# Patent

## Title
Nucleic acids, compositions and uses thereof

## Abstract

The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application Ser. No. 60/981,599, filed Oct. 22, 2007 and U.S. Provisional Application Ser. No. 60/982,623, filed Oct. 25, 2007, the disclosures of which are hereby incorporated by reference in their entirety, including all figures, tables and amino acid or nucleic acid sequences.


The subject invention was made with government support under research projects supported by U.S. Department of Energy grants DE-FG-02GO12026, DE FC36-99GO10476 and DE FC36-00GO10594. The government has certain rights in this invention.


BACKGROUND OF INVENTION
Structural polysaccharides comprise up to 90% of plant cell walls, and include cellulose and hemicellulose fractions as prominent resources renewable through photosynthesis. The hemicellulose fractions constitute from 22 to 30% of the dry weight of lignocellulosic biomass derived from wood and agricultural residues (Kuhad et al., 1997) and the quest for alternatives to petroleum has led to the search and discovery of microorganisms that can serve as biocatalysts for production of fuels and chemical feedstocks from renewable resources.
The major hemicellulose polymer in hardwoods and crop residues is methylglucuronoxylan (MeGAXn), a linear chain of β-1,4-linked D-xylopyranose residues regularly substituted with α-1,2-linked 4-O-methyl-D-glucuronopyranosyl residues. Variable substitutions on xylose residues may include 2′- and 3′-O-acetyl esters, as well as α-1,2- or α-1,3-linked L-arabinofuranosyl residues (Sunna et al., 1997). Additional substituents include O-feruloyl, and O-p-coumaroyl esters linked to hydroxyl groups on the arabinofuranosyl residues.
The natural processing of methylglucuronoxylans is catalyzed by the combined action of endoxylanases, α-glucuronidases, arabinosidases and esterases (Collins et al., 2005; Preston et al., 2003; Sunna et al, 1997). Xylanolytic bacteria secrete endoxylanases of glycohydrolase families GH5, GH10, and GH11 that catalyze the depolymerization of the xylan backbone with the generation of different products (Biely et al., 2000; Preston et al., 2003). The GH10 endoxylanases generate xylobiose, xylotriose, and the aldotetrauronate β-1,4-linked D-xylotriose substituted at the non reducing terminus with α-1,2-linked 4-O-methyl-D-glucuronate. Bacteria that secrete a GH10 endoxylanase may assimilate and metabolize all of the products derived from the depolymerization of MeGAXn. The utilization of the aldouronate requires the expression of genes encoding transporters, α-glucuronidase, and enzymes that convert xylooligosaccahrides to xylose. The glucuronate metabolism gene cluster in Geobacillus stearothermophilus T-6 includes genes that encode required activities, and has been well studied and defined with respect to structural and regulatory genes (Shulami et al., 1999; Shulami et al., 2007). Similar gene clusters have been found in several other bacteria as well (Nelson et al., 1999; Takami et al., 2000).
The isolation and characterization of an aggressively xylanolytic gram-positive endospore-forming bacterium, designated Paenibacillus sp. strain JDR-2, has been reported (St. John et al., 2006). This strain secretes a multimodular GH10 endoxylanase as a cell-anchored protein that catalyzes the depolymerization of MeGAXn (St. John et al., 2006). The rapid and complete utilization of MeGAXn without accumulation of the aldotetrauronate, methylglucuronoxylotriose (MeGAX3) in the medium implicated an efficient system for assimilation and complete metabolism of aldouronates. A structural gene, aguA, has been cloned from genomic DNA of Paenibacillus sp. strain JDR-2 and expressed in E. coli with the formation of a recombinant GH67 α-glucuronidase (AguA) that catalyzes conversion of MeGAX3 to methylglucuronate and xylotriose. This gene is followed by xynA2 encoding an intracellular GH10 endoxylanase catalytic domain (XynA2) that processes the xylotriose product generated by the action of AguA on MeGAX3. (Nong et al., 2005).
Both yeast and bacteria have been developed for the bioconversion of glucose derived from the cellulose fraction, and bacteria have been developed for the bioconversion of pentoses, principally xylose, from the hemicellulose fraction (Dien et al., 2003; Ingram et al., 1999; Kuhad et al., 1997). Pretreatment has relied on a combination of chemical and enzymatic hydrolytic procedures to solubilize the hemicellulose fraction and release fermentable xylose, and to depolymerize the cellulose to fermentable glucose. Pretreatment protocols are still being developed to provide cost-effective production of ethanol and other biobased products from these resources (Lloyd et al., 2005).
BRIEF SUMMARY
The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product from lignocellulosic biomass.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 depicts the genomic organization of aldouronate-utilization operons in Paenibacillus sp. JDR-2. More recent analysis has made changes in the annotation of the polypeptide lengths of lplA (570 aa instead of 556 aa) and lplB (323 aa instead of 286 aa). The intergenic distances between yesM and lplA should be 134 nt and between lplA and lplB should be 89 nt.
FIG. 2 illustrates aldouronate-utilization gene expression in Paenibacillus sp. JDR-2 grown under different nutrient conditions. A colony of Paenibacillus sp. JDR-2 was dispersed in 420 μl Zucker-Hankin (Zucker et al., 1970) salts medium, and 100 μl of this suspension was added to each of four 8-ml culture medium in 250 ml baffled flasks containing 1× Zucker-Hankin, 0.5% yeast extract and either 1) no additional substrate, back slash; 2) 0.5% oat spelt xylan, checkered; 3) 0.5% glucose, stippled; or 4) 0.5% xylose, cross-hatched. The cultures were incubated at 30° C. at 225 rpm for 9 h to O.D.600=0.6. Cells were harvested and RNA was prepared from each cell pellet. RNA (100 ng) was added to each 16 μl real-time RT-PCR reaction. At the end of the reaction, threshold cycle levels were converted to mRNA abundance by predetermined standardization of RT-PCR threshold cycles using genomic DNA concentration as standard.
FIG. 3 shows the transcription regulation and gene expression of the aldouronate-utilization gene cluster.
FIG. 4 relates to a comparison of aldouronate-utilization gene organizations in bacteria in which evidence supports relationships of gene function to substrate utilization.
FIGS. 5A and 5B. Growth and substrate utilization of Paenibacillus sp. JDR-2 on Zucker-Hankin minimal medium supplemented 0.01% yeast extract and either MeGAXn, MeGAX3, or MeGAX1. FIG. 5A: Growth was determined as turbidity (OD600) for MeGAXn (open circles), MeGAX1 (open triangles), and MeGAX3 (open squares); and for MeGAXn as cell protein (closed circles). FIG. 5B: Utilization of substrates was determined by total carbohydrate assay for MeGAXn (open circles), MeGAX1 (open triangles), and MeGAX3 (open squares); and determined by uronic acid assay for MeGAXn (closed circles). Data points are the average values obtained for replicate samples; bars denote the range.
FIG. 6. Comparison of substrate utilization rates during the most rapid growth phase (10 to 20 h) of Paenibacillus sp. JDR-2 on Zucker-Hankin minimal medium supplemented 0.01% yeast extract and either MeGAXn, MeGAX3, or MeGAX1. Utilization of substrates was determined by total carbohydrate assay: MeGAXn (open circles), MeGAXn (open triangles), and MeGAX3 (open squares); and by total uronic acid assay: MeGAXn (closed circles), MeGAXn (closed triangles), and MeGAX3 (closed squares). Curves were generated for best fit as described in the Methods section. Relative rates of utilization, noted as k values for the slopes, were −0.0781 and −0.0748 for MeGAXn; −0.0306 and −0.0361 for MeGAX1; −0.0224 and −0.0181 for MeGAX3. R2 values ranged from 0.975 to 0.997.
FIG. 7. Utilization of MeGAX1, MeGAX3 and sweetgum MeGAXn and product accumulation by Paenibacillus sp. JDR-2. Lane 1: standards of aldouronate, 10 nmoles each; Lane 2: standards of xylose and xylosides, 10 nmoles each; Lanes 3-19: supernates taken at 0, 8, 16, 24, and 32 h for cultures grown on MeGAX1 (Lanes 3-7); taken at 0, 8, 16, 24, 32, and 40 h for cultures grown on MeGAX1 (Lanes 8-13); MeGAX3 (Lanes 14-19). Samples of supernates were spotted at indicated times that contained 100 nmol of xylose equivalents at 0 time. TLC plates were developed and samples detected as described in the Methods section.
FIG. 8. TLC analysis of deglycosylation of aldouronic acids by recombinant AguA. Pure AguA (1 μg) was incubated in assay buffer (pH 6.0) at 30° C. for 16 h and the reaction components were resolved by TLC and detected as descried in Materials and Methods. Lane 1: standards of X1-4, 20 nmoles each; Lane 2: standards of MeGAX1-5, 20 mmoles each; Lanes 3-6: AguA incubated with MeGAX1, MeGAX2, MeGAX3, and MeGAX4, respectively.
FIGS. 9A-9D. HPLC analysis of deglycosylation of aldouronates by recombinant AguA. Pure AguA (1 μg) was incubated with aldouronates in assay buffer (pH 6.0) at 30° C. for 30 min. The reaction components were resolved on a BioRad Aminex HPX 87H column eluted with 0.01 N H2SO4 and detected by differential refractometry. X-axis values indicate the elution time in minutes; Y-axis values indicate amounts determined by differential refractometry detected as millivolts. FIG. 9A. MeGAX1 control (peak: 9.06 min); FIG. 9B. MeGAX1 (peak: 9.06 min) cleaved into MeGA (peak: 10.29 min) and xylose (peak: 12.12 min) by AguA for 30 min; FIG. 9C. MeGAX3 (peak: 8.12 min) control; FIG. 9D: MeGAX3 (peak: 8.12 min) cleaved into xylotriose (peak: 8.75 min) and MeGA (peak: 10.29 min) by AguA for 30 min.
FIG. 10. TLC analysis of deglycosylation of xylosides by XynA2, and aldouronates by AguA with XynA2. Pure AguA and XynA2, (4.0 μg vs 1.9 μg), was incubated in assay buffer (pH 6.0) at 30° C. for 16 h and the reaction components were resolved by TLC and detected as descried in Materials and Methods. Lane 1: standards of X1-4, 10 nmoles/each; Lane 2-4: xylobiose, xylotriose and xyloteterose incubated with XynA2; Lane 5-6: MeGAX2 and MeGAX3 cleaved by XynA2+AguA.



BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO:1 and SEQ ID NO:2 are the polynucleotide and polypeptide sequences, respectively, encoding the yesN CheY-like, Ara C type response regulator.
SEQ ID NO:3 and SEQ ID NO:4 are the polynucleotide and polypeptide sequences, respectively, encoding the yesM Histidine kinase-type transduction protein.
SEQ ID NO:5 and SEQ ID NO:6 are the polynucleotide and polypeptide sequences, respectively, encoding the lplA Substrate binding protein.
SEQ ID NO:7 and SEQ ID NO:8 are the polynucleotide and polypeptide sequences, respectively, encoding the lplB Lipoprotein.
SEQ ID NO:9 and SEQ ID NO:10 are the polynucleotide and polypeptide sequences, respectively, encoding the ytcP Permease activity.
SEQ ID NO:11 and SEQ ID NO:12 are the polynucleotide and polypeptide sequences, respectively, encoding the aguA GH67 α-glucuronidase activity.
SEQ ID NO:13 and SEQ ID NO:14 are the polynucleotide and polypeptide sequences, respectively, encoding the xynA2 GH10 xylanase activity.
SEQ ID NO:15 and SEQ ID NO:16 are the polynucleotide and polypeptide sequences, respectively, encoding the xynB GH43 β-xylosidase activity.
SEQ ID NO:17 and SEQ ID NO:18 are the polynucleotide and polypeptide sequences encoding a NADH-dependent flavin oxidoreductase.
SEQ ID NO:19 and SEQ ID NO:20 are the polynucleotide and polypeptide sequences for the xynA1 gene.
SEQ ID NO:21 is a sequence of 15276 base pairs (bps) that includes the genes identified in FIG. 1 and Table 4. This sequence has been deposited with GenBank as EU024644, which is hereby incorporated by reference in its entirety.
SEQ ID NOs:22-49 are primer sequences.
SEQ ID NOs:50-55 are candidate CcpA binding sites.
DETAILED DISCLOSURE
The subject invention pertains to the genetic transformation of known host cells (e.g., Gram positive or Gram negative ethanogenic bacteria) so as to provide these bacteria with the ability to produce ethanol from lignocellulosic biomass or xylan containing substrates. Thus, the subject invention allows the use of recombinant strains of yeast, Gram positive and/or Gram negative bacteria for the production of ethanol from under-utilized sources of biomass, such as hemicellulose (a major portion of wood and inedible plant parts). Thus, in one aspect of the subject invention yeast, Gram negative and/or Gram positive organisms are transformed with one or more of the disclosed nucleic acid sequences encoding the aldouronate-utilization regulon. The organisms that are transformed may, or may not, contain a naturally occurring aldouronate-utilization regulon. In some embodiments, the transformed organism lacks a naturally occurring aldouronate-utilization regulon.
Another aspect of the invention provides for the co-culture of a host cell (e.g., a yeast, Gram positive or Gram negative bacteria) comprising one or more of the nucleic acid sequences encoding the aldouronate-utilization regulon with another organism that produces a desired product. The organism containing one or more of the nucleic acid sequences encoding the aldouronate-utilization regulon is used to breakdown complex lignocellulosic biomass or xylan containing substrates into a form that the bacteria producing a desired product can utilize (e.g., xylose). In certain aspects of the invention, thermotolerant host cells are preferred (e.g., thermotolerant Bacillus spp. (e.g., thermotolerant B. coagulans).
As defined herein, a “desired product” or “product of interest” can be any product/compound that can be produced by a host cell. Thus, non-limiting examples of a “desired product” or “product of interest” include ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate, or alanine.
To impart to a microorganism the ability to produce one or more of the elements of the aldouronate-utilization regulon disclosed herein, a single nucleic acid comprising all of the elements (e.g., SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15 and 17 [or SEQ ID NO: 21 which encodes the entire regulon]) of the aldouronate-utilization regulon can be provided to a bacterial cell via transformation or any other means (e.g., chromosomal integration). These elements may be used for the direct utilization of aldouronates generated by the chemical and/or enzymatic digestion of the hemicellulose fraction of lignocellulosics. These elements may also be used to construct an expanded cassette to include secreted endoxylanases containing catalytic domains, with and without modular substrate binding domains, for the purpose of depolymerization and direct utilization of fermentable constituents. Constructs may also be generated to include genes encoding enzymes tolerant of acidic conditions (low pH) and high temperatures (greater than 50° C.). Thus, this single nucleic acid can be in the form of a transposon element, genetic construct or a vector, such as a plasmid. Alternatively, individual nucleic acids (e.g., genes) encoding polypeptides of the aldouronate-utilization regulon can be used to transform bacteria. Thus, a single nucleic acid molecule according to the subject invention can contain one or any combination of 2, 3, 4, 5, 6 7, 8 or 9 genes encoding the polypeptides of the aldouronate-utilization regulon. Again, the individual nucleic acids encoding polypeptides of the aldouronate-utilization regulon can be incorporated into a plasmid or other genetic construct which is used to transform a host organism.
As set forth herein, the subject application provides isolated, recombinant, and/or purified polynucleotide sequences comprising:
a) a polynucleotide sequence encoding a polypeptide as set forth in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20;
b) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence encoding a polypeptide as set forth in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20, wherein said polynucleotide encodes a polypeptide having at least one of the activities of SEQ ID NOs: as set forth in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20;
c) a polynucleotide sequence comprising SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or 21;
d) a polynucleotide sequence having at least about 20% to 99.99% identity to the polynucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or 21;
e) a polynucleotide that is complementary to the polynucleotides set forth in (a), (b), (c), or (d);
f) a genetic construct comprising a polynucleotide sequence as set forth in (a), (b), (c), (d), or (e);
g) a vector comprising a polynucleotide or genetic construct as set forth in (a), (b), (c), (d), (e), or (f);
h) a host cell comprising a vector as set forth in (g), a genetic construct according to (f) or a polynucleotide as set forth in any of (a)-(e);
i) a polynucleotide that hybridizes under low, intermediate or high stringency with a polynucleotide sequence as set forth in (a), (b), (c), (d) or (e);
j) a probe comprising a polynucleotide according to (a), (b), (c), (d) or (e) and, optionally, a label or marker; or
k) a host cell as set forth in (h), wherein said host cell is selected from Gluconobacter oxydans, Gluconobacter asaii, Achromobacter delmarvae, Achromobacter viscosus, Achromobacter lacticum, Agrobacterium tumefaciens, Agrobacterium radiobacter, Alcaligenes faecalis, Arthrobacter citreus, Arthrobacter tumescens, Arthrobacter paraffineus, Arthrobacter hydrocarboglutamicus, Arthrobacter oxydans, Aureobacterium saperdae, Azotobacter indicus, Brevibacterium ammoniagenes, divaricatum, Brevibacterium lactofermentum, Brevibacterium flavum, Brevibacterium globosum, Brevibacterium fuscum, Brevibacterium ketoglutamicum, Brevibacterium helcolum, Brevibacterium pusillum, Brevibacterium testaceum, Brevibacterium roseum, Brevibacterium immariophilium, Brevibacterium linens, Brevibacterium protopharmiae, Corynebacterium acelophilum, Corynebacterium glutamicum, Corynebacterium callunae, Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Enterobacter aerogenes, Erwinia amylovora, Erwinia carotovora, Erwinia herbicola, Erwinia chrysanthemi, Flavobacterium peregrinum, Flavobacterium fucatum, Flavobacterium aurantinum, Flavobacterium rhenanum, Flavobacterium sewanense, Flavobacterium breve, Flavobacterium meningosepticum, Micrococcus sp. CCM825, Morganella morganii, Nocardia opaca, Nocardia rugosa, Planococcus eucinatus, Proteus rettgeri, Propionibacterium shermanii, Pseudomonas synxantha, Pseudomonas azoloformans, Pseudomonas fluorescens, Pseudomonas ovalis, Pseudomonas stutzeri, Pseudomonas acidovolans, Pseudomonas mucidolens, Pseudomonas testosteroni, Pseudomonas aeruginosa, Rhodococcus erythropolis, Rhodococcus rhodochrous, Rhodococcus sp. ATCC 15592, Rhodococcus sp. ATCC 19070, Sporosarcina ureae, Staphylococcus aureus, Vibrio metschnikovii, Vibrio tyrogenes, Actinomadura madurae, Actinomyces violaceochromogenes, Kitasatosporia parulosa, Streptomyces coelicolor, Streptomyces flavelus, Streptomyces griseolus, Streptomyces lividans, Streptomyces olivaceus, Streptomyces tanashiensis, Streptomyces virginiae, Streptomyces antibioticus, Streptomyces cacaoi, Streptomyces lavendulae, Streptomyces viridochromogenes, Aeromonas salmonicida, Bacillus pumilus, Bacillus circulans, Bacillus thiaminolyticus, Bacillus coagulans, Escherichia freundii, Microbacterium ammoniaphilum, Serratia marcescens, Salmonella typhimurium, Salmonella schottinulleri, Xanthomonas citri, Thermotoga martima, Geobacillus sterothermophilus and so forth (in certain embodiments, thermotolerant microorganisms, such as a thermotolerant B. coagulans strain are preferred).
“Nucleotide sequence”, “polynucleotide” or “nucleic acid” can be used interchangeably and are understood to mean, according to the present invention, either a double-stranded DNA, a single-stranded DNA or products of transcription of the said DNAs (e.g., RNA molecules). It should also be understood that the present invention does not relate to genomic polynucleotide sequences in their natural environment or natural state. The nucleic acid, polynucleotide, or nucleotide sequences of the invention can be isolated, purified (or partially purified), by separation methods including, but not limited to, ion-exchange chromatography, molecular size exclusion chromatography, or by genetic engineering methods such as amplification, subtractive hybridization, cloning, subcloning or chemical synthesis, or combinations of these genetic engineering methods.
A homologous polynucleotide or polypeptide sequence, for the purposes of the present invention, encompasses a sequence having a percentage identity with the polynucleotide or polypeptide sequences, set forth herein, of between at least (or at least about) 20.00% to 99.99% (inclusive). The aforementioned range of percent identity is to be taken as including, and providing written description and support for, any fractional percentage, in intervals of 0.01%, between 20.00% and including 99.99%. These percentages are purely statistical and differences between two nucleic acid sequences can be distributed randomly and over the entire sequence length. For example, homologous sequences can exhibit a percent identity of 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 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, or 99 percent with the sequences of the instant invention. Typically, the percent identity is calculated with reference to the full length, native, and/or naturally occurring polynucleotide (e.g., any one of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or 21). The terms “identical” or percent “identity”, in the context of two or more polynucleotide or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.
Both protein and nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson et al., 1988; Altschul et al., 1990; Thompson et al., 1994; Higgins et al., 1996; Gish et al., 1993). Sequence comparisons are, typically, conducted using default parameters provided by the vendor or using those parameters set forth in the above-identified references, which are hereby incorporated by reference in their entireties.
A “complementary” polynucleotide sequence, as used herein, generally refers to a sequence arising from the hydrogen bonding between a particular purine and a particular pyrimidine in double-stranded nucleic acid molecules (DNA-DNA, DNA-RNA, or RNA-RNA). The major specific pairings are guanine with cytosine and adenine with thymine or uracil. A “complementary” polynucleotide sequence may also be referred to as an “antisense” polynucleotide sequence or an “antisense sequence”.
Sequence homology and sequence identity can also be determined by hybridization studies under high stringency, intermediate stringency, and/or low stringency. Various degrees of stringency of hybridization can be employed. The more severe the conditions are, the greater the complementarity that is required for duplex formation. Severity of conditions can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under low, intermediate, or high stringency conditions by techniques well known in the art, as described, for example, in Keller and Manak (1987).
For example, hybridization of immobilized DNA on Southern blots with 32P-labeled gene-specific probes can be performed by standard methods (Maniatis et al., 1982). In general, hybridization and subsequent washes can be carried out under intermediate to high stringency conditions that allow for detection of target sequences with homology to the exemplified polynucleotide sequence. For double-stranded DNA gene probes, hybridization can be carried out overnight at 20-25° C. below the melting temperature (Tm) of the DNA hybrid in 6×SSPE, 5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The melting temperature is described by the following formula (Beltz et al., 1983).
Tm=81.5° C.+16.6 Log [Na+]+0.41 (% G+C)−0.61 (% formamide)−600/length of duplex in base pairs.
Washes are typically carried out as follows:
(1) twice at room temperature for 15 minutes in 1×SSPE, 0.1% SDS (low stringency wash);
(2) once at Tm−20° C. for 15 minutes in 0.2×SSPE, 0.1% SDS (intermediate stringency wash).
For oligonucleotide probes, hybridization can be carried out overnight at 10-20° C. below the melting temperature (Tm) of the hybrid in 6×SSPE, 5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. Tm for oligonucleotide probes can be determined by the following formula:
Tm(° C.)=2(number T/A base pairs)+4(number G/C base pairs) (Suggs et al., 1981).
Washes can be carried out as follows:
(1) twice at room temperature for 15 minutes 1×SSPE, 0.1% SDS (low stringency wash);
2) once at the hybridization temperature for 15 minutes in 1×SSPE, 0.1% SDS (intermediate stringency wash).
In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment >70 or so bases in length, the following conditions can be used:
















Low:
1 or 2X SSPE, room temperature



Low:
1 or 2X SSPE, 42° C.



Intermediate:
0.2X or 1X SSPE, 65° C.



High:
0.1X SSPE, 65° C.










