfonic acid (HEPES), 3-(N-morpholino)propane sulfonic acid (MOPS), piperazine-N,N′-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N-tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES), N-tris(hydroxymethyl)methyl-glycine (Tricine), and tris(hydroxymethyl)-aminomethane (Tris).
In some aspects, the method further comprises contacting the substrate with a Aga16B polypeptide. The Ag16B polypeptide can be a polypeptide having an amino acid sequence with at least 70%, 80%, 90%, 95% and 100% sequence identity with an amino acid sequence of SEQ ID NO:1. Variants of Aga16B polypeptides can also be used that maintain Aga16B activity and which conserve the amino acid residues that are shown to be conserved in the polypeptides various domains as shown in FIGS. 2 and 5. In some aspects, the substrate is first contacted with the Aga16B polypeptide.
In a second aspect, the invention is drawn to methods of producing neoagarobiose, comprising: (a) providing a substrate selected from the group consisting of agar, agarose, neoagarotetraose, agarooligosaccharides, and derivatives thereof; (b) contacting the substrate with a first polypeptide having at least 80%, 90%, or 100% sequence identity with an amino acid sequence of SEQ ID NO:9, thereby creating a reaction mix; and (c) incubating the reaction mix under suitable conditions and sufficient time to produce neoagarobiose from the substrate. Variants of the polypeptide comprising an amino acid sequence of SEQ ID NO:9 can also be used, wherein conserved amino acid residues as shown in FIG. 4 are conserved. In some aspects, the method further comprises contacting the substrate with at least one carbohydrate binding module polypeptide having at least 80%, 90% or 100% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs:5, 6 and 7. In yet other aspects, the substrate is contacted with two of the carbohydrate binding module polypeptides of SEQ ID NOs:5, 6 and 7, and in yet other aspects to all three. Variants of polypeptides comprising SEQ ID NOs:5, 6 and 7 can also be used, wherein conserved residues are conserved as shown in FIG. 5. The polypeptides can be fused together in any combination.
In some aspects, the methods further comprise contacting the substrate with a second polypeptide comprising an amino acid sequence having at least 80%, 90% and 100% sequence identity with an amino acid sequence of SEQ ID NO:12. Variants of polypeptides comprising SEQ ID NO:12 can also be used, wherein conserved residues are conserved as shown in FIG. 2. In some aspects, the methods comprising contacting the substrate first with the second polypeptide. Furthermore, the methods can further comprising contacting the substrate with at least one carbohydrate binding module polypeptide having at least 80%, 90% or 100% sequence identity with an amino acid sequence of SEQ ID NO:10 or 11. Variants of polypeptides comprising SEQ ID NOs:10 and 11 can also be used, wherein conserved residues are conserved as shown in FIG. 5. Any of the polypeptides can be provided on solid supports. In some aspects, a single solid support comprises multiple, different polypeptides. In yet other aspects, the polypeptides can be fused in any combination.
In yet another aspect, the invention is drawn to methods of producing neoagarobiose, comprising: (a) providing a substrate selected from the group consisting of agar, agarose, neoagarotetraose, agarooligosaccharides, and derivatives thereof; (b) contacting the substrate with an Aga86E polypeptide of SEQ ID NO:1 and an Aga16B polypeptide of SEQ ID NO:3, thereby creating a reaction mix; and (c) incubating the reaction mix under suitable conditions and sufficient time to produce neoagarobiose from the substrate. In some aspects, the methods coprising contacting the substrate first with the Aga16B polypeptide before being contacted with the Aga86E polypeptide. The reaction mix can incubated at a temperature of about 42° C. Any of the polypeptides can be provided on solid supports. In some aspects, a single solid support comprises multiple, different polypeptides. In yet other aspects, the polypeptides can be fused in any combination.
In yet another aspect, the invention is drawn to systems to produce neoagarobiose, comprising: (a) an isolated Aga86E polypeptide; (b) an isolated Aga16B polypeptide; and (c) a buffer. In some aspects, the systems further comprise a substrate selected form the group consisting of agarose, neoagarotetraose, and agarooligosaccharide. Any of the polypeptides can be provided on solid supports. In some aspects, a single solid support comprises multiple, different polypeptides. In yet other aspects, the polypeptides can be fused in any combination.



BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING
FIG. 1 shows predicted structural features of S. degradans agarases. The indicated domains were identified by sequence similarity. Black box, type II protein secretion signal; white dotted box, GH16 domain; cross-hatched box, GH50 domain; horizontally striped box, GH86 domain; vertically striped box, repeated amino acid linker. Filled triangles indicate family 6 carbohydrate binding modules.
FIG. 2 shows sequence similarities observed in GH16 domains of known or predicted agarases. Regions of agarases exhibiting sequence similarity to Aga16B were aligned using ClustalW. Black boxes indicate identity. Gray boxes similarity. The signature sequence for a GH16 domain is overlined. The amino acid residues of the region exhibiting the indicated sequence similarity is listed as “residues”. Total length of the polypeptide is indicated as the “total”. Aeromonas b-Aga, Aeromonas β-agarase, gi|6073784, residues 32-290/290 total; Pa. atlantica DagA, Pseudoalteromonas atlantica β-agarase I DagA, gi|1220461, residues 24-290/290 total; Zobellia AgaA, Zobellia galactanvorans β-agarase AgaA, gi|16650393, residues 35-295/539 total; Microb. JAMB-A7, Microbulbifer sp. JAMB-A7 β-agarase AgaA7, gi|37665541, residues 22-307/441 total; S. degradans Aga16B, Saccharophagus degradans 2-40 β-agarase Aga16B, AAT67062, residues 31-289/593; Pm ND137, Pseudomonas sp. ND137 agarase, gi|58219335, residues 23-300/591 total; Microb. JAMB-A94, Microbulbifer sp JAMB-A94 β-agarase AgaA, gi|50344693, residues 24-298/433 total; Pm ND137, Pseudomonas sp ND137 β-agarase AagA, gi|17826962, residues 25-299/441 total; Zobellia AgaB, Z. galactanvorans β-agarase AgaB, gi|6650395, residues 54-353/353; Micros. MSI 16, Microscilla sp. PRE1 predicted agarase MS116, gi|14484956, residues 22-386/614 total; Pa. CY24 AgaA, Pseudoalteromonas sp. CY24 β-agarase AgaA, gi|30043922, residues 54-297/453 total; S.c. A3 DagA, Streptomyces coelicolor A3 DagA, gi|21221895, residues 30-309/309 total. SEQ ID NOs are indicated in the figure.
FIG. 3 shows sequence similarities observed in GH50 domains of known or predicted agarases. Regions of agarases exhibiting sequence similarity to the region conserved between AgaA and Aga50D were aligned using ClustalW. V. JT0107 AgaA, Vibrio sp. JT0107 AgaA, gi|497893, residues 505-919/995 total; Agar. JAMB-A11, Agarivorans sp. JAMB-A11 agarase, gi|67423393, residues 507-923, 995 total; Uncult. AguC, Uncultured bacterium AguC, gi|37222154, residues 353-772/772 total; S. degradans AgaA, Saccharophagus degradans 2-40 AgaA, gi|48861348, residues 350-769/769 total; S. degradans Aga50D, Saccharophagus degradans 2-40 Aga50D, gi|48861458, residues 325-747/747 total; S.c. A3 hyd., Streptomyces coelicolor A3 putative hydrolase, gi|6469474, residues 366-788/798 total; V. JT0107 AgaB, Vibrio sp JT0107 β-agarase AgaB, gi|531270, residues 534-955/955 total; Azoto. AVOP, Azotobacter vinlandii AvOP agarase, gi|67157228, residues 427-768/801 total. SEQ ID NOs are indicated in the figure.
FIG. 4 shows sequence similarities observed in GH86 domains of known or predicted agarases. Regions of agarases exhibiting sequence similarity to the region conserved between Aga86C and Aga86E were aligned using Clustal W. S. degradans Aga86C, Saccharophagus degradans 2-40 Aga86C, gi|48861753, residues 147-787/787 total; Micros. MS109, Microscilla sp PRE1 putative β-agarase MS109, pi|14518314, residues 30-647/736 total; Microb. JAMB-A94, Microbulbifer sp. JAMB-A94 AgaO, gi|57864209, residues 488-1175/1175 total; S. degradans Aga86E, S. degradans outer membrane protein Aga86E, gi|48861758, residues 633-1316,1316 total; Micros. MS115, Microscilla sp PRE1 putative agarases MS115, gi|14518320, residues 34-700/1330 total; Pa. atlantica AgrA, Pseudoalteromonas atlantica β-agarase AgrA, gi|94831, residues 27-505/505 total; Rh. baltica AgrA, Rhodopirellula baltica SH1 AgrA, gi|32443741, residues 189-811/811 total. SEQ ID NOs are indicated in the figure.
FIG. 5 shows sequence similarities observed in the predicted CBM domains of S. degradans agarases and known CBM6 modules. Modules identified by SMART analysis in Aga16B and Aga86E were aligned using ClustalW. Module designations are indicated in FIG. 1. Amino acid residues shown are: B1, 322-445; B2, 455-493; E1, 9-148, E2, 162-302; E3, 349-483. SEQ ID NOs are indicated in the figure.
FIG. 6 shows unrooted phylogenetic tree for CBM6 domains identified in the S. degradans 2-40 genome. The scale bar indicates the number of substitutions per position following alignment with MUSCLE (Edgar, 2004) and bootstrap analysis by ClustalW. The tree was generated using neighbor joining and displayed with TreeView (Page, 1996). The bootstrap value (out of a sampling of 100) is shown for the node linking the agarase CBM (bold). Abbreviations: Aga, known agarase; Cbm, protein containing a carbohydrate binding module; Cel, predicted endoglucanase; Glu, predicted β-glucosidase; Lam, candidate laminarinase; Lch, lichenase; Xyn, candidate xylanase.



