Aldouronate utilization in Paenibacillus sp. strain JDR-2: Physiological and enzymatic evidence for coupling of extracellular depolymerization and intracellular metabolism

Applied and Environmental Microbiology

Volumn 75, Issue 13, 2009, Pages 4410-4418

  Nong, Guang ^a   Rice, John D ^a   Chow, Virginia ^a   Preston, James F ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ACID PRETREATMENT; AVERAGE RATE; CELL SURFACES; DILUTE ACIDS; ENDOXYLANASE; ENZYME PRETREATMENT; EXTRACELLULAR; GENE CLUSTERS; GENES ENCODING; GLUCURONIDASE; GLYCOHYDROLASE; INTRACELLULAR METABOLISM; LIGNO-CELLULOSICS; LIGNOCELLULOSIC BIOMASS; MULTI-MODULAR; PRE-TREATMENT; SPECIFIC GROWTH RATE; SWEET GUM; TRANSCRIPTIONAL REGULATOR; XYLOBIOSE; XYLOSE RESIDUES; XYLOSIDASE;

ACIDS; BIOCHEMISTRY; BIOMASS; CELL MEMBRANES; ENCODING (SYMBOLS); ENZYME ACTIVITY; METABOLISM;

GENE ENCODING;

ABC TRANSPORTER; ALDOURONATE; ALPHA GLUCURONIDASE; ARABINOFURANOSIDASE; BIOFUEL; ENDOXYLANASE; GLYCOSIDASE; LIGNOCELLULOSE; METHYLGLUCURONOXYLAN; METHYLGLUCURONOXYLOSE; METHYLGLUCURONOXYLOTRIOSE; TRIOSE; UNCLASSIFIED DRUG; URONIC ACID; XYLAN; XYLAN 1,4 BETA XYLOSIDASE; XYLAN ENDO 1,3 BETA XYLOSIDASE;

BACTERIUM; BIOFUEL; BIOMASS; CELLULOSE; DECIDUOUS TREE; ENZYME ACTIVITY; GENE EXPRESSION; GROWTH RATE; LIGNIN; METABOLISM; PHYSIOLOGY; POLYMERIZATION; PROTEIN; SUGAR;

AGUA GENE; ARTICLE; BIOMASS; CELL METABOLISM; DEPOLYMERIZATION; ENZYME BINDING; GENE; GENE CLUSTER; NONHUMAN; PAENIBACILLUS; PAENIBACILLUS JDR 2; REGULON; TRANSCRIPTION REGULATION; XYNA1 GENE; XYNA2 GENE; XYNB GENE;

BACTERIAL PROTEINS; DISACCHARIDES; ENDO-1,4-BETA XYLANASES; GENE ORDER; GLUCURONIDASE; GLYCOSIDES; GRAM-POSITIVE BACTERIA; LIGNIN; MODELS, BIOLOGICAL; MULTIGENE FAMILY; POLYSACCHARIDES; TRISACCHARIDES; URONIC ACIDS; XYLOSE;

BACTERIA (MICROORGANISMS); LIQUIDAMBAR STYRACIFLUA; PAENIBACILLUS SP.;

EID: 67649622092     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02354-08     Document Type: Article

References (37)