By way of another non-limiting example, procedures using conditions of high stringency can also be performed as follows: Pre-hybridization of filters containing DNA is carried out for 8 h to overnight at 65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65° C., the preferred hybridization temperature, in pre-hybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5−20×106 cpm of 32P-labeled probe. Alternatively, the hybridization step can be performed at 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na citrate. Subsequently, filter washes can be done at 37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by a wash in 0.1×SSC at 50° C. for 45 min. Alternatively, filter washes can be performed in a solution containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS, or 0.1×SSC and 0.1% SDS at 68° C. for 15 minute intervals. Following the wash steps, the hybridized probes are detectable by autoradiography. Other conditions of high stringency which may be used are well known in the art and as cited in Sambrook et al. (1989) and Ausubel et al. (1989) are incorporated herein in their entirety.
Another non-limiting example of procedures using conditions of intermediate stringency are as follows: Filters containing DNA are pre-hybridized, and then hybridized at a temperature of 60° C. in the presence of a 5×SSC buffer and labeled probe. Subsequently, filters washes are performed in a solution containing 2×SSC at 50° C. and the hybridized probes are detectable by autoradiography. Other conditions of intermediate stringency which may be used are well known in the art and as cited in Sambrook et al. (1989) and Ausubel et al. (1989) are incorporated herein in their entirety.
Duplex formation and stability depend on substantial complementarity between the two strands of a hybrid and, as noted above, a certain degree of mismatch can be tolerated. Therefore, the probe sequences of the subject invention include mutations (both single and multiple), deletions, insertions of the described sequences, and combinations thereof, wherein said mutations, insertions and deletions permit formation of stable hybrids with the target polynucleotide of interest. Mutations, insertions and deletions can be produced in a given polynucleotide sequence in many ways, and these methods are known to an ordinarily skilled artisan. Other methods may become known in the future.
It is also well known in the art that restriction enzymes can be used to obtain functional fragments of the subject DNA sequences. For example, Bal31 exonuclease can be conveniently used for time-controlled limited digestion of DNA (commonly referred to as “erase-a-base” procedures). See, for example, Maniatis et al. (1982); Wei et al. (1983).
The present invention further comprises fragments of the polynucleotide sequences of the instant invention. Representative fragments of the polynucleotide sequences according to the invention will be understood to mean any nucleotide fragment having at least 5 successive nucleotides, preferably at least 12 successive nucleotides, and still more preferably at least 15, 18, or at least 20 successive nucleotides of the sequence from which it is derived. The upper limit for such fragments is the total number of nucleotides found in the full-length sequence encoding a particular polypeptide (e.g., a polypeptide such as that of SEQ ID NO: 2). The term “successive” can be interchanged with the term “consecutive” or the phrase “contiguous span”. Thus, in some embodiments, a polynucleotide fragment may be referred to as “a contiguous span of at least X nucleotides, wherein X is any integer value beginning with 5; the upper limit for such fragments is one nucleotide less than the total number of nucleotides found in the full-length sequence encoding a particular polypeptide (e.g., a polypeptide comprising SEQ ID NO: 2).
In some embodiments, the subject invention includes those fragments capable of hybridizing under various conditions of stringency conditions (e.g., high or intermediate or low stringency) with a nucleotide sequence according to the invention; fragments that hybridize with a nucleotide sequence of the subject invention can be, optionally, labeled as set forth below.
The subject invention provides, in one embodiment, methods for the identification of the presence of nucleic acids according to the subject invention in transformed host cells. In these varied embodiments, the invention provides for the detection of nucleic acids in a sample (obtained from a cell culture) comprising contacting a sample with a nucleic acid (polynucleotide) of the subject invention (such as an RNA, mRNA, DNA, cDNA, or other nucleic acid). In a preferred embodiment, the polynucleotide is a probe that is, optionally, labeled and used in the detection system. Many methods for detection of nucleic acids exist and any suitable method for detection is encompassed by the instant invention. Typical assay formats utilizing nucleic acid hybridization includes, and are not limited to, 1) nuclear run-on assay, 2) slot blot assay, 3) northern blot assay (Alwine et al., 1977, 4) magnetic particle separation, 5) nucleic acid or DNA chips, 6) reverse Northern blot assay, 7) dot blot assay, 8) in situ hybridization, 9) RNase protection assay (Melton et al, 1984) and as described in the 1998 catalog of Ambion, Inc., Austin, Tex., 10) ligase chain reaction, 11) polymerase chain reaction (PCR), 12) reverse transcriptase (RT)-PCR (Berchtold, 1989), 13) differential display RT-PCR (DDRT-PCR) or other suitable combinations of techniques and assays. Labels suitable for use in these detection methodologies include, and are not limited to 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, 5) magnetic labels, or other suitable labels. These methodologies and labels are well known in the art and widely available to the skilled artisan. Likewise, methods of incorporating labels into the nucleic acids are also well known to the skilled artisan.
Thus, the subject invention also provides detection probes (e.g., fragments of the disclosed polynucleotide sequences) for hybridization with a target sequence or the amplicon generated from the target sequence. Such a detection probe will comprise a contiguous/consecutive span of at least 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or 21. Labeled probes or primers are labeled with a radioactive compound or with another type of label as set forth above (e.g., 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, or 5) magnetic labels). Alternatively, non-labeled nucleotide sequences may be used directly as probes or primers; however, the sequences are generally labeled with a radioactive element (32P, 35S, 3H, 125I) or with a molecule such as biotin, acetylaminofluorene, digoxigenin, 5-bromo-deoxyuridine, or fluorescein to provide probes that can be used in numerous applications.
Polynucleotides of the subject invention can also be used for the qualitative and quantitative analysis of gene expression using arrays or polynucleotides that are attached to a solid support. As used herein, the term array means a one-, two-, or multi-dimensional arrangement of full length polynucleotides or polynucleotides of sufficient length to permit specific detection of gene expression. Preferably, the fragments are at least 15 nucleotides in length. More preferably, the fragments are at least 100 nucleotides in length. More preferably, the fragments are more than 100 nucleotides in length. In some embodiments the fragments may be more than 500 nucleotides in length.
For example, quantitative analysis of gene expression may be performed with full-length polynucleotides of the subject invention, or fragments thereof, in a complementary DNA microarray as described by Schena et al. (1995, 1996a). Polynucleotides, or fragments thereof, are amplified by PCR and arrayed onto silylated microscope slides. Printed arrays are incubated in a humid chamber to allow rehydration of the array elements and rinsed, once in 0.2% SDS for 1 min, twice in water for 1 min and once for 5 min in sodium borohydride solution. The arrays are submerged in water for 2 min at 95° C., transferred into 0.2% SDS for 1 min, rinsed twice with water, air dried and stored in the dark at 25° C.
mRNA is isolated from a biological sample and probes are prepared by a single round of reverse transcription. Probes are hybridized to 1 cm2 microarrays under a 14×14 mm glass coverslip for 6-12 hours at 60° C. Arrays are washed for 5 min at 25° C. in low stringency wash buffer (1×SSC/0.2% SDS), then for 10 min at room temperature in high stringency wash buffer (0.1×SSC/0.2% SDS). Arrays are scanned in 0.1×SSC using a fluorescence laser scanning device fitted with a custom filter set. Accurate differential expression measurements are obtained by taking the average of the ratios of two independent hybridizations.
Quantitative analysis of the polynucleotides present in a biological sample can also be performed in complementary DNA arrays as described by Pietu et al. (1996). The polynucleotides of the invention, or fragments thereof, are PCR amplified and spotted on membranes. Then, mRNAs originating from biological samples derived from various tissues or cells are labeled with radioactive nucleotides. After hybridization and washing in controlled conditions, the hybridized mRNAs are detected by phospho-imaging or autoradiography. Duplicate experiments are performed and a quantitative analysis of differentially expressed mRNAs is then performed.
Alternatively, the polynucleotide sequences related to the invention may also be used in analytical systems, such as DNA chips. DNA chips and their uses are well known in the art (see for example, U.S. Pat. Nos. 5,561,071; 5,753,439; 6,214,545; Schena 1996b; Bianchi et al., 1997; each of which is hereby incorporated by reference in their entireties) and/or are provided by commercial vendors such as Affymetrix, Inc. (Santa Clara, Calif.). In addition, the nucleic acid sequences of the subject invention can be used as molecular weight markers in nucleic acid analysis procedures.
The subject invention also provides genetic constructs comprising: a) a polynucleotide sequence encoding a polypeptide comprising SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20, or any fragment thereof; b) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence encoding a polypeptide comprising SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20, or any fragment thereof, wherein said polynucleotide encodes a polypeptide having at least one of the activities or a polypeptide comprising SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20; c) a polynucleotide sequence encoding a fragment of a polypeptide comprising SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20, wherein said fragment has at least one of the activities of the polypeptide of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20; d) a polynucleotide sequence comprising SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or 21; e) a polynucleotide sequence having at least about 20% to 99.99% identity to the polynucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or 21) a polynucleotide sequence encoding variant (e.g., a variant polypeptide) of the polypeptide of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20, wherein said variant has at least one of the activities associated with the polypeptide from which it was derived; f) a polynucleotide sequence encoding a fragment of a variant polypeptide as set forth in (e); or g) a polynucleotide that is complementary to the polynucleotides set forth in (a), (b), (c), (d), (e) or (f). Genetic constructs of the subject invention can also contain additional regulatory elements such as promoters and enhancers and, optionally, selectable markers.
Also within the scope of the subject instant invention are vectors or expression cassettes containing genetic constructs as set forth herein or polynucleotides encoding the polypeptides, set forth supra, operably linked to regulatory elements. The vectors and expression cassettes may contain additional transcriptional control sequences as well. The vectors and expression cassettes may further comprise selectable markers. The expression cassette may contain at least one additional gene, operably linked to control elements, to be co-transformed into the organism. Alternatively, the additional gene(s) and control element(s) can be provided on multiple expression cassettes. Such expression cassettes are provided with a plurality of restriction sites for insertion of the sequences of the invention to be under the transcriptional regulation of the regulatory regions. The expression cassette(s) may additionally contain selectable marker genes operably linked to control elements.
The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region, a DNA sequence of the invention, and a transcriptional and translational termination regions. The transcriptional initiation region, the promoter, may be native or analogous, or foreign or heterologous, to the host cell. By “foreign” is intended that the transcriptional initiation region is not found in the organism into which the transcriptional initiation region is introduced.
The subject invention also provides for the expression of a polypeptide, peptide, fragment, or variant encoded by a polynucleotide sequence disclosed herein comprising the culture of a host cell transformed with a polynucleotide of the subject invention under conditions that allow for the expression of the polypeptide and, optionally, recovering the expressed polypeptide.
As discussed above, the subject application also provides host cells transformed by at least one nucleic acid or vector according to the invention. These cells may be obtained by introducing into host cells a nucleotide sequence inserted into a vector as defined above, and then culturing the said cells under conditions allowing the replication and/or the expression of the polynucleotide sequences of the subject invention.