DETAILED DESCRIPTION
The present invention solves the problems of readily providing a source of neoagarobiose. The invention exploits Aga86E of S. degradans, which before the discovery by the current inventors, was thought to be yet another β-agarase without any remarkable enzymatic activity. The inventors discovered that Aga86E has the remarkable ability to exolytically degrade agarose and agarooligosaccharides to release neoagarobiose. Aga86E is therefore not an ordinary agarase; it is a neoagarobiosebiohydralase. Furthermore, the inventors discovered that combining the endolytic activity of another β-agarase, Aga16B, the process of degrading agar or agarose to neoagarobiose was even more efficient. The invention exploits these findings, disclosing methods and systems directed to produce neoagarobiose.
In their study that led to the discoveries that brought about the present invention, traditional genomic library screens and protein expression coupled with bioinformatic analysis of the genome sequence and proteomics were used to identify five agarases encoded by S. degradans 2-40. Several of the agarases, including Aga86E and Aga16B of the present invention, were found to have unusual structural features, such as multiple carbohydrate binding modules from family 6 (CBM6).
The identification of the S. degradans 2-40 agarases was based upon sequence similarity, conserved structural features, agarase activity of expressed genes in E. coli, and/or the phenotype of gene replacement mutants.
Aga16B was unequivocally demonstrated by the inventors to be a secreted β-agarase (see the Examples, below). All agarase-positive clones identified in the S. degradans 2-40 genomic library included aga16B. The enzyme exhibited sequence similarity to a family of GH16-containing agarases, and the signature sequence for a GH16 catalytic domain was present. When cloned to produce a His-tagged derivative, the purified product had agarase activity in zymograms and endolytically degraded agar similarly to a β-agarase I, producing neoagarotetraose as the smallest product. Analysis of culture filtrates of S. degradans 2-40 by mass spectrometry indicated that the enzyme is expressed during bacterial growth where agar was the sole carbon source. Multiple forms of Aga16B were observed in zymograms of affinity-purified preparations. These forms were similar to the forms observed in culture filtrates of S. degradans 2-40, suggesting that Aga16B is the predominant β-agarase I secreted by the bacterium.
Aga86E is a special agarase, a neoagarobiosebiohydralase. Sequence similarity to several other agarases, as well as to a probable GH86 domain found only in agarases, was detected. When cloned to create a His-tagged derivative, the purified product was active in degrading agarose, releasing almost specifically neoagarobiose. This is consistent with exolytic degradation of agarose polymers. The active derivatives of Aga86E appear to be amino-terminal truncations of 100 and 86 kDa. These are proteolytic products lacking one or more of the CBMs but formed even in the presence of broad-spectrum protease inhibitors.
Like most other carbohydrases characterized thus far, the S. degradans 2-40 agarases are modular. The catalytic domains found in these agarases include GH16, GH50, or GH86 domains. GH16 domains are not specific to agarases and have been found in enzymes with other activities, such as β-galactosidases, endoglucanases, lichenases, and carrageenanases (Allouch et al., 2004). The crystal structure of an agarase-active GH16 domain from Zobellia galactanivorans has been characterized (Allouch et al., 2003). This module contains two parallel binding sites that are thought to unwind the helical structure of agarose (Allouch et al., 2004). Since the functional residues are conserved, the endolytic hydrolysis of agarose by Aga16B is similar. There are several regions of sequence conservation within each of the predicted GH50 and GH86 domains that represent conserved active sites and/or binding domains. Like several other GH domains, the GH50 and GH86 domains have been associated with both endolytic and exolytic activities. For example, the GH86 family agarase of a deep-sea Microbulbifer-like strain has been reported to endolytically degrade agarose, but the inventors found that the GH86-containing Aga86E surprisingly exolytically degrades agarose to release neoagarobiose.
More unusual are the presence of multiple CBM6 in Aga16B and Aga86E. Aga16B has two homologs of CBM6, whereas Aga86E has three. While CBM are common in other carbohydrases, a survey for CBM in other agarases revealed only two other agarases with CBM-like domains. The CBM6 found in Aga86E and Aga16B form a distinct subclass within the large CBM6 family. Notably, deletion of the CBM6 did not affect the catalytic activity of either enzyme, as the catalytic GH16 and GH86 domains function independently of other domains. These domains increase the affinity of these enzymes for their substrate or disrupt interactions between adjacent polymers (Xu et al., 2004). Phylogenetic analyses indicate that this CBM6 is most similar to the first and second CBM6 of the exo-acting Aga86E.
In the following sections, the invention is described first by defining terms; therein follows a discussion of the Aga86E and Aga16B polypeptides and polynucleotides that can be used to make the polypeptides. Following the presentation of the polypeptides, various ways of using the Aga86E and Aga16B polypeptides are discussed, followed by examples that further elucidate the invention.
DEFINITIONS
The term, “Aga86E/16B polypeptides” refers to any polypeptide, including, full-length polypeptides, and domain fragments, such as CBMs and catalytic domains, that make up Aga86E polypeptide (SEQ ID NO:1) and Aga16B polypeptide (SEQ ID NO:3). The term is meant to be one of convenience and brings no limitation to the present invention. Examples of Aga86E/16 polypeptides are those represented by SEQ ID NOs:1, 3, 5-7, 9-12. Any combination of these sequences when fused together, with or without repeat sequences such as those of SEQ ID NOs:8 and 13, are also Aga86E/16B polypeptides. An “Aga86E/16B polynucleotide” is a polynucleotide that encodes an Aga86E/16B polypeptide.
A “polynucleotide” is a nucleic acid polymer of ribonucleic acid (RNA), deoxyribonucleic acid (DNA), modified RNA or DNA, or RNA or DNA mimetics (such as, PNAs), and derivatives thereof, and homologues thereof. Thus, polynucleotides include polymers composed of naturally occurring nucleobases, sugars and covalent inter-nucleoside (backbone) linkages as well as polymers having non-naturally-occurring portions that function similarly. Such modified or substituted nucleic acid polymers are well known in the art and for the purposes of the present invention, are referred to as “analogues.” Oligonucleotides are generally short polynucleotides from about 10 to up to about 160 or 200 nucleotides.
“Aga86E/16B variant polynucleotide” or “Aga86E/16B variant nucleic acid sequence” means a Aga86E/16B variant polynucleotide having at least about 60% nucleic acid sequence identity, more preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 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% nucleic acid sequence identity and yet more preferably at least about 99% nucleic acid sequence identity with the nucleic acid sequence of Aga86E/16B. Variants do not encompass the native nucleotide sequence.
Ordinarily, Aga86E/16B variant polynucleotides are at least about 8 nucleotides in length, often at least about 50, 55, 60 nucleotides in length, or even about 75-200 to wild-type full-length nucleotides in length, or more.
“Percent (%) nucleic acid sequence identity” with respect to Aga86E/16B-nucleic acid sequences is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the Aga86E/16B sequence of interest, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining % nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
When nucleotide sequences are aligned, the % nucleic acid sequence identity of a given nucleic acid sequence C to, with, or against a given nucleic acid sequence D (which can alternatively be phrased as a given nucleic acid sequence C that has or comprises a certain % nucleic acid sequence identity to, with, or against a given nucleic acid sequence D) can be calculated as follows:

    
    
        % nucleic acid sequence identity=W/Z·100
        where
        W is the number of nucleotides cored as identical matches by the sequence alignment program's or algorithm's alignment of C and D
        and
        Z is the total number of nucleotides in D.
    
    


When the length of nucleic acid sequence C is not equal to the length of nucleic acid sequence D, the % nucleic acid sequence identity of C to D will not equal the % nucleic acid sequence identity of D to C.
“Consisting essentially of a polynucleotide having a % sequence identity” means, when applied to a polynucleotide, that the polynucleotide does not substantially differ in length, but in sequence. Thus, a polynucleotide “A” consisting essentially of a polynucleotide having 80% sequence identity to a known sequence “B” of 100 nucleotides means that polynucleotide “A” is about 100 nts long, but up to 20 nts can vary from the “B” sequence. The polynucleotide can be longer or shorter due to the addition of 1-15 nucleotides on the termini to produce specific types of probes, primers and other molecular tools, etc., such as the case of when substantially non-identical sequences are added to create intended secondary structures. Such non-identical nucleotides are not considered in the calculation of sequence identity when the sequence is modified by “consisting essentially of.”
The specificity of single stranded DNA to hybridize complementary fragments is determined by the “stringency” of the reaction conditions. Hybridization stringency increases as the propensity to form DNA duplexes decreases. In nucleic acid hybridization reactions, the stringency can be chosen to either favor specific hybridizations (high stringency), which can be used to identify, for example, full-length clones from a library. Less-specific hybridizations (low stringency) can be used to identify related, but not exact, DNA molecules (homologous, but not identical) or segments.
DNA duplexes are stabilized by: (1) the number of complementary base pairs, (2) the type of base pairs, (3) salt concentration (ionic strength) of the reaction mixture, (4) the temperature of the reaction, and (5) the presence of certain organic solvents, such as formamide, which decreases DNA duplex stability. A common approach is to vary the temperature: higher relative temperatures result in more stringent reaction conditions. (Ausubel et al., 1987) provide an excellent explanation of stringency of hybridization reactions.
To hybridize under “stringent conditions” describes hybridization protocols in which nucleotide sequences at least 60% homologous to each other remain hybridized.
The polynucleotides can be prepared by conventional techniques, such as solid-phase synthesis using commercially available equipment, such as that available from Applied Biosystems USA Inc. (Foster City, Calif.; USA), DuPont, (Wilmington, Del.; USA), or Milligen (Bedford, Mass.; USA). Modified polynucleotides, such as phosphorothioates and alkylated derivatives, can also be readily prepared by similar methods known in the art.
In general, a Aga86E/16B variant that preserves Aga86E/16B-like function and includes any variant in which residues at a particular position in the sequence have been substituted by other amino acids, and further includes the possibility of inserting an additional residue or residues between two residues of the parent polypeptide as well as the possibility of deleting one or more residues from the parent sequence. Useful conservative substitutions are shown in Table 1. Conservative substitutions whereby an amino acid of one class is replaced with another amino acid of the same type fall within the scope of the subject invention so long as the substitution does not materially alter the biological activity of the compound. If such substitutions result in a change in biological activity, then more substantial changes, indicated in Table 2 as exemplary, are introduced and the products screened for its ability to degrade agarose or agarooligosaccharides.







TABLE 1







Preferred substitutions









Original

Preferred


residue
Exemplary substitutions
substitutions





Ala (A)
Val, Leu, Ile
Val


Arg (R)
Lys, Gln, Asn
Lys


Asn (N)
Gln, His, Lys, Arg
Gln


Asp (D)
Glu
Glu


Cys (C)
Ser
Ser


Gln (Q)
Asn
Asn


Glu (E)
Asp
Asp


Gly (G)
Pro, Ala
Ala


His (H)
Asn, Gln, Lys, Arg
Arg


Ile (I)
Leu, Val, Met, Ala, Phe, Norleucine
Leu


Leu (L)
Norleucine, Ile, Val, Met, Ala, Phe
Ile


Lys (K)
Arg, Gln, Asn
Arg


Met (M)
Leu, Phe, Ile
Leu


Phe (F)
Leu, Val, Ile, Ala, Tyr
Leu


Pro (P)
Ala
Ala


Ser (S)
Thr
Thr


Thr (T)
Ser
Ser


Trp (W)
Tyr, Phe
Tyr


Tyr (Y)
Trp, Phe, Thr, Ser
Phe


Val (V)
Ile, Leu, Met, Phe, Ala, Norleucine
Leu









Non-conservative substitutions that affect (1) the structure of the polypeptide backbone, such as a β-sheet or α-helical conformation, (2) the charge or (3) hydrophobicity, or (4) the bulk of the side chain of the target site can modify Aga86E/16B polypeptide function or immunological identity. Residues are divided into groups based on common side-chain properties as denoted in Table B. Non-conservative substitutions entail exchanging a member of one of these classes for another class. Substitutions can be introduced into conservative substitution sites or more preferably into non-conserved sites.







TABLE 2







Amino acid classes










Class
Amino acids







hydrophobic
Norleucine, Met, Ala, Val, Leu, Ile



neutral hydrophilic
Cys, Ser, Thr



acidic
Asp, Glu



basic
Asn, Gln, His, Lys, Arg



disrupt chain conformation
Gly, Pro



aromatic
Trp, Tyr, Phe










The variant polypeptides can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis.
“Aga86E/16B polypeptide variant” means an active Aga86E/16B having at least: (1) about 70% amino acid sequence identity with a full-length native Aga86E/16B sequence, (2) a Aga86E/16B sequence lacking a signal peptide, (3) an extracellular domain of a Aga86E/16B, with or without a signal peptide, or (4) any other fragment of a full-length Aga86E/16B sequence. For example, Aga86E/16B variants include those wherein one or more amino acid residues are added or deleted at the N- or C-terminus of the full-length native amino acid sequence. An Aga86E/16B polypeptide variant will have at least about 70% or 80% amino acid sequence identity, preferably at least about 81% amino acid sequence identity, more preferably at least about 82%-98% amino acid sequence identity and most preferably at least about 99% amino acid sequence identity with a full-length native sequence Aga86E/16B sequence. Ordinarily, Aga86E/16B variant polypeptides are at least about 10 amino acids in length, often at least about 20 amino acids in length, more often at least about 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, or 300 amino acids in length, or more.
“Percent (%) amino acid sequence identity” is defined as the percentage of amino acid residues that are identical with amino acid residues in a Aga86E/16B sequence in a candidate sequence when the two sequences are aligned. To determine % amino acid identity, sequences are aligned and if necessary, gaps are introduced to achieve the maximum % sequence identity; conservative substitutions are not considered as part of the sequence identity. Amino acid sequence alignment procedures to determine percent identity are well known to those of skill in the art. Publicly available computer software such as BLAST, BLAST2, ALIGN2 or Megalign (DNASTAR) can be used to align polypeptide sequences.
When amino acid sequences are aligned, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) can be calculated as:

    
    
        % amino acid sequence identity=X/Y·100
        where
        X is the number of amino acid residues scored as identical matches by the sequence alignment program's or algorithm's alignment of A and B
        and
        Y is the total number of amino acid residues in B.
    
    


If the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A.
Useful variants are those that conserve the conserved amino acid residues as shown in FIGS. 2-5, or wherein preferred conservative substitutions have been made.
An “isolated” or “purified” polypeptide, or biologically active fragment is separated and/or recovered from a component of its natural environment. Contaminant components include materials that would typically interfere the use for the polypeptide; such undesirable contaminants would significantly interfere with enzymatic activity (e.g., such as that of the GH domains of the Aga86E and Aga16B polypeptides), or binding activity, such as that of the CBMs. To be substantially isolated, preparations have less than 30% by dry weight of contaminants, more preferably less than 20%, 10% and most preferably less than 5% contaminants. An isolated, recombinantly-produced Aga86E/16B or biologically active portion is usually substantially free of culture medium, i.e., culture medium represents less than 20%, more or less than about 10%, or less than about 5% of the volume of the Aga86E/16B preparation.
Biologically active portions of Aga86E/16B include peptides comprising amino acid sequences sufficiently homologous to, or derived from, the amino acid sequences of Aga86E/16B (SEQ ID NOS:1, 3, 5, 6, 7, 9-12) that include fewer amino acids than the full-length Aga86E/16B, and exhibit at least one activity of a Aga86E/16B. Biologically active portions comprise a domain or motif with at least one activity of native Aga86E/16B, such as endolytic activity on a substrate (Aga16B) or exolytic activity on a substrate (Aga86E), and binding to a carbohydrate moiety (CBMs). A biologically active portion of a Aga86E/16B can be a polypeptide that is 10, 25, 50, 100 or more amino acid residues in length.
Biologically active portions of a Aga86E/16B can have an amino acid sequence shown in SEQ ID NOS:1, 3, 5, 6, 7, 9-12, or be substantially identical to SEQ ID NOS:1, 3, 5, 6, 7, 9-12, and retains the functional activity of the polypeptide of SEQ ID NOS:1, 3, 5, 6, 7, 9-12. Other biologically active Aga86E/16B polypeptides can comprise an amino acid sequence at least 45% identical to the amino acid sequence of SEQ ID NOS:1, 3, 5, 6, 7, 9-12, and retain a functional activity of native Aga86E/16B. Biological activity of Aga86E polypeptides include carbohydrate binding and neoagarobiosebiohydralase activity (e.g., degrading agarose and agarooligosaccharides to neoagarobiose); biological activity of Aga16B polypeptides include carbohydrate binding and degrading agar and agarose to agarooligosaccharides.
“Substantially preserved activity” means that a polypeptide has at least 10% the activity of a wild-type polypeptide when tested in parallel in a biological buffer at an appropriate temperature and for a sufficient time for the reaction to proceed for the wild-type polypeptide with any suitable substrate.
PRACTICING THE INVENTION
Aga86E
In a first embodiment, the invention is direct to methods and systems using Aga86E polypeptides and polynucleotides from S. degradans 2-40. The Aga86 polypeptide (SEQ ID NO:3) and the corresponding polynucleotide (SEQ ID NO:4) are shown in Tables 3 and 4, respectively.







