The L-arabinan utilization system of Geobacillus stearothermophilus

Journal of Bacteriology

Volumn 193, Issue 11, 2011, Pages 2838-2850

  Shulami, Smadar ^a   Raz Pasteur, Ayelet ^b   Tabachnikov, Orly ^a   Gilead Gropper, Sarah ^a   Shner, Itzhak ^a   Shoham, Yuval ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b RAMBAM MEDICAL CENTER   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ABNE PROTEIN; ABNEFJ PROTEIN; ALPHA ARABINOFURANOSIDASE; ARABINAN; ARABINASE; ARABINOSE; ARAP PROTEIN; ARAS PROTEIN; BACTERIAL PROTEIN; BETA LEVO ARABINOPYRANOSIDASE; CARBOHYDRATE BINDING PROTEIN; GLUCOSE; GLYCOSIDASE; LIPOPROTEIN; OLIGOSACCHARIDE; POLYSACCHARIDE; UNCLASSIFIED DRUG; XYLOSE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; BIODEGRADATION; CATABOLISM; CELL WALL; CONTROLLED STUDY; EXTRACELLULAR SPACE; GEL MOBILITY SHIFT ASSAY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE REPRESSION; GEOBACILLUS STEAROTHERMOPHILUS; INTRACELLULAR SPACE; MOLECULAR MECHANICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN MOTIF; SOIL MICROFLORA; THERMOPHILE;

ARABINOSE; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; GENE ORDER; GEOBACILLUS STEAROTHERMOPHILUS; GLUCOSE; MEMBRANE TRANSPORT PROTEINS; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; POLYSACCHARIDES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS;

EID: 79958097056     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00222-11     Document Type: Article

References (80)