The host cell may be chosen from eukaryotic or prokaryotic systems, such as for example bacterial cells, (Gram negative or Gram positive), yeast cells (for example, Saccharomyces cereviseae or Pichia pastoris), animal cells (such as Chinese hamster ovary (CHO) cells), plant cells, and/or insect cells using baculovirus vectors. In some embodiments, the host cells for expression of the polypeptides include, and are not limited to, those taught in U.S. Pat. Nos. 6,319,691, 6,277,375, 5,643,570, or 5,565,335, each of which is incorporated by reference in its entirety, including all references cited within each respective patent.
Another aspect of the invention provides:
a) one or more:
1) isolated, purified, and/or recombinant polypeptides comprising SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20;
2) variant polypeptides having at least about 20% to 99.99% identity, preferably at least 60 to 99.99% identity to the polypeptide of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20 and which has at least one of the activities associated with the polypeptide of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20;
3) a fragment of the polypeptide of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20, or a variant polypeptide, wherein said polypeptide fragment or fragment of said variant polypeptide has substantially the same activity as the polypeptide of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20; or
4) a polypeptide according to embodiments a(1), a(2) or a(3) that further comprises a heterologous polypeptide sequence;
b) a composition comprising a carrier and a polypeptide as set forth in a(1), a(2), a(3) or a(4), optionally wherein said carrier is an adjuvant or a pharmaceutically acceptable excipient; or
c) antibodies that specifically bind to a polypeptide comprising SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20, variants thereof or fragments thereof.
In the context of the instant invention, the terms “oligopeptide”, “polypeptide”, “peptide” and “protein” can be used interchangeably; however, it should be understood that the invention does not relate to the polypeptides in natural form, that is to say that they are not in their natural environment but that the polypeptides may have been isolated or obtained by purification from natural sources or obtained from host cells prepared by genetic manipulation (e.g., the polypeptides, or fragments thereof, are recombinantly produced by host cells, or by chemical synthesis). Additionally, the terms “amino acid(s)” and “residue(s)” can be used interchangeably.
Polypeptide fragments of the subject invention can be any integer in length from at least 3, preferably 4, and more preferably 5 consecutive amino acids to 1 amino acid less than a full length polypeptide of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20.
Fragments, as described herein, can be obtained by cleaving the polypeptides of the invention with a proteolytic enzyme (such as trypsin, chymotrypsin, or collagenase) or with a chemical reagent, such as cyanogen bromide (CNBr). Alternatively, polypeptide fragments can be generated in a highly acidic environment, for example at pH 2.5. Such polypeptide fragments may be equally well prepared by chemical synthesis or using hosts transformed with an expression vector according to the invention. The transformed host cells contain a nucleic acid, allowing the expression of these fragments, under the control of appropriate elements for regulation and/or expression of the polypeptide fragments.
In certain preferred embodiments, fragments of the polypeptides disclosed herein retain at least one property or activity of the full-length polypeptide from which the fragments are derived. Thus, fragments of the polypeptide of SEQ ID NOs: SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20 have one or more of the following properties or activities set forth in Table 4 or any of the activities described within the Example section of this application (e.g., see Results).
A “variant polypeptide” (or polypeptide variant) is to be understood to designate polypeptides exhibiting, in relation to the natural polypeptide, certain modifications. These modifications can include a deletion, addition, or substitution of at least one amino acid, a truncation, an extension, a chimeric fusion, a mutation, or polypeptides exhibiting post-translational modifications. Among these homologous variant polypeptides, are those comprising amino acid sequences exhibiting between at least (or at least about) 20.00% to 99.99% (inclusive) identity to the full length, native, or naturally occurring polypeptide are another aspect of the invention. The aforementioned range of percent identity is to be taken as including, and providing written description and support for, any fractional percentage, in intervals of 0.01%, between 20.00% and, up to, including 99.99%. These percentages are purely statistical and differences between two polypeptide sequences can be distributed randomly and over the entire sequence length. Thus, variant polypeptides can have 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 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, or 99 percent identity with the polypeptide sequences of the instant invention. In a preferred embodiment, a variant or modified polypeptide exhibits at least 60, 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, or 99 percent identity to any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20. Typically, the percent identity is calculated with reference to the full-length, native, and/or naturally occurring polypeptide (e.g., those polypeptides set forth in SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20). In all instances, variant polypeptides retain at least one of the activities associated with the polypeptide set forth in SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20 from which it was derived.
Variant polypeptides can also comprise one or more heterologous polypeptide sequences (e.g., tags that facilitate purification of the polypeptides of the invention (see, for example, U.S. Pat. No. 6,342,362, hereby incorporated by reference in its entirety; Altendorf et al., (1999-WWW, 2000); Baneyx, (1999); Eihauer et al., (2001); Jones et al. (1995); Margolin (2000); Puig et al., (2001); Sassenfeld (1990); Sheibani (1999); Skerra et al., (1999); Smith (1998); Smyth et al., (2000); Unger (1997), each of which is hereby incorporated by reference in their entireties), or commercially available tags from vendors such as such as STRATAGENE (La Jolla, Calif.), NOVAGEN (Madison, Wis.), QIAGEN, Inc., (Valencia, Calif.), or InVitrogen (San Diego, Calif.).
The subject invention also concerns antibodies that bind to polypeptides of the invention. Antibodies that are immunospecific for the polypeptides as set forth herein are specifically contemplated. In various embodiments, antibodies that do not cross-react with other proteins that are substantially related to those disclosed herein (see for example, the polypeptides disclosed in FIG. 2). The antibodies of the subject invention can be prepared using standard materials and methods known in the art (see, for example, Monoclonal Antibodies: Principles and Practice, 1983; Monoclonal Hybridoma Antibodies: Techniques and Applications, 1982; Selected Methods in Cellular Immunology, 1980; Immunological Methods, Vol. II, 1981; Practical Immunology, and Kohler et al., 1975). These antibodies can further comprise one or more additional components, such as a solid support, a carrier or pharmaceutically acceptable excipient, or a label.
The term “antibody” is used in the broadest sense and specifically covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity, particularly neutralizing activity. “Antibody fragments” comprise a portion of a full length antibody, generally the antigen binding or variable region thereof. Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multi-specific antibodies formed from antibody fragments.
The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations that typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al. (1975), or may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567). The “monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al. (1991) and Marks et al. (1991), for example.
The monoclonal antibodies described herein specifically include “chimeric” antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et al., 1984). Also included are humanized antibodies, such as those taught in U.S. Pat. No. 6,407,213 or 6,417,337 which are hereby incorporated by reference in their entirety.
“Single-chain Fv” or “sFv” antibody fragments comprise the VH and VL domains of an antibody, wherein these domains are present in a single polypeptide chain. Generally, the Fv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the sFv to form the desired structure for antigen binding. For a review of sFv see Pluckthun in The Pharmacology of Monoclonal Antibodies (1994) Vol. 113:269-315, Rosenburg and Moore eds. Springer-Verlag, New York.
An “isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In preferred embodiments, the antibody will be purified (1) to greater than 95% by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using Coomassie blue or, preferably, silver stain. Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
Finally, the terms “comprising”, “consisting of” and “consisting essentially of” are defined according to their standard meaning. The terms may be substituted for one another throughout the instant application in order to attach the specific meaning associated with each term. The phrases “isolated” or “biologically pure” refer to material that is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment.
Materials and Methods
Preparation of a cosmid library of Paenibacillus sp. strain JDR-2. Culture media (50 ml) were inoculated with 1/250 volume of a starter culture of Paenibacillus sp. strain JDR-2 (St. John et al., 2006). The culture was grown at 30° C. with vigorous shaking. After reaching mid-log phase (OD600=0.7, 1 OD600=109 cells/ml), cells were collected by centrifugation, resuspended in buffer A (50 mM Tris-HCl, pH 8.0, 1.0 M NaCl), pelleted by centrifugation and resuspended in buffer A again at 4×109 cells/ml. An equal volume of 2% low melt agarose was added to the cell suspension and the cell/agarose mix was poured into 800 μl plug molds. Plugs were further processed according to (Bell et al., 2002).
Partial digestion of genomic DNA. To determine the optimal amount of enzyme to use for digestion, 360 mg of plugs were equilibrated two times in 50 ml TBE (90 mM Tris-borate, 2 mM EDTA, pH 8.0) for 15 min, rinsed with 15 ml 0.1% triton X-100, chopped into a slurry and distributed into six 1.5 ml centrifuge tubes. A brief centrifugation (12,000 g, 30 seconds) packed the agarose slurry and the supernates were removed by aspiration. To each tube containing approximately 60 μl of packed plugs were added 10 μl 40 mM spermidine, 10 μl 10× Hind III reaction buffer, and 1 μl bovine serum albumin (10 mg/ml). Water was added to adjust the final volume to 100 μl. The mixtures were equilibrated on ice for 30 min, varying amounts (0.05-0.7 units) of Hind III added to each tube, equilibrated further for 15 min and finally incubated at 37° C. for 30 min to allow restriction digestion. The reactions were immediately stopped by adding 11 μl 0.5 M EDTA, pH 8.0.
Field inversion gel electrophoresis. Slurries of agarose gel plugs were loaded into the wells of a 1% agarose (Bio-Rad) gel in 0.5×TBE or 1×TAE buffer (40 mM Tris-HCl, 20 mM acetic acid, 1 mM EDTA, pH 8.3). Electrophoresis was carried out using the FIGE MAPPER apparatus (Bio-Rad) set at program 8 which separated DNA fragments in the 25-150 kb range. Initial current was 47-50 mA and the run lasted 20 h. At completion, 0.5 g of an agarose gel piece containing Hind III digested DNA ranging in size 20-48 kb was cut out and treated with 6 units of Gelase (Epicentre) at 45° C. The released DNA was ready to be ligated to the cosmid vector.
Construction of cosmid library. Size-selected Hind III-digested genomic DNA fragments were ligated to the Hind III-digested and dephosphorylated cosmid vector pCC1 (Epicenter). Ligation products were packaged into lambda phage packaging extracts (Epicenter) and electroporated into E. coli EPI300 (Epicenter) as per protocol provided. Transformed E. coli were plated onto LB/chloramphenicol plates (LB broth (Bertani, 1951), in 1.5% bactoagar containing chlamphenicol at 12.5 μg/ml) and the colonies were picked and stored individually in wells of 9×12 microtiter plates supplemented with LB/chloramphenicol media.
Screening of cosmid library for aldouronate-utilization genes. Pooled cultures from 300 transformants were screened for the presence of the aguA gene by PCR using the primers PF54 and PR569 (Table 1). Cosmid DNA preparations from positive clones were sequenced.
Preparation of mRNA. Typically, 8 ml media in 125 ml flasks were each inoculated with a fresh colony of Paenibacillus sp. strain JDR-2 and incubated at 30° C. with vigorous shaking at 240 rpm. Cells were collected by centrifugation when growth reached OD600 nm=0.6 and RNA was isolated as per Cheung et al. (1994). To remove residual genomic DNA in the resultant RNA fraction, DNase (Promega M610A) was added at 20 U/ml and digested at 37° C. for 45 min. The DNase was then inactivated by mixing with five volumes of GTC (4 M guanidine thiocyanate, 25 mM sodium acetate, pH 7.0, 0.1 M β-mercaptoethanol and 0.5% sarkosyl). One volume of 1.0 M sodium acetate, pH 4.4, 6 volumes of water-saturated phenol and one volume of chloroform were added and mixed. The mixtures were centrifuged to separate phases, the aqueous phases were transferred to separate tubes and RNA fractions were precipitated following addition of equal volumes of isopropanol. The RNA precipitates were further rinsed with 75% ethanol and dissolved in 100 μl of water. The DNase treatment was repeated until there were no significant traces of genomic DNA-directed PCR products in the subsequent RT-PCR reactions.