TABLE 3





Aga86E polypeptide sequence


(GenBank Accession No. ZP 00315657: SEQ ID NO: 3)















Met Ser Val Leu Pro Leu Ala Ala Gly Ala Ala Asp Tyr Val Ile Glu


1               5                   10                  15


 


Ala Glu Asn Phe Val Ala Gln Gly Gly Thr Tyr Val Asp Gly Gln Pro


            20                  25                  30


 


Asn Lys Val Ser Val Tyr Ser Val Asn Gly Ala Thr Ala Ile Asn Tyr


        35                  40                  45


 


Val Asn Arg Ala Asp Tyr Thr Asp Tyr Gln Ile Asn Val Ala Thr His


    50                  55                  60


 


Gly Tyr Tyr Asn Val Gln Tyr Ala Ile Gly Thr Ser Val Ala Ser Gly


65                  70                  75                  80


 


Ala Ala Ile Glu Leu Leu Val Gln Asn Gly Ser Ser Trp Glu Ser Gln


                85                  90                  85


 


Gly Gln Thr Asn Val Pro Val Gly His Trp Asp Ser Phe Gln Pro Leu


            100                 105                 110


 


Asn Ala Ser His Glu Val Ile Leu Pro Ala Gly Thr Val Asn Leu Arg


        115                 120                 125


 


Val Tyr Gly Ala Gly Ser Asn Asp Trp Gln Trp Asn Leu Asp Ser Ile


    130                 135                 140


 


Ser Leu Thr Leu Glu Ser Ala Ile Asn Pro Gln Pro Asp Pro Asp Pro


145                 150                 155                 160


 


Asp Pro Ser Pro Gln Leu Val Lys Thr Glu Ala Glu Ala Phe Asn Ala


                165                 170                 175


 


Gln Ser Gly Thr Phe Ala Asp Gly Gln Pro Thr Pro Val Ser Ile Tyr


            180                 185                 190


 


Thr Val Asn Gly Lys Thr Ala Ile Asn Phe Val Asn Lys Gly Asp Ala


        195                 200                 205


 


Val Glu Tyr Asn Leu Val Ala Pro Ala Ala Gly Ser Tyr Ala Leu Lys


    210                 215                 220


 


Tyr Ser Ile Gly Thr Ser Val Ala Ser Gly Ser Glu Val Glu Phe Phe


225                 230                 235                 240


 


Val Leu Lys Asn Asn Val Trp Val Ser Gln Gly Lys Thr Pro Val Pro


                245                 250                 255


 


Ala Val Gly Trp Asp Asn Phe Thr Ser Val Ala Ser Ala Gln Thr Val


            260                 265                 270


 


Glu Leu Ala Ala Gly Ser Asn Lys Val Lys Leu Val Gly Ala Gly Thr


        275                 280                 285


 


Asn Asp Trp Gln Trp Asn Leu Asp Phe Phe Glu Leu Thr Leu Gly Asn


    290                 295                 300


 


Val Glu Pro Glu Pro Glu Pro Glu Pro Glu Pro Glu Pro Glu Pro Glu


305                 310                 315                 320


 


Pro Glu Pro Glu Pro Glu Pro Glu Pro Glu Pro Glu Pro Glu Pro Glu


                325                 330                 335


 


Pro Glu Pro Gln Pro Glu Pro Asp Gly Asp Pro Val Pro Val Ser Gly


            340                 345                 350


 


Ser Phe Lys Leu Glu Ala Glu His Phe Gln Lys Val Gly Gly Glu Val


        355                 360                 365


 


Gln Ile Tyr Ser Leu Ser Pro Gly Asn Ala Val Asn Tyr Phe Asn Ser


    370                 375                 380


 


Gly Asp Tyr Leu Glu Phe Tyr Val Asp Leu Asp Ala Gly Gly Leu Tyr


385                 390                 395                 400


 


Glu Ala Ser Phe Arg Val Gly Thr Gly Val Ala Ser Asp Val Ala Val


                405                 410                 415


 


Gly Leu Met Val Thr Asp His Lys Gly Asp Leu Thr Leu Lys Ser Val


            420                 425                 430


 


Thr Pro Val Thr Asp Gln Gly Gly Trp Asp Ala Phe Tyr Asn Leu Thr


        435                 440                 445


 


Ala Gln Ser Gln Leu Asn Ile Tyr Ser Gly Ile Asn Thr Ile Arg Ile


    450                 455                 460


 


Thr Gly Ala Gly Ser Ala Asp Phe Gln Phe Asn Ile Asp Ser Ile Thr


465                 470                 475                 480


 


Leu Thr Arg Val Gly Pro Ile Asn Pro Ala Leu Asp Gly Asp Asn Asp


                485                 490                 495


 


Gly Val Pro Asp Thr Ser Asp Asn Cys Pro Ser Ser Pro Ala Asn Glu


            500                 505                 510


 


Thr Ala Asn Ala Glu Gly Cys Val Pro Ser Gln Leu Asp Thr Asp Glu


        515                 520                 525


 


Asp Gly Ile Asn Asp Lys Ile Asp Gln Cys Asp Ala Thr Pro Ala Gly


    530                 535                 540


 


Asp Phe Val Asp Ala Leu Gly Cys Thr Ser Thr Gly Gly Asp Asp Asp


545                 550                 555                 560


 


Asp Phe Asp Gly Val Leu Asn Gly Ala Asp Gln Cys Gly Asn Thr Pro


                565                 570                 575


 


Tyr Gly Met Asn Val Asn Ala Gln Gly Cys Ser Val Phe Ser Gly Ser


            580                 585                 590


 


Asp Ala Asp Asn Asp Gly Val Ala Asn Ser Glu Asp Thr Cys Ala Asn


        595                 600                 605


 


Thr Pro Ala Leu Glu Phe Ala Asn Glu Gln Gly Cys Ser Ser Ser Gln


    610                 615                 620


 


Val Ala Asn Thr His Val Val Asn Val Ser Val Asn Ala Asn Phe Lys


625                 630                 635                 640


 


Arg Ser Val Asn Gly Val Phe Asp Phe Gly Arg Arg Arg His Met Thr


                645                 650                 655


 


Ala His Thr Ala Ile His Glu Pro Asp Trp Val Gly His Thr Asp Lys


            660                 665                 670


 


Leu Asn Tyr Leu Phe Asn Thr Leu Asp Val Tyr Met Gly Arg Asp Asn


        675                 680                 685


 


Gly Ser Ala Thr Trp Lys Phe Asn Asp Thr Thr Glu Asp Pro Asn Lys


    690                 695                 700


 


Pro Asn Trp Pro Asn Met Asp Tyr Met Val Glu Arg Gly Lys Gly Leu


705                 710                 715                 720


 


Arg Glu Ala His Asp Gln Asn Pro Leu Phe Lys Arg Phe Ser Ala Glu


                725                 730                 735


 


Lys Gln Leu Leu Ile Ala Gly Thr Asn Pro His Ala Leu Tyr Pro Thr


            740                 745                 750


 


Leu Ser Trp Phe Pro Asn Ala Phe Thr Trp Ser Gly Trp Gln Pro Lys


        755                 760                 765


 


Asn Ile Glu Thr Ser Ala Ala Trp Val Gly Gln Tyr Met Glu His Tyr


    770                 775                 780


 


Phe Ala Asn Ala Ser Asn Gly Tyr Val Gly Glu Gln Leu Pro Glu Tyr


785                 790                 795                 800


 


Trp Glu Val Val Asn Glu Pro Asp Met Lys Met Lys Thr Gly Gln Phe


                805                 810                 815


 


Met Val Thr Asn Gln Glu Ala Ile Trp Glu Tyr His Asn Leu Val Ala


            820                 825                 830


 


Gln Glu Ile Arg Asp His Leu Gly Ala Glu Ala Pro Pro Ile Gly Gly


        835                 840                 845


 


Met Thr Trp Gly Gln His Asp Phe Tyr Arg Arg Asp Gly Ile Ser Arg


    850                 855                 860


 


Phe Ala Asp Asp Ser Tyr Asp Gln Trp Ile Thr Asn Asp Asp Gln Val


865                 870                 875                 880


 


Leu Gln Ala Glu Ala Arg Ala Phe Tyr Arg Asn Ala Met Ala Thr Thr


                885                 890                 895


 


Val Asp Asp Thr Arg Asp Gln Asp Trp Tyr Gln Trp Asp Val Met Trp


            900                 905                 910


 


Lys Gly Phe Met Asp Ala Ala Gly Asp Asn Met Asp Phe Tyr Ser Val


        915                 920                 925


 


His Ile Tyr Asp Trp Pro Gly Glu Asn Val Gly Asp Thr Thr Val Val


    930                 935                 940


 


Arg Arg Gly Gly His Thr Ser Ala Met Leu Glu Met Met Glu Trp Tyr


945                 950                 955                 960


 


Asp Val Lys Arg Asn Gly Phe Asn Asn Arg Lys Pro Ile Val Leu Ser


                965                 970                 975


 


Glu Tyr Gly Ser Val Asn Gly Ala Trp Asp Asn Arg Ala His Glu Glu


            980                 985                 990


 


Arg Tyr Asp Ile Ala Ser Ile Lys Ala Phe Asn Gly Met Leu Met Gln


        995                 1000                1005


 


Phe Leu Glu Arg Pro Asp Tyr Val Ile Lys Ser Leu Pro Phe Thr


    1010                1015                1020


 


Pro Ala Lys Pro Leu Trp Gly Tyr Leu Pro Gly Gly Cys Gly Tyr


    1025                1030                1035


 


Asp Asp Ala Val Ala Cys Thr Thr Arg Tyr His Tyr Ala Met Leu


    1040                1045                1050


 


Ile Glu Asp Glu Leu Asn Ser Gly Asn Trp Glu Trp Ser Ser Tyr


    1055                1060                1065


 


Ile Lys Phe Tyr Glu Leu Trp Ala Asp Ile Asp Gly Thr Arg Val


    1070                1075                1080


 


Asp Ser Lys Ser Ser Asp Val Asp Val Gln Val Asp Ser Tyr Val


    1085                1090                1095


 


Lys Gly Asn Glu Leu Phe Val Ile Leu Asn Asn Leu Glu Ala Ala


    1100                1105                1110


 


Asp Thr Thr Val Asn Leu Asp Val Ser Gly Ile Ala Ser Val Gln


    1115                1120                1125


 


Asn Val Glu Leu Arg Asn Met His Phe Asp Ile Gln Glu Thr His


    1130                1135                1140


 


Leu Asp Arg His His Met Ser Ala Ala Pro Lys Thr Val Thr Leu


    1145                1150                1155


 


Ala Ala Asp Ala Thr Val Val Leu Arg Tyr Thr Leu Ala Ser Ser


    1160                1165                1170


 


Val Ala Val Asn Asn Thr Val Val Glu Lys Lys Tyr Phe Gly Glu


    1175                1180                1185


 


Ser Val Ser Gly Gly Ile Glu Pro His Arg Ile Ser Val Ala Gly


    1190                1195                1200


 


Gly Ala Lys Thr Leu Tyr Ile Asn Asn Val Ser Val Pro Ser Gly


    1205                1210                1215


 


Tyr Ser Glu Ala Ile Leu Arg Leu Thr Val Ser Leu Tyr Pro Asp


    1220                1225                1230


 


Glu Asp Asp Lys Val Gly Gly His Leu Ser Leu Asp Ser Ile Thr


    1235                1240                1245


 


Val Asn Gly Thr Ala Ile Glu Ala Pro Ile Asp Trp Lys Gly Pro


    1250                1255                1260


 