1. Betts, W. B., R. K. Dart, A. S. Ball, and S. L. Pedlar. 1991. Biosynthesis and structure of lignocellulose, p. 139-355. In W. B. Betts, (ed.), Biodegradation of natural and synthetic materials. Springer Verlag, Berlin, Germany.
2. Bi, C., J. D. Rice, and J. F. Preston. 2009. Complete fermentation of xylose and methylglucuronoxylose derived from methylglucuronoxylan by Enterobacter asburiae strain JDR-1. Appl. Environ. Microbiol. 75:395-404.
3. Biely, P., M. Vrsanska, M. Tenkanen, and D. Kluepfel. 1997. Endo-beta-1,4-xylanase families: differences in catalytic properties. J. Biotechnol. 57:151-166. (Pubitemid 27397479)
4. Biely, P., J. Hirsch, D. C. la Grange, W. H. van Zyl, and B. A. Prior. 2000. A chromogenic substrate for a beta-xylosidase-coupled assay of alpha-glucuronidase. Anal. Biochem. 286:289-294.
5. Blumenkrantz, N., and G. Asboe-Hansen. 1973. New method for quantitative determination of uronic acids. Anal. Biochem. 54:484-489.
6. Bounias, M. 1980. N-(1-naphthyl)ethylenediamine dihydrochloride as a new reagent for nanomole quantification of sugars on thin-layer plates by a mathematical calibration process. Anal. Biochem. 106:291-295.
7. Choi, I. D., H. Y. Kim, and Y. J. Choi. 2000. Gene cloning and characterization of alpha-glucuronidase of Bacillus stearothermophilus no.236. Biosci. Biotechnol. Biochem. 64:2530-2537.
8. Chow, V., G. Nong, and J. F. Preston. 2007. Structure, function, and regulation of the aldouronate utilization gene cluster from Paenibacillus sp. strain JDR-2. J. Bacteriol. 189:8863-8870.
9. Collins, T., C. Gerday, and G. Feller. 2005. Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol. Rev. 29:3-23.
10. Dekker, R. F. H. 1983. Bioconversion of hemicellulose: aspects of hemicellulase production by Trichoderma reesii QM9414 and enzymatic saccharification of hemicellulose. Biotechnol. Bioeng. 25:1127-1146.
11. Dien, B. S., M. A. Cotta, and T. W. Jeffries. 2003. Bacteria engineered for fuel ethanol production: current status. Appl. Microbiol. Biotechnol. 63:258-266.
12. Dubois, M., K. A. Gilles, J. K. Hamilton, P. A. Rebers, and F. Smith. 1956. Colorimetric method for the determination of sugars and related substances. Anal. Chem. 28:350-356.
13. Ge, Y., E. G. Antoulinakis, K. R. Gee, and I. Johnson. 2007. An ultrasensitive, continuous assay for xylanase using the fluorogenic substrate 6,8-difluoro- 4-methylumbelliferyl β-D-xylobioside. Anal. Biochem. 362:63-68.
14. Ingram, L. O., H. C. Aldrich, A. C. Borges, T. B. Causey, A. Martinez, F. Morales, A. Saleh, S. A. Underwood, L. P. Yomano, S. W. York, J. Zaldivar, and S. Zhou. 1999. Enteric bacterial catalysts for fuel ethanol production. Biotechnol. Prog. 15:855-866.
15. Jarboe, L. R., T. B. Grabar, L. R. Yamano, K. T. Shanmugam, and L. O. Ingram. 2007. Development of ethanologenic bacteria. Adv. Biochem. Eng. Biotechnol. 108:237-261.
16. Johnson, D. G., M. C. Silva, C. R. Mackenzie, H. Schneider, and J. D. Fontana. 1989. Microbial degradation of hemicellulosic materials. Appl. Biochem. Biotechnol. 20/21:245-258.
17. Khandke, K. M., P. J. Vithayathil, and S. K. Murthy. 1989. Purification and characterization of an α-glucuronidase from a thermophilic fungus, Thermoascus aurantiacus. Arch. Biochem. Biophys. 274:511-517.
18. Kuhad, R. C., A. Singh, and K. E. Eriksson. 1997. Microorganisms and enzymes involved in the degradation of plant fiber cell walls. Adv. Biochem. Eng. Biotechnol. 57:45-125.
19. Lloyd, T. A., and C. E. Wyman. 2005. Combined sugar yield for dilute sulfuric acid pretreatment of corn stover followed by enzymatic hydrolysis of the remaining solids. Bioresour. Technol. 96:1967-1977.
20. Milner, Y., and G. Avigad. 1967. A copper reagent for the determination of hexuronic acids and certain ketohexoses. Carbohydr. Res. 4:359-361.