RT-PCR. Real-time reverse transcription-PCR was performed in 16 μl reactions each containing 100-200 ng of RNA, 3.2 μl of 0.25 μM primer pair mixtures and 8 μl of 2× iScript SYBR mix (Bio-Rad iScript). A typical reaction consisted of the following steps: 1) incubation with reverse transcriptase for 10 minutes at 58° C., 2) melting for 3 minutes at 95° C., 3) 45 cycles of 10 seconds at 95° C., 20 seconds at 58° C. and 20 seconds at 72° C., and 4) one cycle of melt curve determination. The reactions were conducted in the Bio-Rad iCycler iQ Real-Time Detection System. Primer pairs used for RNA transcript detection were rre178f and rre459r for yesN, sbp1081f and sbp1361r for yesM, aguA1069f and aguA1354r for aguA, xy1247f and xy1623r for xynA2, bex948f and bex1291r for xynB and xynA1-2237f and xynA1-2503r for xynA1. Primer pairs for flanking genes were amp10f and amp204r for the aminopeptidase gene and oxr535f and oxr774r for the oxidoreductase gene. The primer pair used for probing the read-through transcript from ytcP to aguA were perm-aguA791f and perm-aguA81r (Table 1). 15,276 bp of cosmid VC2 was sequenced and submitted to GenBank (accession number: 926135).
Results
Cosmid library analysis. The cosmid library was screened by PCR with degenerate primers PF54 and PR569. Two clones, VC1 and VC2, each yielded aguA-specific PCR generated fragments as confirmed by nucleotide sequencing, and therefore contained the gene encoding α-glucuronidase. VC1 had a 28 kb insert while VC2 had a 35 kb insert. Analyses by restriction digestion showed VC1 and VC2 shared a majority of fragments, indicating that they were from the same genomic region.
Sequence organization of the aldouronate gene cluster in cosmid VC2. VC2 yielded the 486 bp aguA-specific product by PCR screening with primers PF54 and PR569. These primers were established as specific for the aguA gene cloned and sequenced from genomic DNA derived from Paenibacillus sp. JDR-2 (Nong et al., 2005). Cosmid VC2 insert DNA was subcloned into pUC19 and 15 kb of the DNA was sequenced. The organization of the genetic content of this 15 kb segment is shown in FIG. 1.
Genes in this segment were identified by BLAST search and defined by identification of open reading frames. Central in this region is an aguA gene encoding a 687 amino acid GH67 α-glucuronidase. This aguA gene was followed by a xynA2 gene encoding a 341 amino acid protein with a GH10 endoxylanase catalytic domain. Following the xynA2 gene was a xynB gene encoding a 521 amino acid protein, classified as β-xylosidase/arabinofuranosidase in the GH43 family. These three genes constituted a triad of structural genes expected to encode enzymes for the processing of the product generated by the anchored multimodular endoxylanase, XynA1, to xylose following assimilation by the cell.
Immediately 5′ to this triad were three genes that are presumed to encode proteins that comprise an ABC transporter complex. The expected translated products from this triad include a substrate binding protein, 570 amino acids; a lipoprotein, 323 amino acids; and a permease protein, 306 amino acids. Immediately 5′ to the ABC transporter triad were genes capable of encoding a transcription regulation element made up of two proteins—a receiver protein of an AraC-type response regulator of 522 amino acids, and a histidine kinase protein of 572 amino acids. An amino peptidase gene was located 349 bp upstream of the transcription regulation unit, while 285 bp downstream of the xynB gene was an NADH-dependent flavin oxidoreductase gene.
Translation start sites of these genes were indicated by the presence of putative ribosome binding sites (canonical sequence—GGAGGG, (McLaughlin et al., 1981)) located 5 to 15 nucleotides 5′ to the translation start sites ATG. These predicted protein products were compared with the archived sequences in GenBank. Genes encoding characterized proteins in the protein databases showing greatest homologies are summarized in Table 2. The average GC content of DNA (approximately 33 kb) of Paenibacillus sp. JDR-2 sequenced so far is 52%.
Identification of transcriptional regulation elements in genes associated with utilization of methylglucuronoxylan. The BPROM program (Softberry, see Worldwide Website: softberry.com) was used to locate bacterial promoters and the high scoring transcription start sites were located at the 5′termini of genes potentially encoding YesN, the receiver protein of the response regulator, UgpB, the substrate binding protein of the ABC transporter and AguA, the α-glucuronidase protein of the glycohydrolase triad in the aldouronate-gene cluster. The promoter 5′ to YesN was identified as having the greatest potential of the cluster. The FindTerm program (Softberry, see Worldwide Website: softberry.com) was used to locate the rho-independent transcription stop sites. The transcription termination site upstream of yesN was located at 14 bp after the termination codon of the preceding amino peptidase gene and consisted of a 14/20 bp stem-9 bp loop followed by a 7/8 AT stretch, and punctuated the beginning of the aldouronate-utilization gene cluster. The site found downstream from xynB, consisting of a 13/14 bp stem-7 bp loop followed by a 8/9 AT stretch, was located at 16 bp after the termination codon for XynB, and punctuated the end of the aldouronate-utilization gene cluster. The same analyses applied to xynA1 (St. John et al., 2006) identified as well a potential promoter immediately upstream and a stop site downstream from xynA1, located 1 bp after the termination codon and consisted of a 18/23 bp stem-4 bp loop followed by a 4/7 AT stretch. The positions for different promoters and termination sites are presented in FIG. 3.
Transcriptional regulation genes. The yesN and yesM genes together made up a two component transcription regulation unit. Sequence homology analysis by CDD Search (See Worldwide Website: ncbi.nlm.nih.gov/Structure/cdd) of yesN indicated it coded for a response regulator protein containing a CheY-like receiver domain at the initial 121 amino acids at the amino terminus with Asp55 as the phosphorylated residue and an AraC-type DNA-binding domain spanning residue 432 to 515 at the carboxyl terminus. We have designated this yesN as homologous to the yesN gene of the gram-positive prototype organism, Bacillus subtilis subsp. subtilus str. 168. YesM on the other hand contained a HAMP (histidine kinase/adenyl cyclase/metal-binding proteins/phosphatases) domain at residues 275-344, a histidine kinase domain at residues 367-450 with His378 as the phosphorylated residue, and an ATPase domain at residues 461-558. Again we designated this yesM for the same reason above. Analysis of this two component unit YesN-YesM by CDD Search identified loci 2109 and 2110 in Bacillus halodurans C-125 to be most similar in amino acid content (42% (221/524) and 45% (261/580) identity respectively) and the above described domain architecture. Another similar loci pair identified was Clostridium cellulolyticum H10 Draft 2754 and 2755.
ABC-type transporter. The genes encoding the ABC-type transporter are found in the operon as a cassette of three open reading frames (orf). The first orf in this cassette, lplA, encodes a protein homologous to the substrate binding periplasmic component, UgpB, and identified by CDD Search to be at residues 52-398. The second coding sequence, lplB, codes for the transmembrane permease component, LplB, which spans the entire 323 residue length and contains the sequence motif EAA-X3-G-X9-I-X-LP (residues 216-235), located in a cytoplasmic loop at a distance of  ̃100 residues from the C-terminus (Schneider 2001). The third coding sequence, ytcP, encodes a protein with another permease component, spanning residues 16-305. Sequence homology analyses showed this ABC transporter to be most similar to Bacillus halodurans C-125 loci 2111-2113 (49% (272/555), 73% (210/287) and 65% (193/293) amino acid identity respectively). Another similar ABC transporter identified was in Clostridium cellulolyticum H10 Draft, loci 2757-2759.
Aldouronate processing functions. An aguA gene was identified encoding a GH67 α-glucuronidase with a calculated molecular weight of 77,876 Da and a pI of 5.4. This was the same aguA gene cloned and sequenced from genomic DNA, and shown to encode a functional α-glucuronidase when expressed in E. coli (Preston et al., 2003). Identities derived from GenBank entries were: 63% to Aeromonas punctata, 62% to Geobacillus stearothermophilus T-6, 61% to Bacillus halodurans C-125, and 57% to Clostridium cellulolyticum H10. This protein is highly conserved with respect to catalytic sites. Based upon alignment with the two bacterial GH67 α-glucuronidases of G. stearothermophilus T-6 and Cellvibrio japonicus for which catalytic mechanisms have been elucidated (Golan et al., 2004; Nagy et al., 2003), glutamate and aspartate residues that participate in the acid/base catalyzed reactions can be discerned. In AguA from Paenibacillus sp. JDR-2 Glu401 and Asp373 are homologs of residues Glu392 and Asp364 in G. stearothermophilus T-6 and Glu393 and Asp365 in C. japonicus, which together with a water molecule constitute the catalytic general base. Similarly, Glu294 in Paenibacillus sp. JDR-2 probably corresponds to Glu285 in G. stearothermophilus T-6 and Glu292 in C. japonicus as the catalytic general acid. Catalysis results in the hydrolysis of the α-1,2-glycosidic bond between the 4-O-methylglucuronic acid residue and the xylose residue in the aldo-oligouronate substrate by an inverting mechanism.
A xynA2 gene, encoding the catalytic domain for a GH10 endoxylanase without a signal sequence, (determined by SignalP (Bendtsen et al., 2004)), follows aguA. It has a calculated molecular weight of 39,457 Da and a calculated pI of 5.3, and showed 60-61% identity to GH10 xylanase catalytic domains presumed to function as an intracellular enzyme in other bacteria, e.g., Geobacillus stearothermophilus T-6 and Thermotoga maritima MSB8.
The last gene in this triad and the last gene in this aldouronate-utilization cluster, xynB, encodes a protein of 521 amino acids with an internal family GH43 β-xylosidase, α-arabinofuranosidase defined within residues 11-288. It did not have a signal peptide, had a calculated molecular weight of 57,783 Da and a calculated pI of 4.9. A gap of 285 noncoding bases was found between this last gene and the next, encoding a putative NADH-dependent flavin oxidoreductase. This xylosidase contained a 40% identity to that found in Bacillus clausii KSM-K16 and 40% with that found in Geobacillus thermoleovorans. 
Effects of xylan, glucose and xylose on the relative expression levels of aldouronate-utilization genes. Real-time RT-PCR analysis of the amount of mRNA produced under these growth conditions (FIG. 2) suggested a concerted effect of induction and repression of genes in this cluster, as well as the xynA1 encoding the secreted multimodular GH10 endoxylanase. When growing in only 0.5% yeast extract, all six genes (yesN, lplA, aguA, xynA2, xynB and xynA1) were expressed with aguA and xynB mRNAs slightly more abundant. With these mRNA levels at 0.5% yeast extract considered as points of reference, we found that when 0.5% xylan was added to the yeast extract-containing media, gene expressions of the six were dramatically enhanced, from 18-fold, in the case of the response regulator yesN, to more than 200-fold, in the case of the substrate binding protein, lplA and the β-xylosidase, xynB. Interestingly, when glucose was added to supplement yeast in the media instead of xylan, the relative mRNA molecule pools of the six monitored genes were all variously reduced to about two-thirds (67%, xynA2) and to as much as one-tenth (10% aguA) of basal level. Xylose, on the other hand, slightly induced expression resulting in a 2.7-fold increase (xynA1) to 19-fold increase (xynA2) over basal level. In addition, by performing real-time RT-PCR with the primer pair perm-aguA791f and perm-aguA81r, read-through transcripts from ytcP to aguA were also identified.
In separate experiments, relative expression analyses of the 5′ gene (encoding putative aminopeptidase) and the 3′ gene (encoding putative oxidoreductase) that flank this 8 orfs comprising the aldouronate-utilization gene cluster showed modest variations in response fluctuating from a 3-fold increase to a 3-fold decrease of growth on different carbon sources compared to the basal level with yeast-extract alone.
Glucose repression and CcpA binding sites. In the real-time RT-PCR analyses, expressions of aldouronate-utilization genes were reduced up to 10-fold for genes within the cluster and more than 3-fold for xynA1 outside this cluster when glucose was added to the culture media containing yeast extract. Glucose catabolite repression in G. stearothermophilus (Cheung et al., 1994) led to the identification of a 14-base canonical sequence within or immediately preceding genes responsive to such transcription repression. With visual inspection of Paenibacillus sp. JDR-2 sequences and analysis with the Prokaryotic Promoter Prediction program, at least five such sequences were detected—a sequence 5′ to the response regulator yesN, a second 5′ to lplA, a third about 100 bp 3′ from the translation start site of lplA, a fourth 5′ to xynA2 and a fifth 5′ to xynA1—the endoxylanase gene located distal to this cluster (Table 3).