Lys Ala Asn Arg Ala Glu Arg Phe Phe Gly Val Leu Asp Ile Pro


    1265                1270                1275


 


Val Pro Val Glu Leu Leu Gln Ser Thr Asn Thr Ile Ala Val Asp


    1280                1285                1290


 


Phe Arg His Asn Gly Glu Leu Thr Val Ala Asn Leu Ile Val Ser


    1295                1300                1305


 


Glu Phe Thr Ser Glu Pro Asn Arg


    1310                1315
















TABLE 4





Aga86E polynucleotide sequence (SEQ ID NO: 4)















atgcgaaatt taaataaaaa taaagtacat atattgcgag cagcaattgc tgcaagcatg


  60


 


agtgtactgc cacttgctgc tggtgccgcc gattatgtaa tcgaagcgga aaactttgtg


 120


 


gcgcagggtg gcacctacgt ggacggacaa cccaataaag ttagcgttta tagtgttaat


 180


 


ggcgcaaccg ctattaacta tgtaaaccga gcagactata ccgattacca aattaatgta


 240


 


gctacccacg gttattacaa tgtgcaatat gctattggta catctgtagc cagtggtgcg


 300


 


gctattgagt tactcgtaca aaatggcagt agctgggaat cgcaggggca aacaaatgtg


 360


 


cctgttggtc attgggatag ttttcagcct ttaaatgcaa gtcatgaggt aatcttacct


 420


 


gcgggcactg taaatttacg tgtatatggt gcggggtcta atgattggca atggaattta


 480


 


gattctattt ctctcaccct agagagcgct attaaccctc agcctgatcc agatcccgat


 540


 


cctagccctc aattagtaaa aactgaagcc gaagccttta atgcgcagag cggaactttc


 600


 


gccgatggtc agcctacacc ggtgagtatt tatactgtta atggaaaaac ggcgataaac


 660


 


tttgtaaaca aaggcgatgc cgttgaatac aacttagttg ctccggctgc cggttcatac


 720


 


gcattaaaat actctattgg taccagtgtt gcttccggta gtgaagtaga gttttttgtt


 780


 


ttaaaaaata atgtttgggt ttcacagggt aaaacacctg tgccggctgt tggttgggat


 840


 


aactttacct ctgttgccag tgcgcaaacc gttgagttag ctgctggctc aaataaagtt


 900


 


aaacttgttg gtgctggcac taatgactgg cagtggaatt tagatttctt cgagctcacc


 960


 


ctgggaaatg ttgaaccaga accagaacca gaaccagagc cagaaccaga gccagagcca


1020


 


gagccagagc cagagccaga gccagagcca gaaccagagc cagaaccaga acctcagcca


1080


 


gagcccgatg gcgaccccgt tcctgtaagt ggctcgttta agttagaagc cgagcacttt


1140


 


caaaaggtag gtggcgaagt acaaatttat tctctatcgc caggcaacgc ggttaattat


1200


 


tttaacagcg gtgattacct agagttctat gtcgacttag atgcaggcgg tttgtatgaa


1260


 


gccagcttca gagtgggtac tggtgtggcc tctgatgtag ccgttggcct aatggttaca


1320


 


gatcacaaag gtgacttaac attgaagagt gttacacccg taacggatca aggtggttgg


1380


 


gatgcatttt ataatctcac cgcgcaaagc cagctgaata tttatagtgg tataaacact


1440


 


attcgtatta caggtgcagg gtctgctgat tttcaattta atattgatag catcactttg


1500


 


actcgtgttg ggccaattaa cccagcgcta gatggggata acgatggtgt accagataca


1560


 


tcagataact gcccaagtag ccccgccaat gaaacggcaa acgctgaagg ttgtgtaccg


1620


 


tcgcaattag acactgatga agatggtatt aacgataaaa ttgatcaatg cgatgcaaca


1680


 


ccagcaggag attttgttga cgccttaggt tgtacaagta ctggtggtga cgacgatgac


1740


 


tttgatggcg ttttaaacgg tgccgatcaa tgtggtaata cgccttacgg tatgaacgtt


1800


 


aatgcccaag ggtgtagtgt gttttctgga agcgatgccg ataacgacgg tgttgcaaac


1860


 


agcgaagaca cctgcgcaaa tacgcctgcg ttagaattcg ctaacgaaca gggttgttct


1920


 


tcgtcgcaag tggcaaatac acatgttgtt aacgtaagtg ttaatgctaa ctttaagcgc


1980


 


tctgtaaatg gtgtatttga tttcggccgc cgtcgtcaca tgactgctca cacggctatt


2040


 


cacgagccag attgggtagg gcataccgat aagttaaatt acctattcaa caccctagat


2100


 


gtttacatgg ggcgtgataa cggttcggca acgtggaagt ttaacgacac taccgaagat


2160


 


cctaataagc ccaactggcc aaatatggac tacatggttg agcgcggtaa agggttgcga


2220


 


gaagcgcatg accaaaaccc attgttcaaa cgttttagtg ccgaaaaaca attattaatt


2280


 


gccggtacta acccgcacgc gttgtaccct accttaagtt ggttccctaa cgcgtttacc


2340


 


tggagcggtt ggcagcctaa aaatattgaa acatctgcag catgggtggg acagtatatg


2400


 


gagcattatt ttgcgaacgc ttcaaacggc tatgtaggtg agcagctgcc cgagtattgg


2460


 


gaagtagtaa acgaaccgga tatgaaaatg aaaaccggtc agtttatggt aaccaatcaa


2520


 


gaggccatct gggagtacca caacttggtt gcgcaagaaa ttcgcgatca ccttggcgca


2580


 


gaagcacctc ccattggtgg tatgacttgg ggacagcacg acttctatcg tcgcgatggc


2640


 


atttcgcgtt ttgccgatga ctcttacgat cagtggatta caaacgatga ccaagtattg


2700


 


caggcagaag ctcgcgcttt ttatcgcaat gctatggcta ccactgtaga tgatactcgc


2760


 


gaccaagatt ggtatcagtg ggatgtaatg tggaaaggct ttatggatgc ggccggcgac


2820


 


aacatggact tttactctgt gcacatttat gactggccag gagagaatgt tggtgatact


2880


 


actgttgttc gtcgtggtgg gcacacctct gccatgctag aaatgatgga gtggtacgat


2940


 


gtaaaacgta acggctttaa caaccgtaaa ccaatcgtac tttcggagta cggctcagtt


3000


 


aatggggctt gggataatcg cgcccacgaa gagcgttacg atattgcaag tatcaaagcg


3060


 


tttaatggca tgttaatgca gttcctagag cgcccagact acgtaataaa atctctacca


3120


 


tttactcctg ccaaaccttt gtggggctac ctgcctggtg gttgtggcta cgatgatgca


3180


 


gtggcctgta ctactcgtta ccattacgcc atgttaattg aggatgagct caacagtggt


3240


 


aattgggaat ggtcttctta cataaagttc tacgagttgt gggcagatat agacggcact


3300


 


cgtgtcgatt ctaaatcgtc tgatgtggat gtacaggttg actcttatgt gaaaggtaac


3360


 


gagctgttcg ttattcttaa caacttagaa gcggccgaca caacggtcaa ccttgatgta


3420


 


agcggtatag ccagcgtgca aaatgttgaa ttgcgcaaca tgcatttcga tattcaagag


3480


 


acgcatcttg atcgccatca tatgagcgct gcacctaaaa cggttactct agccgccgat


3540


 


gcgactgtgg tattacgtta tacgcttgca agcagtgttg cggtaaataa caccgtagta


3600


 


gagaaaaagt actttggtga gagtgtaagt ggcggtatag aaccacatcg catttcggtt


3660


 


gcaggcggtg ctaaaacgct ttatatcaat aacgtttcgg ttccaagtgg ctacagcgaa


3720


 


gcaatattgc gcttaactgt atcgctttac ccagacgaag acgataaagt gggcggccat


3780


 


ttaagcctag atagcattac tgttaacggc actgccatag aggcgccaat agattggaaa


3840


 


ggcccgaaag caaaccgtgc agaacgattc ttcggcgtac ttgatattcc agtacctgta


3900


 


gaattattgc aatctactaa taccatcgca gtggacttcc gccacaatgg tgagttaacg


3960


 


gtagcaaact taattgtgtc ggaatttact tctgagccaa atagataa


4008









Any derivatives of Aga86E can be used in the invention, provided that the catalytic activity of the polypeptide is substantially preserved (e.g., the polypeptide has at least 10% the activity per polypeptide of wild-type Aga86E in phosphate buffer at 42° C. for 1 hour with any suitable substrate, such as agarose or agarooligosaccharides).
The wild-type Aga86E has three carbohydrate binding modules (CBM6s) located in the amino-terminus of Aga86E as follows: CBM6-E1, aa 9 to 148 (SEQ ID NO:5), CBM6-E2, aa 162 to 302 (SEQ ID NO:6), and CBM6-E3, aa 349 to 483 (SEQ ID NO:7); these are underscored once in Table 3. A repetitive linker sequence of (P-X) separate the first and second CBM6 of Aga86E (italicized in Table 3; SEQ ID NO:8, wherein X is any amino acid); the second and third CBM6 are separated by an (E-P) repeat (SEQ ID NO:13; double-underscored in Table 3). Aga86E also has four thrombospondin type 3 repeats between aa 511 and 643. A cleavable type II secretion signal is located at the amino terminus.
A glycoside hydrolase-like domain is found from aa 633 to 1316 aa (single underscored and italicized; SEQ ID NO:9); this domain harbors the catalytic activity of the Aga86E polypeptide.
Thus, in one embodiment, the invention utilizes a polypeptide comprising SEQ ID NO:9. In another embodiment, the invention utilizes a polypeptide comprising SEQ ID NO:9 and at least one CBM, comprising at least one selected from the group consisting of SEQ ID NOs:5, 6 and 7. In yet other embodiments, the invention uses a polypeptide comprising SEQ ID NO:9 and at least two CBMs, wherein the CBMs are separated by a plurality of repeat sequences of SEQ ID NO:8 and/or SEQ ID NO:13, wherein the number of repeats can be, in any combination of SEQ ID NOs:8 and 9: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50 or more. In another embodiment, the invention exploits the full-length Aga86E polypeptide (SEQ ID NO:3).
The invention is also directed to methods and systems using Aga16B polypeptides and polynucleotides from S. degradans 2-40. The Aga16B polypeptide (SEQ ID NO:1) and the corresponding polynucleotide (SEQ ID NO:2) are shown in Tables 5 and 6, respectively.







TABLE 5





Aga16B polypeptide















Met Arg Pro Ser Cys Ala Phe Phe Ser Thr Pro Leu Met Ala Ala Asp


1               5                   10                  15


 


Trp Asp Gly Ile Pro Val Pro Ala Asp Pro Gly Asn Gly Asn Thr Trp


            20                  25                  30


 


Glu Leu Gln Ser Leu Ser Asp Asp Phe Asn Tyr Ala Ala Pro Ala Asn


        35                  40                  45


 


Gly Lys Arg Thr Thr Phe Tyr Ser Arg Trp Ser Glu Gly Phe Ile Asn


    50                  55                  60


 


Ala Trp Leu Gly Pro Gly Gln Thr Glu Phe Tyr Gly Pro Asn Ala Ser


65                  70                  75                  80


 


Val Glu Gly Gly His Leu Ile Ile Lys Ala Thr Arg Lys Pro Gly Thr


                85                  90                  95


 


Thr Gln Ile Tyr Thr Gly Ala Ile His Ser Asn Glu Ser Phe Thr Tyr


            100                 105                 110


 


Pro Leu Tyr Leu Glu Ala Arg Thr Lys Ile Thr Asn Leu Thr Leu Ala


        115                 120                 125


 


Asn Ala Phe Trp Leu Leu Ser Ser Asp Ser Thr Glu Glu Ile Asp Val


    130                 135                 140


 


Leu Glu Ser Tyr Gly Ser Asp Arg Ala Thr Glu Thr Trp Phe Asp Glu


145                 150                 155                 160


 


Arg Leu His Leu Ser His His Val Phe Ile Arg Gln Pro Phe Gln Asp


                165                 170                 175


 


Tyr Gln Pro Lys Asp Ala Gly Ser Trp Tyr Pro Asn Pro Asp Gly Gly


            180                 185                 190


 


Thr Trp Arg Asp Gln Phe Phe Arg Ile Gly Val Tyr Trp Ile Asp Pro


        195                 200                 205


 


Trp Thr Leu Glu Tyr Tyr Val Asn Gly Glu Leu Val Arg Thr Val Ser


    210                 215                 220


 


Gly Pro Glu Met Ile Asp Pro Tyr Gly Tyr Thr Asn Gly Thr Gly Leu


225                 230                 235                 240


 


Ser Lys Pro Met Gln Val Ile Phe Asp Ala Glu His Gln Pro Trp Arg


                245                 250                 255


 