1. Abo-Amer, A. E., et al. 2004. DNA interaction and phosphotransfer of the C4-dicarboxylate-responsive DcuS-DcuR two-component regulatory system from Escherichia coli. J. Bacteriol. 186:1879-1889.
2. Abramovich-Naveh, E. 2007. Structure-function studies on arabinases from Geobacillus stearothermophilus. Ph.D. thesis. Technion-Israel nstitute of Technology, Haifa, Israel.
3. Alhassid, A., et al. 2009. Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with ts substrate. Biochem. J. 422:73-82.
4. Alper, H., and G. Stephanopoulos. 2009. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential. Nat. Rev. icrobiol. 7:715-723.
5. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
6. Anantharaman, V., and L. Aravind. 2000. CaChe-a signaling domain common to animal Ca(2)-channel subunits and a class of prokaryotic hemotaxis receptors. Trends Biochem. Sci. 25:535-537.
7. Baraquet, C., et al. 2006. TorT, a member of a new periplasmic binding protein family, triggers induction of the Tor respiratory system upon trimethylamine N-oxide electron-acceptor binding in Escherichia coli. J. Biol. Chem. 281:38189-38199.
8. Barnard, A., A. Wolfe, and S. Busby. 2004. Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce ifferent regulatory outcomes. Curr. Opin. Microbiol. 7:102-108.
9. Bayer, E. A., J. P. Belaich, Y. Shoham, and R. Lamed. 2004. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu. Rev. Microbiol. 58:521-554.
10. Blanco, A. G., M. Sola, F. X. Gomis-Ruth, and M. Coll. 2002. Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator. Structure 10:701-713.
11. Bordi, C., et al. 2004. Genes regulated by TorR, the trimethylamine oxide response regulator of Shewanella oneidensis. J. Bacteriol. 186:4502-509.
12. Bravman, T., et al. 2003. Detailed kinetic analysis of a family 52 glycoside hydrolase: a beta-xylosidase from Geobacillus stearothermophilus. iochemistry 42:10528-10536.
13. Brüx, C., et al. 2006. The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role f the three catalytic residues. J. Mol. Biol. 359:97-109.
14. Czjzek, M., et al. 2005. Enzyme-substrate complex structures of a GH39 beta-xylosidase from Geobacillus stearothermophilus. J. Mol. Biol. 53:838-846.
15. Dassa, E., and P. Bouige. 2001. The ABC of ABCS: a phylogenetic and functional classification of ABC systems in living organisms. Res. Microbiol. 52:211-229.
16. Demain, A. L., M. Newcomb, and J. H. Wu. 2005. Cellulase, clostridia, and ethanol. Microbiol. Mol. Biol. Rev. 69:124-154.
17. de Vries, R. P., and J. Visser. 2001. Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiol. Mol. Biol. Rev. 5:497-522.
18. Doner, L. W., and P. L. Irwin. 1992. Assay of reducing end-groups in oligosaccharide homologues with 2,2'-bicinchoninate. Anal. Biochem. 202:50-3.
19. Eitinger, T., D. A. Rodionov, M. Grote, and E. Schneider. 2011. Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol. Rev. 35:3-67.
20. Faergeman, N. J., B. W. Sigurskjold, B. B. Kragelund, K. V. Andersen, and J. Knudsen. 1996. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry. Biochemistry 35:14118-14126.
21. Farrell, A. E., et al. 2006. Ethanol can contribute to energy and environmental goals. Science 311:506-508.
22. Ferreira, M. J., and I. de Sa-Nogueíra. 2010. A multitask ATPase serving different ABC-type sugar importers in Bacillus subtilis. J. Bacteriol. 92: 5312-5318.
23. Fontes, C. M., and H. J. Gilbert. 2010. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. nnu. Rev. Biochem. 79:655-681.
24. Foussard, M., et al. 2001. The molecular puzzle of two-component signaling cascades. Microbes Infect. 3:417-424.
25. Galazka, J. M., et al. 2010. Cellodextrin transport in yeast for improved biofuel production. Science 330:84-86.
26. Gallegos, M. T., R. Schleif, A. Bairoch, K. Hofmann, and J. L. Ramos. 1997. Arac/XylS family of transcriptional regulators. Microbiol. Mol. Biol. ev. 61:393-410.
27. Gat, O., A. Lapidot, I. Alchanati, C. Regueros, and Y. Shoham. 1994. Cloning and DNA sequence of the gene coding for Bacillus stearothermophilus T-6 xylanase. Appl. Environ. Microbiol. 60:1889-1896.
28. Gilbert, H. J. 2010. The biochemistry and structural biology of plant cell wall deconstruction. Plant Physiol. 153:444-455.
29. Gilson, E., et al. 1988. Evidence for high affinity binding-protein dependent transport systems in gram-positive bacteria and in Mycoplasma. EMBO. 7:3971-3974.
30. Gírio, F. M., et al. 2010. Hemicelluloses for fuel ethanol: a review. Bioresour. Technol. 101:4775-4800.
31. Helmann, J. D. 1995. Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res. 23: 2351-2360.
32. Higgins, C. F., et al. 1990. Binding protein-dependent transport systems. J. Bioenerg. Biomembr. 22:571-592.
33. Hövel, K., et al. 2003. Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J. 22:4922-932.
34. Ichinose, H., et al. 2009. A beta-l-arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27. J. Biol. hem. 284:25097-25106.
35. Inácio, J. M., I. L. Correia, and I. de Sa-Nogueíra. 2008. Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in acillus subtilis. Microbiology 154:2719-2729.
36. Inácio, J. M., and I. de Sa-Nogueíra. 2008. Characterization of abn2 (yxiA), encoding a Bacillus subtilis GH43 arabinanase, Abn2, and its role in arabinopolysaccharide degradation. J. Bacteriol. 190:4272-4280.
37. Jarmer, H., et al. 2001. Sigma A recognition sites in the Bacillus subtilis genome. Microbiology 147:2417-2424.
38. Johnson, J. L. 1981. Genetic characterization, p. 450-472. In P. Gerhardt, R. G. E. Murray, E. W. Costilow, W. A. Nester, N. R. Wood, R. Krieg, and G. B. Philips (ed.), Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC.
39. Khasin, A., I. Alchanati, and Y. Shoham. 1993. Purification and characterization of a thermostable xylanase from Bacillus stearothermophilus T-. Appl. Environ. Microbiol. 59:1725-1730.