Gene organization and regulation of gene expression. Based upon similarities to homologs defined in other bacteria, the ABC transporter located 5′ to the aguA gene are most likely concerned with the import of oligoaldouronate substrate for intracellular degradation. Conners et al. (2005) in a recent study of the ABC transporters in Thermotoga maritima concluded that ABC transporters for carbohydrate uptake are probably controlled by local regulators responsive to the transport substrate or a key metabolic degradation product. Shulami et al. (2007) reported that the two component response regulator and ABC transporter found upstream of the glycohydrolases (GH67, GH52) in Geobacillus stearothermophilus T-6 regulated the expression of this cluster. The organization of the genes in Paenibacillus sp. JDR-2 encoding putative transcriptional regulators, transporters, and glycohydrolases, as well as their coordinate regulation, is consistent with these interpretations. The identification of cre motifs within selected genes within each triad further defines the basis for this regulation.
Data from real-time RT-PCR indicated the genes within the aldouronate-utilization cluster in Paenibacillus sp. JDR-2 were regulated as a unit by the same transcription signals and were differentially expressed compared to the flanking genes encoding amino peptidase and oxidoreductase. The coordinate expression of the aldouronate-utilization gene cluster along with the expression of the xynA1 gene encoding the multimodular and cell anchored GH10 endoxylanase supports the case made earlier for the coupling of the depolymerization of methylglucuronoxylan with assimilation and processing of the product, MeGAX3 (St. John et al., 2006). The aldouronate-utilization gene cluster, itself comprised of three potential operons coordinately responding to induction or repression (FIG. 3), may thus be considered a regulon. The coordinate response of these genes with xynA1 expands the scope of this regulon to the function of methylglucuronoxylan or xylan-utilization. Further definition of these processes awaits development of transformation systems in Paenibacillus sp. JDR-2, or the expression of these systems in Bacillus spp. amenable to transformation.
Comparative genomic organizations of aldouronate-utilization clusters. The organization of the aldouronate-utilization gene clusters in bacteria that have been studied for this function is presented in FIG. 4. While there are parallels as noted above, there are also salient differences. There were no nucleotide-binding domains identified in this Paenibacillus sp. ABC transporter cassette. Neither were genes encoding ATP-binding proteins detected in the four open reading frames (orfs) that precede the aguA gene in Geobacillus stearothermophilus T-6, where the first two orfs were identified as an interrupted substrate binding protein and the last two orfs were identified as permeases (Shulami et al., 1999). It has been noted in different gram-positive bacteria that a single ATPase may serve more than one set of substrate-binding and membrane-associated proteins that comprise typical ABC transporter systems (Quentin et al., 1999; Schneider, 2001). In the case of Thermologa maritima MSB8 (Nelson et al., 1999) where five orfs were located adjacent to aguA, two orfs were identified as genes encoding ATP-binding proteins, and located between genes encoding a substrate binding protein and two permeases.
Another feature distinguishing each of these aldouronate-utilization clusters is the relationship to the secreted GH10 endoxylanase, as well the structural properties of the GH10 endoxylanase itself. Both Paenibacillus sp. JDR-2 and Thermotoga maritima MSB8 secrete large multimodular enzymes that include family 22 carbohydrate binding modules (CBM) as well as the GH10 catalytic domain that is distinctive for its generation of the aldotetrauronate MeGAX3. The Paenibacillus sp. JDR-2 secretes a 1467 amino acid endoxylanase comprised of three family 22 CBMs followed by a GH10 catalytic domain followed by a single family 9 CBM and triplicate surface layer homology domains (SLH) on the C-terminus. This enzyme is cell bound, presumably anchored by the C-terminal SLH modules, and the MeGAX3 and xylooligosaccharides are rapidly assimilated as they are released during depolymerization of methylglucuronoxylan (St. John et al., 2006). The xynA1 gene encoding this enzyme is located distal from the aldouronate-utilization gene cluster, as it is not found in cosmids containing 35 kb inserts that include the 14 kb aldouronate-utilization cluster it self. Thermotoga maritima secretes a multimodular 1059 amino acid GH10 endoxylanase that contains two family CBMs followed by a GH10 catalytic domain but lacks SLH domains, and has not been shown to be cell-associated. The xynA1 gene encoding this enzyme is found adjacent to the permease gene for the ABC transporter, and its transcription is in a direction opposite for the genes encoding ABC transporter proteins and AguA. Geobacillus sterothermophilus T6 secretes a 407 amino acid GH10 endoxylanase comprised of a catalytic domain and a 28 amino acid signal peptide, lacking modules to associate with glucan or xylan polymers, or to anchor the enzyme to the cell surface. The xynA1 gene encoding this enzyme is located near the aldouronate-utilization cluster, separated by ten genes most of which encode enzymes involved in glucuronate metabolism (Shulami et al., 1991). Evidence for coordinate expression of aldouronate-utilization genes has been demonstrated, but not for the expression of the xynA1 gene that encodes the secreted GH10 endoxylanase.
Development of bacteria for bioconversion of methylglucuronoxylan. The rapid and complete utilization of methylglucuronoxylan, along with the synchronized induction and repression of the genes comprising the xylan-utilization regulon supports further development of Paenibacillus sp. JDR-2 for the direct conversion of methylglucuronoxylan to biobased products. Growth under conditions of oxygen limitation allow formation of minor amounts of acetate, lactate, succinate and ethanol.
The compact configuration of the aldouronate-utilization gene cluster from Paenibacillus sp. JDR-2 and its coordinate control recommend it as a cassette for transformation of other gram-positive bacteria that have been or may be developed for efficient fermentation of xylose. Additional transformation with the xynA1 gene encoding the multimodular GH10 endoxylanase may provide the products for assimilation and subsequent metabolism. The presence of carbohydrate binding modules for interaction with cellulosic polysaccharides and surface layer homology domains that anchor the catalytic domain and associated substrate to the surface of the cell generate products that are in turn rapidly assimilated into the cell. The collective properties that allow extracellular depolymerization, assimilation and metabolism are presumably the basis for the aggressive xylanolytic activity of Paenibacillus sp. JDR-2. Through genetic engineering, gram-positive bacterial biocatalysts may then be developed for the digestion and vectoral conversion of the hemicellulose fraction of cellulosic resources to renewable fuels and chemicals.
Example 2
Materials and Methods
Cultivation of Paenibacillus sp. Strain JDR-2 and Substrate Utilization.
Paenibacillus sp. strain JDR-2 was isolated and identified in this laboratory as previously described (St. John et al., 2006). Viable cultures were stored in 30% (v/v) glycerol at −70° C. and resuscitated in Zucker-Hankin medium (Zucker et al., 1970) supplemented with 0.5% oat-spelt xylan, 0.01% yeast extract as needed. A stock culture has been deposited with the Bacillus Genetic Stock Center (See Worldwide Website: bgsc.org) under accession number 35A1. Resuscitated cultures were maintained at 30° C. for 2 to 3 weeks with daily transfers in liquid cultures of Zucker-Hankin medium supplemented with 0.5% oat-spelt xylan.
To establish the growth curve, a single colony of Paenibacillus sp. JDR-2 was inoculated in Zucker-Hankin medium supplemented with 0.2% of yeast extract, and then, the cells were grown to early exponential phase at 30° C. with shaking on a G-2 gyrotary shaker (New Brunswick Scientific) at 200 rpm. The culture was used to inoculate, as 5% of final volume, fresh Zucker-Hankin medium supplemented with different carbon sources (0.2% of sweetgum xylan, MeGAX1 or MeGAX3) and 0.01% of yeast extract in replicate. Samples (150 μl) were removed to measure the growth as turbidity (OD600). Following centrifugation of the samples, cell pellets were collected for protein assay and the supernatants were transferred to fresh 0.5-ml centrifuge tubes for total carbohydrate assay, uronic acid assay and TLC analysis. Best fit linear curves were defined with Excel for maximum rates of utilization of substrates.
Preparation of Aldouronates.
MeGAXn was prepared from sweetgum (Liquidamber styrachiflua) sawdust and structurally defined by 13C-NMR. MeGAX3 (4-O-methyl-D-glucuronate α-1,2-linked to the reducing terminal xylose of β-1,4-xylotrioside) was obtained as a major aldouronate following the depolymerization of MeGAXn with the GH10 xylanase XynA1 catalytic domain from Paenibacillus sp. strain JDR-2 in 0.1 M potassium phosphate (pH 6.5) at 45° C. Following filtration through a YM-3 membrane (Amicon) and concentration of the reaction mixture by flash evaporation at 50° C., oligomers were resolved on a 2.5 cm by 150 cm P-2 column (Bio-Rad) using 0.05 M formic acid as the eluent. Pooled fractions comprising the MeGAX3 peak were lyophilized, dissolved in 0.22 μm filtered distilled water, analyzed for composition as above and authenticated by thin layer chromatography on silica gel 60 plates as described below. MeGAX4 (4-O-methyl-D-glucuronate α-1,2-linked to the xylose residue penultimate to the reducing terminal xylose of β-1,4-xylotetraoside) was prepared as a limit product following incubation of pure GH11 endoxylanase from Trichoderma longibrachiatum (Hampton Research, Laguna Niguel, Calif. 92677) in 0.05 M sodium acetate (pH 5.5) at 30° C. and purified as for MeGAX3. This preparation also included a small amount of MeGAX5. Purified MeGAX1 and MeGAX2 were obtained as aldouronate products of the hydrolysis of MeGAXn with 0.5% H2SO4 at 120° C. for 60 min. Upon cooling to room temperature, the hydrolysate was neutralized with BaCO3 to a pH of approximately 3.5, cooled at −20° C. for 30 minutes, and filtered through a GF-C filter. Acidic oligomers were bound to AG2-X8 resin (Bio-Rad) in the acetate form by placing on a gyrotory shaker for 1 hour. The slurry was poured into a 2.5 cm by 20 cm glass column and rinsed with distilled water until no reaction to the total carbohydrate assay was observed in the eluate. Bound oligomers were bulk eluted by displacement with 20% acetic acid, concentrated by flash evaporation, subjected to P-2 column chromatography and analyzed as above.
Determination of Growth and Substrate Utilization
Culture growth was followed by turbidity determined as optical density at 600 nm (OD600), measured in a 1.00 cm cuvette on a Beckman DU500 series spectrophotometer. When necessary, cultures were diluted to provide OD600 readings between 0.2 and 0.8 which were then corrected for dilution to provide data for growth curves. For biomass determination, cells were collected by centrifugation and assayed for total protein. Cell pellets were resuspended in 200 μl of 1 N NaOH and incubated in a water bath at 85° C. for 10 min. Samples were cooled to room temperature, neutralized with an equal normal of 1 N HCl, and assayed for total protein following the procedures of BCATM Protein Assay Kit (Pierce chemical Co., Rockford, Ill. 61105) using bovine serum albumin as a standard.
Utilization of substrates was determined by the disappearance of total carbohydrate in medium samples using the phenol sulfuric acid method with xylose as a standard (Dubois et al., 1956). The utilization of aldouronates was separately determined by quantifying uronic acid concentrations in a colorimetric assay using glucuronic acid as a standard (Bluemenkrantz et al., 1973). To determine the consumption of different carbon substrates (MeGAX1, MeGAX3, MeGAXn), the supernates (containing 100 nmoles of xylose equivalent determined as total carbohydrate) of media samples taken at different times were loaded on a TLC plate (Silica gel 60, 0.25 mm thickness, EM Laboratories, Inc.). The plate was developed in with chloroform/acetate acid/water (6:7:1, v/v) using 2×4 h double ascension (Zhou et al., 2001). Plates were air-dried for 10 min and sprayed with 6.5 mM N-(1-naphthyl)-ethylenediamine dihydrochloride in methanol containing 3% (v/v) of sulfuric acid (Bounias 1980). The stained plate was baked in an oven at 90° C. for 10 min for visualization.
Cloning and Sequencing.
The identification of relevant genes started with the application of PCR to detect, clone and sequence a gene (aguA) encoding a GH 67 α-glucuronidase. Degenerate primers (F750-GCATTAATGCAATTTCAATTAATAAYGTNAAYGT (SEQ ID NO:22), R1201-CAGATGTTTTTGTTGGCCTGTRTAYTCYTGNGT (SEQ ID NO:23)) of aguA gene were designed. Using the genomic library of Paenibacillus sp. JDR-2 as template, a PCR reaction was run under the touchdown protocol: 1 cycle of 60 seconds at 98° C.; 21 cycles of 20 seconds at 95° C., 30 seconds per cycle starting at 60° C., decreasing setpoint temperature after cycle 2 by 0.5° C. per cycle, and extension for 40 seconds at 72° C.; 20 cycles of 20 seconds at 95° C., 30 seconds at 50° C. and extension for 40 seconds at 72° C.; and an additional extension for 10 minutes at 72° C. PCR products were identified following electrophoresis in 1.5% of agarose gel slabs. The predominant band of the predicted size was detected by ethidium bromide staining and excised from gel for cloning into pCR2.1-TOPO vector. Following transformation into E. coli TOP10 and growth on LB agar containing 100 μg·ml−1 of ampicillin. Colonies were selected for sequencing. The sequences obtained were used to design sequence-specific primers (F54-CGAGAGACATTCCTTATTACGGAGA (SEQ ID NO:24), R569-CATCTGGTTGGTATGCTCCATCG (SEQ ID NO:25)) that were applied to screen the genomic library for determination aguA and contiguous gene sequences in the genome.
Expression Constructs of aguA and xynA2 Genes.