Asp Glu Gln Gly Thr Ala Pro Pro Thr Asp Ala Glu Leu Ala Asp Ser


            260                 265                 270


 


Ser Arg Asn Gln Phe Leu Ile Asp Trp Val Arg Phe Tyr Lys Pro Val


        275                 280                 285


 


Ala Ser Asn Asn Gly Gly Gly Asp Pro Gly Asn Gly Gly Thr Pro Gly


    290                 295                 300


 


Asn Gly Gly Ser Gly Asp Thr Val Val Val Glu Met Ala Asn Phe Ser


305                 310                 315                 320


 


Ala Thr Gly Lys Glu Gly Ser Ala Val Ala Gly Asp Thr Phe Thr Gly


                325                 330                 335


 


Phe Asn Pro Ser Gly Ala Asn Asn Ile Asn Tyr Asn Thr Leu Gly Asp


            340                 345                 350


 


Trp Ala Asp Tyr Thr Val Asn Phe Pro Ala Ala Gly Asn Tyr Thr Val


        355                 360                 365


 


Asn Leu Ile Ala Ala Ser Pro Val Thr Ser Gly Leu Gly Ala Asp Ile


    370                 375                 380


 


Leu Val Asp Ser Ser Tyr Ala Gly Thr Ile Pro Val Ser Ser Thr Gly


385                 390                 395                 400


 


Ala Trp Glu Ile Tyr Asn Thr Phe Ser Leu Pro Ser Ser Ile Tyr Ile


                405                 410                 415


 


Ala Ser Ala Gly Asn His Thr Ile Arg Val Gln Ser Ser Gly Gly Ser


            420                 425                 430


 


Ala Trp Gln Trp Asn Gly Asp Glu Leu Arg Phe Thr Gln Thr Asp Ala


        435                 440                 445


 


Asp Thr Gly Thr Asn Pro Pro Ser Thr Ala Ser Ile Ala Val Glu Ala


    450                 455                 460


 


Glu Asn Phe Asn Ala Val Gly Gly Thr Phe Ser Asp Gly Gln Ala Gln


465                 470                 475                 480


 


Pro Val Ser Val Tyr Thr Val Asn Gly Asn Thr Ala Ile Asn Tyr Val


                485                 490                 495


 


Asn Gln Gly Asp Tyr Ala Asp Tyr Thr Ile Ala Val Ala Gln Ala Gly


            500                 505                 510


 


Asn Tyr Thr Ile Ser Tyr Gln Ala Gly Ser Gly Val Thr Gly Gly Ser


        515                 520                 525


 


Ile Glu Phe Leu Val Asn Glu Asn Gly Ser Trp Ala Ser Lys Thr Val


    530                 535                 540


 


Thr Ala Val Pro Asn Gln Gly Trp Asp Asn Phe Gln Pro Leu Asn Gly


545                 550                 555                 560


 


Gly Ser Val Tyr Leu Ser Ala Gly Thr His Gln Val Arg Leu His Gly


                565                 570                 575


 


Ala Gly Ser Asn Asn Trp Gln Trp Asn Leu Asp Lys Phe Thr Leu Ser


            580                 585                 590


 


Asn
















TABLE 6





Aga16B polynucleotide (SEQ ID NO: 2)















atgcgcccta gctgcgcctt cttcagtacc cctcttatgg ctgcagattg ggacggaatt


  60


 


cctgtcccag cggacccagg gaatggcaac acctgggagc tacagtccct ttctgacgat


 120


 


ttcaactatg cggccccagc taacggcaaa cgcaccacct tctatagccg ctggagcgaa


 180


 


ggctttatca atgcttggct cggcccgggg caaaccgagt tttacggccc caatgcttcg


 240


 


gtagaaggcg gccaccttat tattaaggcc actcgcaagc caggtactac tcaaatttac


 300


 


actggagcaa ttcactccaa tgaaagtttt acctacccat tgtatttgga agcgcgcacc


 360


 


aaaattacaa acctcaccct cgccaacgca ttttggctac taagctcaga ttccaccgaa


 420


 


gagattgatg tgctggagtc ttacggcagc gaccgtgcaa cagaaacgtg gtttgacgaa


 480


 


cgcctacact taagccatca cgtttttatc cgccagccat ttcaagacta ccaaccgaaa


 540


 


gatgcaggca gctggtaccc caaccccgat ggcggcactt ggcgcgacca atttttccgt


 600


 


ataggtgttt attggataga cccatggaca ctggagtatt acgtgaatgg cgaattagtg


 660


 


cgcactgtaa gcggcccaga aatgattgac ccgtacggtt acaccaacgg cacaggccta


 720


 


agtaaaccca tgcaagttat tttcgatgca gagcatcagc cttggcgcga cgaacaaggt


 780


 


actgccccac ccaccgacgc agagctagcc gactcgagtc gcaatcaatt cttaattgac


 840


 


tgggtgcgat tctacaaacc cgtggcaagc aacaatggtg gcggcgaccc aggcaatggc


 900


 


ggcaccccag gtaatggtgg cagtggcgat actgtagtgg tagaaatggc caacttctct


 960


 


gccacaggta aagaaggctc tgcagttgca ggcgacactt tcacaggctt caaccccagc


1020


 


ggcgcgaaca acatcaacta caacacctta ggggattggg cagactacac ggtgaacttc


1080


 


cccgctgccg gtaattacac cgtaaaccta attgcagcct cgccggttac atctgggctg


1140


 


ggtgcagata ttttggtaga cagcagttac gcaggcacca tacctgttag cagcaccgga


1200


 


gcttgggaga tatacaacac ctttagcttg cccagctcga tttatatcgc aagcgcaggc


1260


 


aatcatacta ttcgcgtaca aagctccggc ggtagcgctt ggcagtggaa cggcgacgaa


1320


 


cttcgcttta cccaaacgga tgcggataca ggcaccaatc cacccagtac agccagcata


1380


 


gcggttgaag ccgaaaactt taacgcggtg ggcggcacct ttagcgatgg tcaagctcaa


1440


 


cctgttagcg tttacaccgt taacggcaac actgccatta actacgtaaa ccaaggcgat


1500


 


tatgccgact acaccattgc tgttgcccaa gcgggtaact acaccattag ctatcaagct


1560


 


ggcagtggcg taacaggtgg tagcatagag tttttggtta acgaaaacgg aagctgggcc


1620


 


agtaaaaccg ttaccgccgt accaaaccaa ggttgggata acttccaacc cttaaacgga


1680


 


ggcagcgttt acctaagcgc aggcacccac caagttcgtt tacacggcgc tggcagcaac


1740


 


aactggcagt ggaacctaga taagttcacg cttagcaact aa


1782









Any derivatives of Aga16B can be used in the invention, provided that the catalytic activity of the polypeptide is substantially preserved (e.g., the polypeptide has at least 10% the activity per polypeptide of wild-type Aga16B in phosphate buffer at 42° C. for 1 hour with any suitable substrate, such as agar or agarose).
The wild-type Aga16B has two CBM6s located in the carboxy-terminus of Aga16B as follows: CBM6-B1, aa 322 to 445 (SEQ ID NO:10), and CBM6-B2, aa 455 to 593 (SEQ ID NO:11); these are underscored once in Table 5.
A glycoside hydrolase-like domain is found from aa 31 to 289 (single underscored and italicized; SEQ ID NO:12); this domain harbors the catalytic activity of the Aga16B polypeptide.
Thus, in one embodiment, the invention utilizes a polypeptide comprising SEQ ID NO:12. In another embodiment, the invention utilizes a polypeptide comprising SEQ ID NO:12 and at least one CBM, comprising at least one selected from the group consisting of SEQ ID NOs:10 and 11. In another embodiment, the invention exploits the full-length Aga16B polypeptide (SEQ ID NO:1).
The two catalytic domains of Aga86E and Aga16B can be fused into a single polypeptide. Thus in yet another embodiment, the invention utilizes a polypeptide comprising SEQ ID NO:9 and SEQ ID NO:12. In a further embodiment, the invention utilizes a polypeptide comprising SEQ ID NOs:9 and 12 along with at least one CBM selected from the group consisting of SEQ ID NOs:5, 6, 7, 10, and 11. The CBMs can be separated from each other with any number of repeats of SEQ ID NOs:8 and 13, including 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50 or more sets of repeats. Noteworthy, too, is that the catalytic domain of Aga86E (SEQ ID NO:9) can be combined with any CBM (SEQ ID NOs:5, 6, 7, 10 and 11), which CBMs can be separated by any number of repeats, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50 or more sets of repeats of SEQ ID NOs:8 and 13, while the Aga16B catalytic domain (SEQ ID NO: 12) is absent.
Substrates
In one embodiment of the invention, at least one polypeptide having a catalytic activity is contacted with a suitable substrate. The substrate is selected from the group consisting of agar, agarose, neoagarotetraose, agarooligosaccharides, and derivatives thereof. Derivatives include partially cross-linked molecules, substituted molecules, and the like. In some embodiments, the substrates can be molten.
In some embodiments, the ultimate product of contacting a substrate with a polypeptide having catalytic activity is neoagarobiose (formula T), shown below. Neoagarobiose is a disaccharide of β-D-galactose and 3,6-anhydro-α-L-galactose, which when linked together, constitutes agarose. In one embodiment, an Aga86E polypeptide is contacted with agarose or an agarooligosaccharide to produce neoagarobiose. In another embodiment, agar or agarose is contacted with an Aga16B polypeptide, to produce mixed-length agarooligosaccharides; these agarooligosaccharides are then contacted with an Aga86E polypeptide to produce from exolytic cleavage, neoagarobiose.