21. Nagy, T., K. Emami, C. M. Fontes, L. M. Ferreira, D. R. Humphry, and H. J. Gilbert. 2002. The membrane-bound α-glucuronidase from Pseudomonas cellulosa hydrolyzes 4-O-methyl-D-glucuronoxylooligosaccharides but not 4-O-methyl-D-glucuronoxylan. J. Bacteriol. 184:4925-4929.
22. Nelson, K. E., R. A. Clayton, S. R. Gill, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, W. C. Nelson, K. A. Ketchum, L. McDonald, T. R. Utterback, J. A. Malek, K. D. Linher, M. M. Garrett, A. M. Stewart, M. D. Cotton, M. S. Pratt, C. A. Phillips, D. Richardson, J. Heidelberg, G. G. Sutton, R. D. Fleischmann, O. White, S. L. Salzberg, H. O. Smith, J. C. Venter, and C. M. Fraser. 1999. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329. (Pubitemid 29318123)
23. Nelson, N. 1944. A photometric adaptation of the Somogyi method for the determination of glucose. J. Biol. Chem. 153:375-380.
24. Preston, J. F., J. C. Hurlbert, J. D. Rice, A. Ragunathan, and F. J. St. John. 2003. Microbial strategies for the depolymerization of glucuronoxylan: leads to biotechnological applications of endoxylanases, p. 191-210. In S. D. Mansfield and J. N. Sadler (ed.), Applications of enzymes to lignocellulosics. American Chemical Society, Washington, DC.
25. Puls, J., O. Schmidt, and C. Granzow. 1987. α-Glucuronidase in two microbial xylanolytic systems. Enzyme Microb. Technol. 9:83-88.
26. Rodriquez, M. E., A. Martinez, S. W. York, K. Zuobi-Hasona, L. O. Ingram, K. T. Shanmugam, and J. F. Preston. 2003. Properties of the hemicellulose fractions of lignocellulosic biomass affecting bacterial ethanol production, abstr. P-535. Abstr. 101st Gen. Meet. Am. Soc. Microbiol., Orlando, FL. American Society for Microbiology, Washington, DC.
27. Ruile, P., C. Winterhalter, and W. Liebl. 1997. Isolation and analysis of a gene encoding alpha-glucuronidase, an enzyme with a novel primary structure involved in the breakdown of xylan. Mol. Microbiol. 23:267-279.
28. Shanmugam, K. T., and L. O. Ingram. 2008. Engineering biocatalysts for production of commodity chemicals. J. Mol. Microbiol. Biotechnol. 15:8-15.
29. Shao, W., S. Obi, J. Puls, and J. Wiegel. 1995. Purification and characterization of the (alpha)-glucuronidase from Thermoanaerobacterium sp. strain JW/SL-YS485, an important enzyme for the utilization of substituted xylans. Appl. Environ. Microbiol. 61:1077-1081.
30. Shulami, S., O. Gat, A. L. Sonenshein, and Y. Shoham. 1999. The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6. J. Bacteriol. 181:3695-3704.
31. Shulami, S., G. Zaide, G. Zolotnitsky, Y. Langut, G. Feld, A. L. Sonenshein, and Y. Shoham. 2007. A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus. Appl. Environ. Microbiol. 73:874-884.
32. Smith, D. C., and C. W. Forsberg. 1991. α-Glucuronidase and other hemicellulase activities of Fibrobacter succinogenes S85 grown on crystalline cellulose or ball-milled barley straw. Appl. Environ. Microbiol. 57:3552-3557.
33. 1: a novel system for methylglucuronoxylan utilization. Appl. Environ. Microbiol. 72:1496-1506.
34. Sunna, A., and G. Antranikian. 1997. Xylanolytic enzymes from fungi and bacteria. Crit. Rev. Biotechnol. 17:39-67.
35. Takami, H., K. Nakasone, Y. Takaki, G. Maeno, R. Sasaki, N. Masui, F. Fuji, C. Hirama, Y. Nakamura, N. Ogasawara, S. Kuhara, and K. Horikoshi. 2000. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res. 28:4317-4331. (Pubitemid 30838225)
36. Zhou, S., and L. O. Ingram. 2001. Simultaneous saccharification and fermentation of amorphous cellulose to ethanol by recombinant Klebsiella oxytoca SZ21 without supplemental cellulase. Biotechnol. Lett. 23:1455-1462.
37. Zucker, M., and L. Hankin. 1970. Regulation of pectate lyase synthesis in Pseudomonas fluorescens and Erwinia carotovora. J. Bacteriol. 104:13-18.