Specific primers with the addition of restriction enzyme sites of the aguA gene (F-GGCCATGGGAGACAACGGATACGC (SEQ ID NO:26), R-CACCTCGAGTGAATCGATTTGCCCCGC (SEQ ID NO:27)) and xynA2 (F-CGGACATGTCATATACTTCGGAGTTGCC (SEQ ID NO:28), R-CACCTCGAGTGAATCGATTTGCCCCGC (SEQ ID NO:29)) were designed for PCR amplification. The PCR products of 3,119 bp fragment including aguA and xynA2 genes and 1,037 bp fragment of xynA2 gene were produced by PCR using the enzyme blend of ProofStart and Taq DNA polymerase (Qiagen) under the conditions: 1 cycle of 2 minutes at 98° C.; 5 cycles of 10 seconds at 95° C., 60 seconds at 55° and extension for 4 minutes at 68° C.; 30 cycles of 10 seconds at 95° C., 4 minutes at 68° C.; and an additional extension for 10 minutes at 72° C. The PCR products purified from agarose gel were double-digested with NcoI plus XhoI or BspLU 11I plus XhoI to produce the 3,119 bp and 1,026 bp fragments, and cloned into vector pET-32 digested with NcoI and XhoI.
In Vitro Protein Expression and Purification.
Constructs of aguA and xynA2 genes cloned into vector pET-32 were transformed into host E. coli Rosetta (DE3) containing pRare plasmid. Transformants were selected on LB plates containing 100 μg·ml−1 of ampicillin and 34 μg·ml−1 of chloramphenicol. Single colonies were inoculated into 100 ml of LB medium containing ampicillin and chloramphenicol and incubated overnight. The cells of an overnight culture were centrifuged and resuspended in 250 ml of fresh LB containing 200 μg·ml−1 of ampicillin and 34 μg·ml−1 of chloramphenicol for over-expression under the induction with 0.2 mM and 0.5 mM of IPTG for aguA and xynA2 genes at 23° C. for 2 h. The cells were harvested, suspended in 10 ml of His.Tag binding buffer without NaCl, and disrupted with 2 passages through a French Pressure Cell (SLM Instruments Inc.) at a differential pressure of 20,000 psi. This treatment was followed by sonication on ice for 2 min at power level 7 using a model W-185E Sonifier Cell Disruptor (Ultrasonics, Inc., NY). Cell lysates were purified on His.Tag columns (HiTrap Chelating HP, GE Healthcare Bio-Sciences Corp, Piscataway, N.J. 08855), binding in the Binding buffer (500 mM NaCl in 20 mM sodium phosphate buffer, pH 7.4) and eluting with the elution buffer (500 mM imidazole in the binding buffer) as described in the protocol provided by the company. The eluate from the His.Tag column was desalted on a PD-10 column (GE Healthcare Bio-Sciences Corp), and the protein was eluted with 50 mM NaOAc (pH6.0).
Determination of Activities and Substrate Specificities of AguA and XynA2
Recombinant AguA was assayed for enzyme activity at 37° C. in 50 mM NaOAc (pH6.0) buffer by determination of reducing termini on methylglucuronate residues released from aldouronates (Milner et al., 1967). Recombinant XynA2 activity was determined at 30° C. in the same buffer by the standard Nelson assay of reducing termini released from xylooligosaccharides (Nelson, 1944). One unit of enzyme activity is defined as the amount that releases 1 μmol reducing termini per min at the designated temperature. Protein concentrations were determined by the BCA assay kit using a bovine serum albumin standard as described above. Activities were also determined by quantification of substrates by HPLC. MeGAX1 or MeGAX3 was incubated as 88 nmol in a volume of 50 μl with enzyme (1 μg) in 50 mM sodium acetate (pH 6.0) for 30 min at 37° C. After heating in a boiling water bath for 10 min to stop the reaction, products were resolved on an Aminex HPX-87H (Bio-Rad) column eluted with 0.01 N H2SO4 and detected by differential refractometry.
Relative preferences and specificities of AguA for MeGAX1, MeGAX2, MeGAX3 and MeGAX4 as substrates were determined upon incubation of purified enzyme (1 μg/μl of protein) with 10 mM of substrate in 100 μl of reaction buffer (50 mM of sodium acetate, pH 6.0) at 30° C. for approximately 16 h. The digested products (20 μl of a complete digestion, 20 nmol equivalents of product) were spotted on a TLC plate (Silica gel 60, EM Laboratories, Inc.), along with 20 nmol of xylooligosaccharide (X1, X2, X3 and X4) and aldouronate (MeGAX1, MeGAX2, MeGAX3 and MeGAX4) standards. The plate was developed, stained and visualized as described above for analysis of media samples.
To determine the respective roles of AguA and XynA2 in processing aldouronates, the activities of XynA2 and AguA were evaluated individually and together with xylooligosaccharides (X2, X3 and X4) and aldouronates (MeGAX2, MeGAX3 and MeGAX4) as substrates. The purified enzyme(s) XynA2 (1.9 μg) or AguA (4.0 μg) with XynA2 (1.9 μg) were incubated in 50 μL of reaction buffer (50 mM of sodium acetate, pH 6.0) at 30° C. for 16 h and the reaction components were resolved by TLC and detected following the above procedures.
Optimal Temperature and pH for the Activities of α-glucuronidase (AguA) and XynA2.
To determine the optimal temperature, the purified AguA (6.0 μg) was incubated with 10 mM of MeGAX1 in 200 μl of reaction in 50 mM of sodium acetate buffer (pH 6.0) for 30 min at different temperatures, 30° C., 40° C., 50° C., 60° C. and 70° C. Reactions assayed in triplicate for AguA activity by determination of uronic acid reducing termini (Milner et al., 1967), using D-glucuronic acid as a standard. To determine the optimal pH, the reactions were run in different buffers of pH 4.0 to 7.0 (50 mM, NaOAc buffer) and pH 7.1 to 8.5 (50 mM, Tris-HCl buffer) for 30 min at 37° C., and assayed as above.
To determine the optimal temperature of XynA2, the purified enzyme (10.0 μg) was incubated with 100.0 μg of xylotriose in 500 μl of reaction in 50 mM of sodium acetate buffer (pH 6.0) for 4 h at different temperature from 25° C. to 80° C. The digestion reaction was run in triplicate for colorimetric assay of XynA2 activity to assay the generation of new reducing termini as a measure of glycosidic bond cleavage, using D-xylose as a standard (Nelson, 1944). To determine the optimal pH, the reactions were run in different buffers of pH 5.0 to 6.5 (50 mM, NaOAc buffer) and pH 7.1 to 8.5 (100 mM, potassium phosphate buffer) for 4 h at 30° C.
Results
Growth and Consumption of Carbohydrate Substrates
The Paenibacillus sp strain JDR-2 strain showed markedly different growth rates (FIG. 9A) with the polysaccharide compared to the aldouronates MeGAX1 (generated by acid hydrolysis) or MeGAX3 (generated by GH10 xylanase catalyzed hydrolysis). The rapid growth on MeGAXn between 8 to 20 h determined by OD600 was followed by a rapid decline phase that indicated cell lysis, possibly associated with sporulation. A similar pattern with a slight temporal shift was observed for growth based upon the determination of total cell protein. The growth in media supplemented with MeGAX1 and MeGAX3 increased slowly and steadily from 8 to 34 h with a lower growth rate compared to growth on MeGAXn, with growth patterns determined by total cell protein similar to those determined by OD600 (data not shown). The utilization of substrates, determined by total carbohydrate or uronic acid, mirrored the growth curves for each substrate (FIG. 9B), indicating growth was quantitatively correlated with the consumption of each substrate.
The regions of growth curves showing the highest rate of growth and substrate utilization were selected to compare the rates of utilization of the polysaccharide, MeGAXn, with MeGAX1 and MeGAX3. The relationships between substrate utilization and time over this time frame provided a quantitative basis for this comparison as determined for the disappearance of total carbohydrate and uronic acid (FIG. 10), and similar rates of utilization were found for a given substrate using both assays. The slopes of the best fit curves relating substrate utilization to time were −0.0765 for MeGAXn, −0.0334 for MeGAX1, and −0.0203 for MeGAX3. The respective rates of utilization of MeGAXn, MeGAX1, and MeGAX3 were 149.8, 59.4 and 54.3 μg xylose equivalent·ml−1·h−1, and the respective growth rates determined for MeGAXn, MeGAX1, and MeGAX3 sole carbon sources were 62.7, 4.3 and 4.8 μg cell protein·ml−1·h−1. While both aldouronates generated by enzyme mediated (MeGAX3) or acid (MeGAX1) served as effective carbon sources, the rate of growth on MeGAXn identified the marked preference for the polysaccharide.
TLC analysis of medium samples (FIG. 7) showed that MeGAXn was depolymerized and consumed within 31 hours with little of no accumulation of intermediate products. MeGAX1 and MeGAX3 as individual substrates for growth were completely utilized by 40 h without the appearance of intermediates prior to their assimilation.
Gene Cloning and Sequence Analysis
Genes cloned from PCR products generated from genomic DNA were identified by BLAST search and defined by identification of open reading frames. Based upon homolog comparisons, an aguA gene was identified encoding a 687 amino acid GH67 α-glucuronidase with a calculated molecular weight of 77,876 Da and a calculated pI of 5.4. Amino acid sequence identities with AguA homologs derived from GenBank entries were: 63% to Aeromonas punctata, 62% to Geobacillus stearothermophilus T-6, 61% to Bacillus halodurans C-125, and 57% to Clostridium cellulolyticum H10. This aguA gene was followed by a xynA2 gene encoding a 341 amino acid catalytic domain for a GH10 endoxylanase without a signal peptide sequence detectable with SignalP program. This XynA2 has a calculated molecular weight of 39,457 Da and a calculated pI of 5.3, and showed 60-61% amino acid sequence identity to GH10 xylanase catalytic domains presumed to function as an intracellular enzyme in other bacteria, e.g. Geobacillus stearothermophilus T-6 and Thermotoga maritima MSB8.
In Vitro Expression and Properties of AguA and XynA2
The expression of recombinant aguA and xynA2 in E. coli was evaluated by SDS-PAGE analysis of insoluble (cell pellets) and soluble (supernates) following French Pressure Cell lysis, sonication and centrifugation. Based upon stained gel patterns (data not shown), expression of aguA identified a predominant protein of 94.8 kDa with 20% in the cell pellet and 80% in the supernate. The expression of xynA2 and similar analysis identified predominant protein of 55.7 kDa with 20% in the pellet and 80% in the supernate. Following purification of soluble fractions on His-Tag resins and desalting on PD-10 columns, the yields of AguA and XynA2 were 24.9 mg·liter−1 and 10.4 mg·liter−1, respectively.
With MeGAX1 as substrate, AguA activity at 37° C. was 4.69, 5.54, 5.11, 5.10, 3.55, 1.77, and 0.052 U·mg−1 protein at pH 5.0, 5.5, 6.0, 6.5, 7.1, 7.5, and 8.0, respectively. At pH 6.0, AguA activity was 3.62, 4.82, 2.62, 0.60, and 0.34 U·mg−1 protein at temperatures 30, 40, 50, 60, and 70° C., respectively. With xylotriose as substrate, XynA2 activity at 30° C. was 0.10, 0.13, 0.14, 0.13, 0.12, 0.12, and 0.11 U·mg−1 protein at pH 5.0, 5.5, 6.0, 6.5, 7.0, 7.5 and 8.0 respectively. At pH 6.0, xynA2 activity was 0.13, 0.14, 0.134, 0.104, 0.084, 0.064, 0.061, 0.059, and 0.059 U·mg−1 protein at temperatures 25, 30, 35, 40, 45, 50, 60, 70, and 80° C., respectively. AguA maintained 85% and XynA2 maintained 71% of their respective optimal activities at pH 5.0, and both showed significant activity at 50° C. (AguA, 54%; XynA2, 46%), supporting their application as moderately acid-tolerant and thermotolerant catalysts.
Products Generated by the Action of AguA and XynA2
Using the colorimetric assay, the specific activities of AguA released 4-O-methyl-D-glucuronate from aldobiouronate (MeGAX1) and aldotetrauronate (MeGAX3) at a concentration of 2 mM substrate were determined at pH 6.0, 37° C., to be 1.0 and 2.8 U·mg−1 protein, respectively.
With TLC analysis (FIG. 8), the activity of AguA on different aldouronates (MeGAX1-4) showed that AguA cleaved MeGAX1-3 to MeGA, and xylose, xylobiose and xylotriose, respectively. The MeGA displayed a mobility slightly less than xylose and was not resolved from xylose in the products generated from MeGAX1. The mobilities of xylose, xylobiose, and xylotriose as standards (Lane 1) were slightly less than found for the saccharides generated by the action of AguA on MeGAX1, MeGAX2, and MeGAX3 (Lanes 3, 4, 5), possibly affected by the components of the assay reaction. AguA exhibited no activity on MeGAX4 or MeGAX5 generated by a GH11 endoxylanase from Trichoderma longibrachiatum. HPLC analysis of reaction mixtures containing either MeGAX1 or MeGAX3 as substrates quantitatively confirmed the activity of AguA on both of these aldouronates (FIG. 9). AguA cleaved MeGAX1 (FIG. 9B) to generate stoichiometric quantities of MeGA (peak: 10.29 min) and xylose (peak: 12.12 min). AguA cleaved MeGAX3 (FIG. 9D) into xylotriose (peak: 8.75 min) and MeGA (peak: 10.29 min).
XynA2 is an endoxylanase classified as a member of glycohydrolase family GH10 lacking a secretion signal sequence that is active with methylglucuronoxylan as substrate (data not shown). Using xylobiose, xylotriose and xylotetraose as substrates, the TLC results (FIG. 10) showed that XynA2 cleaved xylotriose and xylotetraose to form xylose and xylobiose as limit products. With xylotriose as substrate and HPLC analysis of products, XynA2 catalyzed the formation of xylobiose equivalent to 67% and xylose equivalent to 33% of total amount of products (and equivalent to the starting amount of xylotriose) indicating that one molecule of xylotriose produced one xylose and one xylobiose. With xylotetraose as substrate, XynA2 catalyzed the formation of xylobiose equivalent to 83% of total amount of products, and xylose equivalent to 17%. Based on these results, XynA2 was able to cleave xylotetraose to form xylobiose or xylotriose and xylose, and then cleave the xylotriose to form xylobiose and xylose. With either substrate, xylobiose was a limit product requiring further processing for metabolism. The combined activities of AguA and XynA2 showed formation of MeGA and xylobiose from MeGAX2 and MeGA, xylobiose and xylose from MeGAX3 (FIG. 10), supporting their cooperative role in the intracellular processing the aldouronate MeGAX3 derived from the extracellular action of the multimodular cell-associated XynA1.
All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.