Making Aga86E/16B polypeptides
The invention is directed to using Aga86E/16B polypeptides, and biologically-active portions, derivatives, fragments, analogs or homologs thereof. Aga86E/16B polypeptides can be isolated from cells and tissues, produced by recombinant DNA techniques or chemically synthesized.
An Aga86E/16B “chimeric polypeptide” or “fusion polypeptide” comprises Aga86E/16B fused to a non-Aga86E/16B polypeptide, or fused with various combinations of CBM6 and GH86 or GH16 domains. A non-Aga86E/16B polypeptide is not substantially homologous to Aga86E/16B (SEQ ID NOS:1, 3, 5, 6, 7, 9-12). An Aga86E/16B fusion polypeptide can include any portion to an entire Aga86E/16B, including any number of biologically active portions.
Other fusion partners can aid in purify Aga86E/16B polypeptides, such as Histidine tags, and for linking to solid supports, such as nickel-coated supports.
Fusion polypeptides can be easily created using recombinant methods. A polynucleotide encoding Aga86E/16B can be fused in-frame with a non-Aga86E/16B encoding polynucleotide, to the Aga86E/16B N- or C-terminus, or internally. Fusion genes can also be synthesized by conventional techniques, including automated DNA synthesizers and PCR amplification using anchor primers that give rise to complementary overhangs between two consecutive gene fragments that can subsequently be annealed and reamplified to generate a chimeric gene sequence (Ausubel et al., 1987).
Any vector can be used, including plasmids, viral vectors, etc. Recombinant expression vectors that comprise a Aga86E/16B (or fragment(s)) regulate a Aga86E/16B transcription by exploiting one or more host cell-responsive (or that can be manipulated in vitro) regulatory sequences that is operably-linked to Aga86E/16B.
Vectors can be introduced in a variety of organisms and cells, which methods, organisms and cells are well-known to those of skill in the art. Alternatively, the vectors can be transcribed and translated in vitro, for example, using T7 promoter regulatory sequences and T7 polymerase.
Solid Supports
In some embodiments, the Aga86E/16B polypeptides are linked to solid supports. The advantage of this approach is that the Aga86E/16B polypeptides can easily be removed from the reaction mix, essentially purifying the resulting products, such as neoagarobiose.
The solid support can be any material known to those of ordinary skill in the art to which the polypeptides can be attached. For example, the solid support can be a test well in a microliter plate or a nitrocellulose or other suitable membrane. Alternatively, the support can be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride. The support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Pat. No. 5,359,681. The binding agent can be immobilized on the solid support using a variety of techniques known to those of skill in the art, which are amply described in the patent and scientific literature. “Immobilization” refers to both noncovalent association, such as adsorption, and covalent attachment (that can be a direct linkage between the agent and functional groups on the support or can be a linkage by way of a cross-linking agent). In such cases, adsorption can be achieved by contacting the binding agent, in a suitable buffer, with the solid support for a suitable amount of time. Such binding should not interfere with the ability of the bound polypeptide to carry out its function, whether to cleave a polysaccharide or bind carbohydrates. Alternatively, the polypeptides can be bound to microparticles that have previously been coated with streptavidin (or avidin) or biotin. Alternatively, the polypeptides can be bound using microparticles that have been previously coated with anti-Aga86E/16B antibodies or derivatives thereof. Moreover, the solid support can be derivatized to allow reactivity with various functional groups on the polypeptides. Such derivatization requires the use of certain coupling agents such as maleic anhydride, N-hydroxysuccinimide and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. Many useful coupling agents are currently available from Pierce Biotechnology, Inc. (Thermo Scientific; Rockford, Ill.).
Substrate Degradation
The methods of the invention include contacting a substrate with at least an enzymatically active domain of Aga86E, such as the GH domain of SEQ ID NO:9 or a functional derivative thereof. The digestion of the substrate, especially when the substrate is agar or agarose, can be hastened by the addition of Aga86E CBMs, and further so by the addition of an Aga16B enzymatically active domain (or in some cases, pre-contacting the substrates with a enzymatically active domain of Aga16B, such as that of SEQ ID NO:12 and functional derivatives thereof), and further addition of CBMs particular to Aga16B. In one embodiment, a substrate is contacted with an Aga86E polypeptide of SEQ ID NO:1; in yet another embodiment, the substrate is contacted with Aga86E polypeptide of SEQ ID NO:1 and an Aga16B polypeptide of SEQ ID NO:3. A substrate can be contacted sequentially with Aga16B polypeptides, and the enzymatically-produced products (agarooligosaccharides of various lengths) then contacted with Aga86E polypeptides. It is unnecessary to remove any remaining Aga16B polypeptides from the reaction mix before contacting the reaction mix with an Aga86E polypeptide.
In one embodiment, the polypeptides are linked to solid supports. One solid support may comprise all of the Aga16B/Aga86E polypeptides; in other embodiments, one solid support may comprise only Aga16B polypeptides, and another solid support may comprise only Aga86E polypeptides. In one embodiment, the substrate is first incubated with Aga16B polypeptides linked to solid supports, followed by the addition of Aga86E polypeptides linked to solid supports. Optionally, before adding the Aga86E polypeptide-coated supports, the Aga16B polypeptide-coated solid supports are first removed. Removal can be accomplished by any physical method, such as simple centrifugation, or in the case of magnetic supports, using magnetic fields, or a combination of physical separation methods.
The substrates and Aga86E/16B polypeptides are suspended in solution for the reaction to optimally proceed. In most embodiments, a biological buffer is used; such buffers can maintain desirable pH and other reaction conditions. Any suitable buffer can be used. Examples of suitable biological buffers include Hank's Balanced Salt Solution (HBSS), sodium phosphate-based buffers, N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-Tris), N-(2-hydroxyethyl)piperazine-N′3-propanesulfonic acid (EPPS or HEPPS), glyclclycine, N-2-hydroxyehtylpiperazine-N′-2-ethanesulfonic acid (HEPES), 3-(N-morpholino)propane sulfonic acid (MOPS), piperazine-N,N′-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N-tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES), N-tris(hydroxymethyl)methyl-glycine (Tricine), and tris(hydroxymethyl)-aminomethane (Tris). Salt solutions that can be used to manipulate osmotic conditions include Alseverr's Solution, Dulbecco's Phosphate Buffered Saline (DPBS), Earle's Balanced Salt Solution, Gey's Balanced Salt Solution (GBSS), Puck's Saline A, Tyrode's Salt Solution, St. Thomas Solution and University of Wisconsin Solution.
In some cases, water alone is sufficient.
The Aga86E/16B polypeptides can be used over a wide range of pH. Optimal pHs are those that are slightly alkaline, such as pH 7.2-8.0. But any pH can be used that does not affect the substrate or polypeptide integrity, such as pH 5, 6, 7, 8, 9, and 10, or any increment therein.
The Aga86E/16B polypeptides are contacted with a substrate, creating a reaction mix, in a buffer for a time sufficient to produce neoagarobiose. The time can vary due to the activity of a particular lot of Aga86E/16B polypeptides, the combination of the various domains used in the reaction mix, the amount of substrate, the type of substrate, the concentration of the enzymatically active domains, etc. Generally, the reaction mix is incubated from 1 minute to 5 days; more typical times include 30 minutes, 60 minutes, 2 hours, 4 hours, 8 hours, 12 hours, 24 hours, etc. The optimal reaction time for a particular production of Aga86E/16B polypeptides, substrates, etc., can easily be determined by one of skill in the art.
Temperature can influence the speed at which the digestion proceeds. In some embodiments, a temperature of approximately 42° C. is desirable. However, other temperatures can be used, from 25° C. to 50° C., such as 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 40, 42, 45, 47 and 50° C. The temperature can be varied during the incubation time.
In some embodiments, the reaction mix is agitated and/or aerated during substrate digestion.
EXAMPLES
The following examples are for illustrative purposes only and should not be interpreted as limitations of the claimed invention. There are a variety of alternative techniques and procedures available to those of skill in the art which would similarly permit one to successfully perform the intended invention.
Example 1
Materials and Methods
Bacterial Strains and Plasmids
Saccharophagus degradans 2-40T (ATCC 43961; DSMZ17024; American Type Culture Collection (ATCC); Manassus, Va.) was grown in minimal medium containing (per liter) 2.3% INSTANT OCEAN® (Aquarium Systems, Mentor, Ohio), 0.5% ammonium chloride, and 50 mM Tris-HCl, pH 7.6. Carbon sources were added to a final concentration of 0.2%. Agar (1.5%) was added to solid media. Cultures of S. degradans 2-40 were incubated at 28° C. Escherichia coli EPI300, DH5α, and Tuner strains were grown at 37° C. in Luria-Bertani (LB) broth or agar supplemented with the appropriate antibiotics. Antibiotics were added to media at the indicated concentrations (in μg/ml): ampicillin, 200; chloramphenicol, 30; and kanamycin (Kan), 50.
Molecular Biology Protocols
DNA manipulations were performed using standard procedures. Restriction enzymes and T4 DNA ligase were obtained from New England Biolabs (Ipswich, Mass.). The pETBlue-2 expression vector was purchased from Novagen (Madison, Wis.). All other reagents and substrates were obtained from Sigma-Aldrich (St. Louis, Mo.) unless otherwise noted. Polymerase chain reactions (PCRs) employed either Taq (Invitrogen, Carlsbad, Calif.) or ProofPro (Continental Lab Products, San Diego, Calif.) polymerase by use of the manufacturer's recommended conditions. The nucleotide sequences of plasmid DNA or gel-purified PCR products were obtained at the UMBI sequencing facility.
Construction and Initial Screen of the S. degradans Genomic Library.
Genomic DNA was isolated from S. degradans 2-40 by using cetyltrimethylammonium bromide (Sambrook and Russell, 2001). The chromosomal DNA was used to construct a genomic library composed of 40-kb fragments cloned into pCC1Fos (Beta version; Epicentre Technologies, Madison, Wis.) by following the manufacturer's recommendations. The fosmid was packaged into lambda phage and used to transfect E. coli EPI300 (Epicentre). A pitting phenotype on LB agar plates was used initially to screen Cmr transfectants for agarase activity.
Determination of the Nucleotide Sequences of aga50A and aga16B
Sau3A fragments of 5 to 10 kb were ligated into BamHI-digested pUC19 and transformed into E. coli DH5α. Random pUC19 derivatives were selected, and a partial DNA sequence of the insert was obtained by using commercially available M13REV and the M13(−21) primers. The nucleotide sequences of candidate agarases were completed by primer walking using synthetic oligonucleotides (Table 7)







TABLE 7







Sequences used in cloning and manipulating agarases












SEQ ID



Primer
Sequence
NO:
Use





aga16B-f
aactgcagatccatgaaaaccacaaatgc
47
Cloning of





aga16B


 


aga16B-r
ccatcgatcttatctaggttccactgcca
48
Cloning of





aga16B


 


ga16B968R
ccatcgatacctgtggcagagaagttg
49
Truncation of





aga16B


 


ga16B853R
ccatcgatgtagaatcgcacccagtcaat
50
Truncation of





aga16B


 


aga16B736F
cttggcgcgccggcgcgacgaacaaggta
51
Truncation of





aga16B


 


aga16B1371R
ccatcgaatgtactgggtggattggtg
52
Truncation of





aga16B


 


aga86E-f
cttggcgcgccgagtcgcttttatcat
53
Cloning of





aga86E


 


aga86E-r
ccatcgattctatttggctcagaagt
54
Cloning of





aga86E


 


aga16B767R
ccatcgatgcgccaaggctgatgctgt
55
Cloning of





aga86E


 


aga86E-CF
ctctcatcaaccgtggcgaggtcggcgcaaactgtca
56
Deletion of





aga86E


 


aga86E-CR
acacattgcgatagtcacgc
57
Deletion of





aga86E


 


aga86E-NE
ccgctgcgctgtgagtatc
58
Deletion of





aga86E


 


aga50A-CF
ctctcatcaaccgtgggcttatttacgcagtgttagg
59
Deletion of





aga50A


 


aga50A-CR
ctctttcgcgttagcatctaa
60
Deletion of





aga50A


 


aga50A-NF
cagagccttctttacctgtg
61
Deletion of





aga50A


 