40. Kumar, R., S. Singh, and O. V. Singh. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J. Ind. Microbiol. iotechnol. 35:377-391.
41. Langut, Y. 2006. Characterization of XylR, the repressor of the xylanolytic system in Geobacillus stearothermophilus. M.S. thesis. Technion-Israel nstitute of Technology, Haifa, Israel.
42. Li, M., et al. 2007. Gram-positive three-component antimicrobial peptidesensing system. Proc. Natl. Acad. Sci. U. S. A. 104:9469-9474.
43. Margulies, M., et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376-380.
44. Marmur, J. 1961. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J. Mol. Biol. 3:208-218.
45. Miwa, Y., et al. 1997. Catabolite repression of the Bacillus subtilis gnt operon exerted by two catabolite-responsive elements. Mol. Microbiol. 23:1203-1213.
46. Mohnen, D. 2008. Pectin structure and biosynthesis. Curr. Opin. Plant Biol. 11:266-277.
47. Moran, C. P. 1990. Measuring gene expression in Bacillus, p. 267-293. In C. R. Harwood and S. M. Cutting (ed.), Molecular biological methods for acillus. John Wiley & Sons, Chichester, United Kingdom.
48. Moran, C. P., Jr., et al. 1982. Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis. Mol. Gen. Genet. 86: 339-346.
49. Mota, L. J., L. M. Sarmento, and I. de Sa-Nogueíra. 2001. Control of the arabinose regulon in Bacillus subtilis by AraR in vivo: crucial roles of operators, cooperativity, and DNA looping. J. Bacteriol. 183:4190-4201.
50. Nagy, T., et al. 2002. The membrane-bound alpha-glucuronidase from Pseudomonas cellulosa hydrolyzes 4-O-methyl-D-glucuronoxylooligosaccharides but not 4-O-methyl-D-glucuronoxylan. J. Bacteriol. 184:4925-4929.
51. Nataf, Y., et al. 2010. Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma actors. Proc. Natl. Acad. Sci. U. S. A. 107:18646-18651.
52. Nataf, Y., et al. 2009. Cellodextrin and laminaribiose ABC transporters in Clostridium thermocellum. J. Bacteriol. 191:203-209.
53. Ouyang, J., M. Yan, D. Kong, and L. Xu. 2006. A complete protein pattern of cellulase and hemicellulase genes in the filamentous fungus richoderma reesei. Biotechnol. J. 1:1266-1274.
54. Pearson, W. R., and D. J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U. S. A. 85:2444-2448.
55. Ragauskas, A. J., et al. 2006. The path forward for biofuels and biomaterials. Science 311:484-489.
56. Ren, N., A. Wang, G. Cao, J. Xu, and L. Gao. 2009. Bioconversion of lignocellulosic biomass to hydrogen: potential and challenges. Biotechnol. Adv. 7:1051-1060.
57. Rhodius, V. A., and S. J. Busby. 1998. Positive activation of gene expression. Curr. Opin. Microbiol. 1:152-159.
58. Robinson, V. L., D. R. Buckler, and A. M. Stock. 2000. A tale of two components: a novel kinase and a regulatory switch. Nat. Struct. Biol. 7:626-33.
59. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, Y.
60. Scheller, H. V., and P. Ulvskov. 2010. Hemicelluloses. Annu. Rev. Plant Biol. 61:263-289.
61. Schneider, E. 2001. ABC transporters catalyzing carbohydrate uptake. Res. Microbiol. 152:303-310.
62. Shallom, D., et al. 2002. Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase. J. Biol. Chem. 277:43667-43673.
63. Shallom, D., et al. 2005. Biochemical characterization and identification of the catalytic residues of a family 43 beta-D-xylosidase from Geobacillus tearothermophilus T-6. Biochemistry 44:387-397.
64. Shallom, D., and Y. Shoham. 2003. Microbial hemicellulases. Curr. Opin. Microbiol. 6:219-228.
65. Shoham, Y., R. Lamed, and E. A. Bayer. 1999. The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides. Trends Microbiol. 7:275-281.
66. Shoham, Y., et al. 1992. Delignification of wood pulp by a thermostable xylanase. Biodegradation 3:161-170.
67. Shulami, S., O. Gat, A. L. Sonenshein, and Y. Shoham. 1999. The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6. Bacteriol. 181:3695-3704.
68. Shulami, S., et al. 2007. A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus. Appl. Environ. Microbiol. 73:874-884.
69. Taylor, L. E., II, et al. 2006. Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T. J. Bacteriol. 88:3849-3861.
70. Tian, Y., et al. 2007. Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein. Protein ci. 16:2240-2250.
71. Timmerman, K. P., and C. P. Tu. 1985. Complete sequence of IS3. Nucleic Acids Res. 13:2127-2139.
72. Tsujibo, H., et al. 2004. Molecular characterization of a high-affinity xylobiose transporter of Streptomyces thermoviolaceus OPC-520 and its ranscriptional regulation. J. Bacteriol. 186:1029-1037.
73. van der Heide, T., and B. Poolman. 2002. ABC transporters: one, two or four extracytoplasmic substrate-binding sites? EMBO Rep. 3:938-943.
74. Volz, K. 1993. Structural conservation in the CheY superfamily. Biochemistry 32:11741-11753.
75. von Heijne, G. 1989. The structure of signal peptides from bacterial lipoproteins. Protein Eng. 2:531-534.
76. Warnecke, F., et al. 2007. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560-565.
77. Watanabe, S., T. Kodaki, and K. Makino. 2006. Cloning, expression, and characterization of bacterial L-arabinose 1-dehydrogenase involved in an alternative pathway of L-arabinose metabolism. J. Biol. Chem. 281:2612-2623.
78. Wiseman, T., S. Williston, J. F. Brandts, and L. N. Lin. 1989. Rapid measurement of binding constants and heats of binding using a new titration alorimeter. Anal. Biochem. 179:131-137.
79. Yu, H., et al. 2007. Microbial community succession and lignocellulose degradation during agricultural waste composting. Biodegradation 18:793-802.
80. Zaide, G., et al. 2001. Biochemical characterization and identification of catalytic residues in alpha-glucuronidase from Bacillus stearothermophilus -6. Eur. J. Biochem. 268:3006-3016.