TABLE 1







List of nucleotide sequences of primers used








Primer
Nucleotide sequence












PF54
CGAGAGAGAGACATTCCTTATTACG
(SEQ ID NO: 30)


 


PR569
CATCTGGTTGGTATGCTCCATCG
(SEQ ID NO: 31)


 


rre178f
GTGCTGGACGGATTGGAGCTTA
(SEQ ID NO: 32)


 


rre459r
CTCCGAGAACTGGCCTTGAACA
(SEQ ID NO: 33)


 


sbp1081f
AACTCGTATGGCGTAGGCAACC
(SEQ ID NO: 34)


 


sbp1361r
TGGCCTGTATAGTCGCTCCAGA
(SEQ ID NO: 35)


 


agua1069f
CGGACGCTTCAAGGACAATGTG
(SEQ ID NO: 36)


 


agua1354r
GGCCGTAATGCCGCTATGAGTA
(SEQ ID NO: 37)


 


xy1247f
CATACGCTGGTGTGGCACAATC
(SEQ ID NO: 38)


 


xy1623r
CCGTGAATCGGCACTTGCTTAG
(SEQ ID NO: 39)


 


bex948f
GGACAAGTCGGTGACCACCAAG
(SEQ ID NO: 40)


 


bexl291r
CTTGCGCCATCGCCGTTACAAG
(SEQ ID NO: 41)


 


xynA1-
GCGTCGGAATGCAAGGCCATTA
(SEQ ID NO: 42)


2237f




 


xynA1-
TCTCGGCTCTCCAGCTTGTGTT
(SEQ ID NO: 43)


2503r




 


amp10f
GATCTGGCAGCTTCCTGCATTC
(SEQ ID NO: 44)


 


amp204r
TCCAGTCCGCGGCTCTTATCAA
(SEQ ID NO: 45)


 


oxr535f
TCACGGCGCGAACACTTATCTC
(SEQ ID NO: 46)


 


oxr774r
GCTCATCACAGGCGGAAGGTAT
(SEQ ID NO: 47)


 


perm-
TAACGGCGGTTACGCCAACCTC
(SEQ ID NO: 48)


agua791f




 


perm-
CCAGCCTGCGTATTGCTCCAAG
(SEQ ID NO: 49)


agua81r
















TABLE 2







Identification of the relevant xylanolytic genes in the 15 kb genomic segment

















Homologous


ORF
Protein
COG#
Function
E valueb
protein/% identityc





yesNa
YesN
4753
Response regulator containing
3e−51
Bacillus subtilus subsp.





CheY-like receiver domain and

subtilus str. 168,





AraC-type DNA-binding

GeneID: 938764/40%





domain [Signal transduction

(64/159)





mechanisms]


yesMa
YesM
2972
Predicted signal transduction
1e−48
Bacillus subtilus subsp.





protein with a C-terminal

subtilus str. 168,





ATPase domain [Signal

GeneID: 936078/23%





transduction mechanisms]

(138/592)


lplAa
UgpB
1653
ABC-type sugar transport
4e−10
Bacillus subtilus subsp.





system, periplasmic component

subtilus str. 168,





[Carbohydrate transport and

GeneID: 936079/25%





metabolism]

(49/191)


lplBa
LplB
4209
ABC-type polysaccharide
3e−92
Bacillus subtilus subsp.





transport system, permease

subtilus str. 168,





component [Carbohydrate

GeneID: 936088/39%





transport and metabolism]

(112/285)


ytcPa
UgpE
0395
ABC-type sugar transport
9e−41
Bacillus subtilus subsp.





system, permease component

subtilus str. 168,





[Carbohydrate transport and

GeneID: 938095/34%





metabolism]

(102/294)


aguA
AguA
pfam03648
Glycosyl hydrolase family 67.
0.0
Geobacillus





Family of alpha-glucuronidase.

stearothermophilus T-







6, Alpha-glucuronidase







Chain A, gi: 37926810/







67% (422/680)


xynA2
XynA2
smart00633
Endoxylanase, Glycosyl
8e−90
Geobacillus





hydrolase family 10

stearothermophilus,







Intra-cellular xylanase







IXT6,







gi: 114054545/







60% (199/327)


xynBa
XynB
pfam04616/
Arabinofuranosidase
2e−74/
Geobacillus




3507
Glycohydrolase family 43/
8e−86
stearothermophilus,





Beta-xylosidase.

Intra-cellular xylanase







IXT6, XynB,







gi: 114054567/32%







(178/540)





aGene name is assigned to that closest in homology found in Bacillus subtilus, subtilus str. 168.


bsimilarity to the functional protein family assignment as determined by CD SEARCH, NCBI.


cPercent identity is the number of residues of the major portion of the query protein identical to those of the subject protein as determined by the NCBI BLAST program.













TABLE 3







Candidate CcpA binding sites and their locations 5′ of


aldouronate-utilization


genes in Paenibacillus sp. JDR-2











SEQ
Homology ratio to



Binding site sequence & Distance from
ID
canonical sequence



translation start site
NO:
(Cho et al., 1999)
Gene





5′-TGWAANCGNTNWCA
50
14/14
Cho et





al., 1999


5′-TGAAATCGCTTACAa---145nt---ATG---
51
14/14
yesN


5′-TGAAAGTGCTTACAa---38nt---ATG---
52
13/14
lplA


5′-ATG---146nt---TGAAGCGGATGACAb---
53
12/14
lplA


5′-TGAACCGCTGGCAGb---183nt---ATG---
54
12/14
xynA2


5′-TGTAAGCGCTTAATb---30nt---ATG---
55
12/14
xynAl





aidentified by PPP (Prokaryotic Promoter Prediction) program (Groningen Biomolecular Sciences and Biotechnology Institute, Haren, the Netherlands, http://bioinformatics.biol.rug.nl/websoftware/ppp/ppp_start.php)


bidentified by manual scanning of the upstream region of these genes













TABLE 4





Activities of the aldouronate-utilization gene


products isolated from Paenibacillus sp. JDR-2

















SEQ ID NO: 1
yesN
CheY-like, Ara C type response regulator


SEQ ID NO: 3
yesM
Histidine kinase-type transduction protein


SEQ ID NO: 5
lplA
Substrate binding protein


SEQ ID NO: 7
lplB
Lipoprotein


SEQ ID NO: 9
ytcP
Permease activity


SEQ ID NO: 11
aguA
GH67 α-glucuronidase activity


SEQ ID NO: 13
xynA2
GH10 xylanase activity


SEQ ID NO: 15
xynB
GH43 β-xylosidase activity


SEQ ID NO: 17

NADH-dependent flavin oxidoreductase
















TABLE 5







List of start and stop nucleotide number of


genes coded in the two sequences EU024644 (SEQ


ID NO: 21) and AJ938162 (SEQ ID NO: 19)











Gene
Start
Stop











GenBank # EU024644











yesN
620
2188



yesM
2204
3922



lplA
4056
5768



lplB
5858
6829



ytcP
6869
7789



aguA
7886
9949



xynA2
9977
11002



xynB
10999
12564



oxidoreductase
12775
13899



hypothetical protein
14019
14726







GenBank #AJ938162











xynA1
1
4401







NB. The AJ938162 sequence is 4401 nucleotides long. Therefore the coding sequence is the entire nucleotide sequence of that submission.






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## Claims

1. An isolated nucleic acid comprising a polynucleotide that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 12, wherein said polypeptide has α-glucuronidase activity.

2. The isolated nucleic acid of claim 1, wherein said polynucleotide comprises the nucleotide sequence of SEQ ID NO: 11.

3. A genetic construct comprising the polynucleotide of claim 1.

4. The genetic construct of claim 3, wherein said polynucleotide comprises the nucleotide sequence of SEQ ID NO: 11.

5. A vector comprising the polynucleotide of claim 1.

6. The vector of claim 5, wherein said polynucleotide comprises the nucleotide sequence of SEQ ID NO: 11.

7. A host cell transformed with the nucleic acid of claim 1.

8. The host cell of claim 7, wherein said nucleic acid comprises a polynucleotide comprising the nucleotide sequence of SEQ ID NO: 11.

9. The host cell of claim 7, wherein said host cell is a Bacillus spp.

10. The host cell of claim 9, wherein said Bacillus spp is Bacillus coagulans.

11. A probe that hybridizes with the nucleic acid of claim 1.

12. The probe of claim 11, wherein said probe hybridizes with the nucleotide sequence of SEQ ID NO: 11.

13. An isolated polynucleotide that hybridizes under intermediate stringency or high stringency conditions to the nucleic acid of claim 1, wherein said intermediate or high stringency conditions comprise a hybridization step at 60° C. in the presence of a 5×SSC buffer and washes performed in a solution containing 2×SSC at 50° C. or a hybridization step at 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15M NaC1 and 0.05 M Na citrate, washes at 37° C. for 1 hour in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% B SA, followed by a wash in 0.1×SSC at 50° C. for 45 minutes, respectively.

14. The isolated polynucleotide of claim 13, wherein said nucleic acid comprises the nucleotide sequence of SEQ ID NO: 11.

15. A composition comprising a host cell transformed with a polynucleotide that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 12, wherein said polypeptide has α-glucuronidase activity.

16. The composition of claim 15, wherein said host cell is contained in a solid medium.

17. The composition of claim 16, wherein said medium is a liquid medium.

18. An isolated nucleic acid that comprises a polynucleotide, wherein said polynucleotide is the full complement of the polynucleotide of claim 1.