aga50A-NR
cgatgatggttgagatgtgtttatgtctgatggctaaacga
62
Deletion of





aga50A









Bioinformatic Approaches
Protein modules and domains were identified in deduced products by using the Simple Modular Architecture Tool ((Letunic et al., 2006; Schultz et al., 1998), the Pfam database (Finn et al., 2006), and the Carbohydrate-Active enZYme database (Coutinho and Henrissat, 1999a). Similarity searches were performed using the BLAST algorithm at the National Center for Biotechnology Information (NCBI) server (Altschul et al., 1990) or surveys of the S. degradans 2-40 genome (GenBank accession: CP000282). Type II secretion signals were identified using the SignalP version 1.1 program (Bendtsen et al., 2004). Molecular masses of polypeptide products were estimated using the peptide mass tool at the ExPASy server of the Swiss Institute of Bioinformatics (Gasteiger et al., 2005; Wilkins et al., 1997). The annotated genomic sequence of S. degradans 2-40 is Genbank Accession no. CP000282. Sequences were aligned using Clustal W (Thompson et al., 1994) or ClustalX (Thompson et al., 1997). The percent G+C content (% G+C) of whole genes and the % G+C at the third position of synonymous codons (GC3s) were calculated using CodonW (Peden, J. P., 2005; available from Sourceforge (Mountain View, Calif.)). Because a significant number of S. degradans 2-40 genes exhibit high similarity to genes found in diverse taxonomic units, a core set of genes was established to minimize the potential impact of horizontally acquired genes on baseline values. As approximately 20% of S. degradans 2-40 gene models exhibit similarity at the nucleotide level to a gene in a fluorescent pseudomonad (974 genes), most of which are annotated as basic metabolism and housekeeping genes, S. degradans 2-40 genes exhibiting at least 50% identity at the nucleotide level with a Pseudomonas sp. gene were used to calculate baseline % G+C, GC3s, and codon usage patterns. This core gene set included a total of 1,153,863 nucleotides (nt) of sequence data. The core gene set had a % G+C of 46.3, which is slightly higher than the total genome % G+C of 45.8% (Gonzalez and Weiner, 2000).
Zymograms
The samples were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in an 8% polyacrylamide gel supplemented with 0.1% agarose. Gels were then washed twice in 20 ml PIPES-Triton buffer (20 mM PIPES [piperazine-N,N′-bis(2-ethanesulfonic acid)], pH 6.8, and 2.5% Triton X-100) for 20 min at room temperature and then incubated in PIPES-Triton buffer overnight at 4° C. Gels were washed twice with 20 ml PIPES buffer and incubated at 42° C. for 2 h. Agarase activity of S. degradans 2-40 lysates was maximal at 42° C. and was stable at this temperature (Whitehead et al., 2001). Zymograms were developed using Gram's iodine solution.
Protein Expression and Purification
Genes of interest were amplified by PCR using tailed primers (see Table S1 in the supplemental material). Each fragment was digested with the designed restriction enzyme, ligated into pETBlue-2, and transformed into E. coli Tuner or E. coli DH5α cells. A 50-ml culture of each transformant carrying a clone of interest was grown at 37° C. to an optical density at 600 nm of 0.5 and induced with 1 mM (final concentration) isopropyl-β-D-thiogalactopyranoside (TPTG). After growth for 4 h at 37° C., cells were harvested and frozen at −20° C. His fusions were purified from cell lysates by using Ni-nitrilotriacetic acid resin (QIAGEN, Valencia, Calif.) according to the manufacturer's recommendations.
Assay of Agarase Activity and Identification of Reaction Products.
Reactions with purified agarase and agarose were performed in 50-μl reaction mixtures containing an aliquot of the purified His-tagged agarase in phosphate-buffered saline and 5 μl of molten 1% agarose. The reaction mixtures were incubated at 42° C. and then applied to a Whatman silica gel 60 A plate with a 250-μm layer. Neoagarohexaose, neoagarotetraose, neoagarobiose, and D-galactose (5 μg) were used as standards. The plates were developed with 2:1:1 N-butanol:acetic acid:water solution and stained with 2:1 ethanolic sulfuric acid:naphthoresorcinol solution (Duckworth and Yaphe, 1970). Degradation products were visualized by being baked at 80° C. for 10 min.
Mass Spectrometry
Culture filtrates of agarose-grown cells were concentrated about 25-fold by ultrafiltration, and protein concentrations were determined using a bicinchoninic acid protein assay (Pierce). Proteins were denatured by incubation in 100 mM Tris buffer, pH 8.5, containing 8 M urea and 10 mM dithiothreitol, and the denatured proteins were alkylated in 50 mM iodoacetate. The denatured, reduced, alkylated samples were digested overnight at 37° C. by using proteomics-grade trypsin (Promega) at a 1:50 enzyme-to-substrate ratio. Digestions were stopped in 1% formic acid and analyzed by reverse-phase high-pressure liquid chromatography (HPLC)-tandem mass spectrometry (MS) at the UMCP College of Life Sciences Mass Spectrometry facility with a Waters 2960 HPLC system linked to a Finnigan LCQ tandem mass spectrometer. Alternatively, culture supernatants were fractionated on 8% SDS-PAGE gels containing 0.1% agarose and stained with SYPRO Ruby red (Molecular Probes). Regions of interest were excised and were equilibrated with 50% 200 mM ammonium bicarbonate and 50% acetonitrile. The treated samples were submitted to the Stanford University Mass Spectrometry Laboratory for analysis by electrospray ionization-quadrupole time-of-flight MS following trypsin digestion. Identification of peptide fragments employed SEQUEST (Eng et al., 1994) and MASCOT (Perkins et al., 1999) algorithms and the amino acid sequence translations of all gene models in the S. degradans 2-40 genome as well as the nonredundant mass spectrometry database (compiled by Dr. D. N. Perkins; Imperial College School of Medicine; London, UK).
Immunoblots
Proteins were fractionated by SDS-PAGE as described above and electroblotted onto supported nitrocellulose membranes (0.45-mm pore size; Osmotics, Trevose, Pa.). Membranes were blocked with 1% alkali-soluble casein (Novagen) and incubated with rabbit anti-AgaE antibodies (1:100). Membranes were washed twice and incubated with horseradish peroxidase-conjugated donkey anti-rabbit antibody (Amersham). Immunoreactive proteins were visualized using an ECL detection kit (Amersham Pharmacia Biotech).
Marked Chromosomal Gene Replacements
The procedures used to generate gene replacement mutants in an Acinetobacter sp. (Metzgar et al., 2004) were adapted for use with S. degradans 2-40. Briefly, the 1-kb regions upstream and downstream of the gene of interest were amplified from genomic DNA by PCR employing a standard design primer and a splicing primer containing 5′ tails complementary to the primers used to amplify a Kan resistance cassette. Aliquots of the upstream- and downstream-region amplicons were mixed directly with an amplified Kan cassette in a splicing PCR mixture containing both standard design primers in excess. After amplification for 30 cycles, the complete splicing PCR mixture was added to a culture of S. degradans 2-40 outgrown from stationary phase in minimal medium plus glucose for 4 h and allowed to incubate with shaking at 28° C. for 2 h. Cells were harvested, washed once in outgrowth medium, and plated onto selective media containing glucose and 100 μg/ml Kan. After 3 to 4 days, cells from appearing colonies were screened in batches for gene replacements by PCR using one of the standard design primers and the correctly oriented primer specific for the kanamycin cassette. Positive colonies were screened with the opposite primer combination to confirm the insertion.
Nucleotide Sequence Accession Numbers
The nucleotide sequences for Aga50A, Aga16B, Aga86C, Aga50D, and Aga86E have been reported to the GenBank database under accession nos. ZP—00315251, AAT67062, ZP—00315652, ZP—00315360, and ZP—00315657, respectively.
Example 2
Predicted Agarases Encoded by S. degradans Genome
Relatively limited genetic tools are available for use in S. degradans 2-40, as stable transformants carrying commonly used narrow- or broad-host-range plasmids could not be isolated and traditional transposon mutagenesis strategies were ineffective. In order to identify agarase-encoding genes, E. coli EPI300 transfectants carrying a genomic library of S. degradans 2-40 created in the copy control fosmid pCClFos were screened on solid agar media for a pitting phenotype. Pitting colonies indicative of the hydrolysis of agar were detected at a frequency of 1.7×10−3 only when cells were grown under single-copy conditions for the fosmid. This was comparable to the expected frequency for a single gene in this library. A total of nine transfectants that pitted agar were identified, and one, EPI300(pNE10), was chosen for sequence analysis. All Aga+ fosmids were highly unstable in several E. coli strains, with less than 1% of transformants retaining an Aga+ phenotype in repeated plasmid isolation/transformation into fresh hosts. The Aga+ colonies were substantially smaller than those of the Aga− transformants.
Due to the phenotypic instability of the Aga+ fosmids, sequence analysis was used to identify resident agarase genes. The sequence of subcloned fragments of pNE10 revealed two open reading frames that could be involved in the degradation of agar. The first, aga50A, encoded a deduced product of a 776-amino-acid (aa) polypeptide with a predicted molecular mass of 86 kDa that was 45% identical and 62% similar to a putative secreted hydrolase from Streptomyces coelicolor A3 (Allouch et al., 2003) (NP627690) and that also exhibits similarity to a β-agarase identified in Vibrio sp. strain JT0107 (S46651) (Table 8). The second open reading frame, aga16B, was predicted to encode a 593-aa product with a predicted mass of 64 kDa. The amino-terminal 278-aa region of Aga16B is 54% identical and 69% similar to a β-agarase of Pseudomonas sp. strain ND137 (BAD88713) and is 64% identical and 73% similar to a β-agarase from Microbulbifer sp. strain JAMB-A7 (BAC99022). aga50A appeared to be divergently expressed from aga16B by a shared 424-bp promoter region. Immediately downstream of aga16B is the gene for a tRNASer. A PCR screen revealed that aga50A and aga16B were present in all Aga+ E. coli EPI300 transfectants carrying the S. degradans 2-40 genomic library but were specifically absent from spontaneously arising Aga− derivatives of pNE10.







TABLE 8







Properties of candidate agarases identified in the S. degradans 2-40 genome

















Homolog





GenBank
Size of predicted

GenBank accession


Gene
accession no.
product (kDa)a
Representative homologb
no.
% Sc
% Ic
















agaSQA
ZP 0031251
87
β-Agarase of Vibrio sp.
S46651
62
44





strain JT0107


agal6B
AAT67062
64
Agarase of Pseudomonas sp.
BAB88713
54
69





strain ND137


aga86C
ZP 000315652
86
β-Agarase of
AAA25696
38
55





Pseudoalteromonas atlantica


aga50D
ZP 000315360
89
β-Agarase of Vibrio sp.
S46651
43
60





strain JT0107


aga86E
ZP 000315657
146
β-Agarase of Microbulbifer
BAD86832
60
72





sp. strain JAMB-A94





aAs estimated by the ExPASy peptide mass tool.


bAs determined by a BLASTP search of the nonredundant database.


cPercent similarity (% S) and percent identity (% I) as calculated by BLASTP alignment.






Upon the release of the S. degradans 2-40 genome sequence by the U.S. Department of Energy Joint Genome Institute (Walnut Creek, Calif.), genes for three additional candidate agarases were identified by sequence similarity to known agarases. The first, aga86C, encoded a 789-aa, 86-kDa protein with a domain that shares 38% identity to a β-agarase of Pseudoalteromonas atlantica (AAA25696) and 29% identity and 45% similarity to an agarase from Microbulbifer sp. strain JAMB-A94 (BAD86832) (Table 2). Aga86C did not share obvious similarity to either Aga50A or Aga16B. A gene for another candidate agarase, aga50D, produced a 795-aa product with a predicted mass of 88.6 kDa. A portion of Aga50D exhibited 45% identity and 61% similarity to a putative secreted hydrolase from S. coelicolor (NP627690) and 43% identity and 60% similarity to an agarase from Vibrio sp. strain JT0107 (S46651). Aga50D also shared sequence similarity with a domain of the S. degradans 2-40 Aga50A. A third putative agarase gene, aga86E, yielded a 1,335-aa, 146-kDa deduced polypeptide. The carboxy-terminal 679-aa region was 30% identical and 44% similar to the β-agarase of P. atlantica and also exhibited 29% identity and 44% similarity to a domain of the S. degradans 2-40 Aga86C. A homolog to a GH96 domain characteristic of α-agarases was not apparent in the genome.







TABLE 9







Sequence features for gene models predicted to encode agarases

















No. of







amino acids



Gene
Chromosomal
% G +

with variant


Gene(s)
modela
addressb
Cc
GC3sd
codon usagee















Aga50A
1176
1513741-1516074
45.3
38.6
6f


Aga16B
1175
1513481-1511685
52.4
52.6
6g


aga86C
2650
3352440-3354803
46.8
44.8
8h


aga50D
2644
3345735-3343354
46.3
42.9
1i


aga86E
2655
3369919-3365912
46.1
37.3
7j


Core


46.3
42


genesk





aGene numbers assigned in the 15 Jun. 2005 annotation of the genome from Genome Analysis and System Modeling Group of the Life Sciences Division of Oak Ridge National Laboratory (Oak Ridge, TN).


bNucleotide address of the apparent coding sequence within the assembled 15 Jun. 2005 version of the S. degradans 2-40 genome. The nucleotide address of the deduced start codon is listed first, followed by the address of the last nucleotide of the apparent stop codon.


c% G + C calculated for the indicated predicted coding sequence.


d% G + C in the third position of synonymous codons within the deduced coding sequence.


eA two-tailed Fisher exact analysis of the codon usage for each amino acid with synonymous codons was performed, comparing codon usage within the predicted coding sequence to that within the core gene set. A P value that indicates the probability that the codon usage is the same as that for the core set was generated. The number of amino acids for which the P value was less than 0.1 is shown.


fVariant codon usage was detected for Arg, Cys, Gly, His, Pro, and Ser.


gVariant codon usage was detected for Asn, Asp, Gly, Phe, Ser, and Tyr.


hVariant codon usage was detected for Ala, Asp, Glu, Gly, Leu, Ser, Tyr, and Val.


iVariant codon usage was detected for Asp.


jVariant codon usage was detected for Arg, Glu, Gly, Pro, Ser, Thr, and Val.


kThe core gene set represents the 974 genes with at least 50% similarity to a gene in a Pseudomonas aeruginosa PAO1 genome.






The putative agarase genes were located in two regions of the S. degradans 2-40 genome. Aga50A and aga16B clustered as gene models 1176 and 1175, respectively, located between nucleotides 1511685 and 1516074, in the 15 Jun. 2005 annotation of the S. degradans 2-40 genome (Table 9). Flanking aga50A is a gene for a candidate β-galactosidase (galA), but the annotations of other nearby genes did not indicate obvious predicted roles in CP metabolism. The gene models for aga86C (gene model 2650), aga50D (gene model 2644), and aga86E (gene model 2655) loosely cluster in a 26,565-nt region beginning at nucleotide 3343354. Most intervening genes do not appear to be associated with degradation of agar or other CPs, but a candidate sugar transporter is present in this region.
Variation in % G+C and codon usage can indicate acquisition from another organism. Using simple % G+C analysis of the coding sequences, only the aga16B coding sequence differed substantially from that of the core gene set (Table 9). In contrast, the GC3s differed from that of the core set by at least 3% in aga50A, aga16B, aga86C, and aga86E, suggestive of acquisition from another organism. These genes also differed in their codon usage patterns relative to the core set of genes. Using a two-tailed Fisher exact test to statistically compare codon usage of the agarase genes to that of the chosen core gene set (Plotkin et al., 2004), codon usage for at least 6 of the 18 amino acids with synonymous codons had less than a 10% chance of being the same as that for the core set (Table 2). In contrast, aga50D was similar to the core set in all traits evaluated except codon usage for Asp. A survey of the nonredundant databases for nucleotide sequence similarities revealed only localized sequence similarities, located primarily within conserved domains of the agarases. Because four of five agarases present in the Microscilla sp. strain PRE1 agarolytic plasmid had extensive similarity to S. degradans 2-40 agarases, the S. degradans 2-40 genome was surveyed for other similarities with the Microscilla agarolytic plasmid. No similarities were detected at the nucleotide level between the agarolytic plasmid of Microscilla sp. strain PRE1 and the S. degradans 2-40 genome, but extensive similarities (nt 58656 to 62741) to a 3-kb region internal to the aga50D-aga86C-aga86E cluster that exhibited extensive synteny were detected.
Example 3
Modular Structure of the Agarases Encoded by S. degradans 
Hydrolases typically carry conserved glycoside hydrolase (GH) domains that function in catalysis and sometimes also carry CBMs (Coutinho and Henrissat, 1999b). Although commonly used domain recognition algorithms, such as SMART, did not identify conserved GH domains within the predicted S. degradans 2-40 agarases, three distinct GH domains were detected when the localized regions of sequence conservation in Aga16B, Aga50A/Aga50D, and Aga86C/Aga86E were analyzed (FIG. 1). The 120-aa region of Aga16B that shares sequence similarity with seven known β-agarases (aa 31 to 289) contains a GH16 domain (FIG. 2). The signature sequence for GH16 (E-[LIV]-D-[LIVF]-X-E-XX-[GQ]-[KRNF]-X-[PSTA]; SEQ ID NO:26) is partially conserved in Aga16B, and both critical Glu residues are retained (Juncosa et al., 1994). In the agarases, the GH16 domain is located in the amino-terminal region of the polypeptide, immediately adjacent to a signal peptide. It is unclear whether this represents an orthologous relationship or a functional requirement for the domain location. The region in common between Aga50A and Aga50D (aa 350 to 769 and aa 325 to 747, respectively) is similar to the GH50 domains of the Vibrio sp. strain JT0107 agarases (FIG. 3). A partially conserved region extends for at least 375 aa and is located in the carboxy-terminal end of the polypeptides. As mentioned before, it has not been established whether this is a functional requirement for the domain. The region conserved between Aga86C and Aga86E (aa 147 to 787 and aa 633 to 1316, respectively) shows sequence similarity to the GH86 domain of P. atlantica AgrA (FIG. 4). This region, however, is highly divergent, with only localized regions of sequence similarity apparent.
Unusual for agarases, two apparent CBM6 were identified in the carboxy-terminal region of Aga16B (CBM6-B1, aa 322 to 445, and CBM6-B2, aa 455 to 593) and three predicted CBM6 were located in the amino-terminal 650-aa region of Aga86E (CBM6-E1, aa 9 to 148, CBM6-E2, aa 162 to 302, and CBM6-E3, aa 349 to 483) (FIG. 1 and FIG. 5). Phylogenetic analyses indicated that predicted CBM6 of the agarases are distinct from other CBM6 found in the S. degradans 2-40 genome (FIG. 6). CBM6-E1, -E2, and -B2 were most closely related to each other, whereas CBM6-E3 and -B1 formed a second group strongly supported by bootstrap analysis (see FIG. S4). A repetitive linker sequence of (P-X)i7(SEQ ID NO: 63) separated the first and second CBM6 of Aga86E; the second and third CBM6, were separated by an (E-P)17 (SEQ ID NO: 64) repeat. Four thrombospondin type 3 repeats were also identified between aa 511 and 643. The function of these repeats is unknown. As expected for secreted proteins, cleavable type II secretion signals were detected in the amino termini of Aga50A, Aga16B, Aga86C, Aga50D, and Aga86E. A predicted lipoprotein acylation site (d'Enfert et al., 1989) was identified in the amino terminus of Aga86C.
Example 4
Activities of the Candidate agarases 
To determine whether the candidate agarases have the predicted activities, each was cloned into pETBIue-2 to create carboxy-terminal His6-tagged (SEQ ID NO: 65) derivatives. E. coli Tuner (pLac1)(pNEaga16B1) expressing Aga16B-His rapidly pitted agar plates, which was usually apparent after overnight growth, even in the absence of induction. Upon purification of Aga16B-His, the expected 65-kDa product and an 85-kDa derivative were detected in immunoblots probed with anti-His antibodies, as well as by mass spectrometry. Anomalous migration of S. degradans 2-40 proteins appears to be common, as several S. degradans 2-40 carbohydrases expressed in E. co/i migrate at higher-than-predicted molecular masses for unknown reasons.
In order to determine the biochemical activity of Aga16B, the products of Aga16B-mediated degradation of agarose were characterized by thin-layer chromatography. Digestion of agarose by Aga16B-His released neoagarotetraose and neoagarohexaose, but neoagarobiose could not be detected, even after long-term incubation. These results are consistent with endolytic β-agarase I-like activity. In contrast, only D-galactose was detected when agarose was digested with cell-free lysates of S. degradans 2-40, indicating the expression of additional enzymes to degrade neoagarooligosaccharides.
E. coli transformants expressing Aga86E-His also exhibited agarase activity. E. coli Tuner(pLacI)(pNEaga86E1) slowly pitted agar plates, requiring several weeks before the phenotype was evident. Spontaneously forming Aga86E-His amino-terminal truncations with masses of 100 and 86 kDa exhibited agarase activity in zymograms, but the full-length 146-kDa Aga86E-His lacked activity. It was unclear whether the absence of activity at the expected molecular mass for full-length Aga86E represented a precursor state for the enzyme or the failure to renature the full-length polypeptide under the conditions of the zymogram.
When the products resulting from the activity of purified Aga86E-His were analyzed by thin-layer chromatography, only neoagarobiose was released from agarose by Aga86E-His digestion after extended incubation (1 to 2 days). This is consistent with the slow-pitting phenotype of the Tuner transfectants expressing Aga86E-His. Because only neoagarobiose appears to be released by Aga86E activity, this enzyme appears to exolytically degrade agarose similarly to a β-agarase II.
It is unusual for agarases to carry CBM6. Like other carbohydrases, the CBM6 of Aga16B and Aga86E do not appear to be required for agarase activity. Truncated His-tagged derivatives of aga16B lacking one or both CBM6 exhibited agarase activity indistinguishable from that of the full-length form. Similarly, the spontaneously occurring amino-terminal truncations of Aga86E that are missing one or more of the resident CBM6 also retained agarase activity under laboratory conditions.
For unknown reasons, it was not possible to express Aga50A, Aga86C, and Aga50D in E. coli. The genes could be cloned into the nonexpressing E. coli strain DH5α-E, but attempts to transfer these clones into expressing strains, such as E. coli Tuner(DE3)(pLysS), were unsuccessful. Although some codons rarely used in E. coli were present in these genes, the expressible agarases also contained these codons at similar frequencies.
Aga16B, Aga86C, and Aga86E are Expressed and Secreted by S. degradans During Growth on Agar
To determine if any of the demonstrated or predicted agarases are expressed during growth on agarose, clarified and concentrated culture filtrates from agarose-grown cells were surveyed by HPLC-coupled tandem MS. Fragments indicative of Aga16B, Aga86C, and Aga86E were detected in total culture filtrates of agarose-grown S. degradans 2-40, but several predicted cytoplasmic proteins were also detected in these samples, which limited interpretation of the data. Only Aga86E was detected during similar analyses of culture filtrates from glucose-grown cells. When specific size-classed proteins from culture filtrates were analyzed by mass spectrometry, fragments consistent with the presence of Aga86C were detected in the agarase-active 85-kDa sample and Aga86E was the dominant component of the 150-kDa fraction. The data confirm that Aga16B, Aga86C, and Aga86E are expressed and secreted during the degradation of agarose.
Example 5
Aga50A and Aga86E are Required for Agar Metabolism
The mosaicism of the S. degradans 2-40 genome and the identification of the components of an apparent competence system within the genome sequence suggested that S. degradans 2-40 can be naturally competent. If so, the mutagenesis procedures developed for an Acinetobacter sp. (Metzgar et al., 2004) should be applicable to S. degradans 2-40. This strategy employs linear mutagenic fragments that recombine into the genome by homologous recombination.
Mutagenic constructs for S. degradans 2-40 were assembled by fusing the 1-kb segments flanking each side of a gene of interest to an antibiotic resistance cassette by using splicing PCR (Metzgar et al., 2004; Murphy, 1998). Each of the resulting linear mutagenic constructs (5′ flank:nptI:3′ flank) was added to a newly inoculated, exponentially growing culture of S. degradans 2-40, and after 2 h of incubation, potential transformants carrying gene replacements were selected. Kanr colonies appeared at a frequency of 6×10−6. Approximately 20% of these apparent transformants appeared to be gene replacements, as indicated by the presence of diagnostic PCR fragments. By this procedure, Δaga50A::nptI (S. degradans NE-A1) and Δaga86E::nptI (S. degradans NE-E1) mutants were created.
In order to evaluate the role of the demonstrated or predicted agarases in the degradation of agar, the constructed agarase mutants were screened for agarase complement in zymograms of cell lysates and their ability to utilize agar as a sole carbon source. Neither mutant was able to grow on agar as the sole carbon source, whereas a similarly constructed ΔchiA:nptI mutant retained this ability. When grown on media supplemented with glucose, the mutants pitted the medium slowly, but less so than wild-type S. degradans 2-40. The zymograms of the S. degradans NE-A1 and S. degradans NE-E1 lysates revealed no change in agarase activity relative to that of the wild type, although immunoblots showed S. degradans NE-E1 to lack Aga86E. These results indicate that the phenotype of the mutants is unlikely to be due to altered expression of other agarases but can be attributed to an essential role for the deleted gene product.
Example 6
The Agarolytic System of S. degradans 2-40 Requires Additional Components
To clarify the essential components of the agarolytic system, the cloned agarases were transformed into E. coli in an attempt to assemble a functional agarolytic system. The Aga+ pNE10 identified during the screen of the S. degradans 2-40 genomic library carries both aga50A and aga16B as well as the β-galactosidase-like galA gene. This plasmid was transformed into Gal+ E coli DH5α or HB101 and Gal−E. coli DH5α-E or TOP10 (Invitrogen) with or without pSHAga86E2 expressing aga86E. None of the resulting strains, however, were able to metabolize agarose as a sole carbon and energy source. Since the Gal+ transformants carrying both plasmids were highly unstable, an alternative test was performed. Gal− Aga+ strains of E. coli carrying either pNE10 or pSHAga86E2 were cross-streaked on several indicator media lacking an added carbon source and then overlaid with a Gal+ indicator strain. Galactose production was not detected in any medium, suggesting that the agarolytic system employs additional components not closely associated with aga50A, aga16B, or aga86E to convert agarose to galactose.
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## Claims

1. A method of producing neoagarobiose, comprising:
(a) providing a substrate selected from the group consisting of agar, agarose, neoagarotetraose, agarooligosaccharides, and derivatives thereof;
(b) contacting the substrate with a Saccharophagus degradans glycoside hydrolase (GH) polypeptide having at least 80% sequence identity with the amino acid sequence of SEQ ID NO:9, wherein the Saccharophagus degradans glycoside hydrolase (GH) polypeptide has exo-acting β-agarase activity, thereby creating a reaction mix; and
(c) incubating the reaction mix under suitable conditions and sufficient time to produce neoagarobiose from the substrate.

2. The method of claim 1, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:9.

3. The method of claim 1, wherein the polypeptide consists of the amino acid sequence of SEQ ID NO:9.

4. The method of claim 1, further comprising contacting the substrate with at least one carbohydrate binding module polypeptide having at least 80% sequence identity with an amino acid sequence selected from the group consisting of SEQ ID NOs:5, 6 and 7.

5. The method of claim 4, wherein the at least one carbohydrate binding module polypeptide has at least 90% sequence identity with the amino acid sequence selected from the group consisting of SEQ ID NOs:5, 6 and 7.

6. The method of claim 4, wherein the at least one carbohydrate binding module polypeptide is selected from the group consisting of SEQ ID NOs:5, 6 and 7.

7. The method of claim 4, wherein the substrate is contacted with a carbohydrate binding module of SEQ ID NO:5, a carbohydrate binding module of SEQ ID NO:6, and a carbohydrate binding module of SEQ ID NO:7.

8. The method of claim 1, further comprising contacting the substrate with a second polypeptide comprising an amino acid sequence having at least 80% sequence identity with an amino acid sequence of SEQ ID NO:12.

9. The method of claim 8, wherein the second polypeptide comprises an amino acid sequence having at least 90% sequence identity with the amino acid sequence of SEQ ID NO:12.

10. The method of claim 8, wherein the second polypeptide comprises an amino acid sequence of SEQ ID NO:12.

11. The method of claim 8, wherein the substrate is first contacted with the second polypeptide.

12. The method of claim 8, further comprising contacting the substrate with at least one carbohydrate binding module polypeptide having at least 80% sequence identity with an amino acid sequence of SEQ ID NO:10 or 11.

13. The method of claim 8, further comprising contacting the substrate with at least one carbohydrate binding module polypeptide having at least 90% sequence identity with an amino acid sequence of SEQ ID NO:10 or 11.

14. The method of claim 8, further comprising contacting the substrate with at least one carbohydrate binding module polypeptide comprising an amino acid sequence of SEQ ID NO:10 or 11.

15. A method of producing neoagarobiose, comprising:
(a) providing a substrate selected from the group consisting of agar, agarose, neoagarotetraose, agarooligosaccharides, and derivatives thereof;
(b) contacting the substrate with a Saccharophagus degradans polypeptide having at least 90% sequence identity with the amino acid sequence of SEQ ID NO:9, wherein the Saccharophagus degradans polypeptide has exo-acting β-agarose activity, thereby creating a reaction mix; and
(c) incubating the reaction mix under suitable conditions and sufficient time to produce neoagarobiose from the substrate.