Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40

Journal of Bacteriology

Volumn 185, Issue 11, 2003, Pages 3352-3360

  Howard, Michael B ^a   Ekborg, Nathan A ^a   Taylor, Larry E ^a   Weiner, Ronald M ^a,b   Hutcheson, Steven W ^a  

^a UNIVERSITY OF MARYLAND   (United States)

^b NATIONAL SCIENCE FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4 METHYLUMBELLIFERYL BETA DEXTRO N,N' DIACETYLCHITOBIOSIDE; 4 METHYLUMBELLIFERYL BETA DEXTRO N,N',N'' TRIACETYLCHITOTRIOSIDE; BACTERIAL ENZYME; CHITIN; CHITIN BINDING PROTEIN; CHITIN DEPOLYMERASE; CHITIN DERIVATIVE; CHITINASE; CHITODEXTRINASE; CYTOPLASM PROTEIN; GLUTAMIC ACID; GLYCOSIDASE; N ACETYL BETA GLUCOSAMINIDASE; N ACETYLGLUCOSAMINE; PROTEIN CHIA; PROTEIN CHIB; PROTEIN CHIC; UNCLASSIFIED DRUG;

AMINO ACID METABOLISM; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIOPLANKTON; CARBOHYDRATE METABOLISM; ENZYME ACTIVITY; ESCHERICHIA COLI K 12; GENE SEQUENCE; GENOME ANALYSIS; GRAM NEGATIVE BACTERIUM; KIDNEY POLYCYSTIC DISEASE; MICROBULBIFER DEGRADANS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE ANALYSIS;

ALTEROMONADACEAE; BACTERIAL PROTEINS; CHITIN; CHITINASE; CULTURE MEDIA, CONDITIONED; CYTOPLASM; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PERIPLASM; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); ESCHERICHIA; ESCHERICHIA COLI K12; MICROBULBIFER DEGRADANS; NEGIBACTERIA; PROKARYOTA; UNCULTURED MARINE BACTERIUM;

EID: 0038191046     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.11.3352-3360.2003     Document Type: Article

References (52)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Andrykovich, G., and I. Marx. 1988. Isolation of a new polysaccharide digesting bacterium from a salt marsh. Appl. Microbiol. Biotechnol. 54:1061-1062.
3. Bannai, H., Y. Tamada, O. Maruyama, K. Nakai, and S. Miyano. 2002. Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18:298-305.
4. Bassler, B., P. Gibbons, C. Yu, and S. Roseman. 1991. Chemotaxis to chitin oligosaccharides by Vibrio furnissii. J. Biol. Chem. 266:24268-24275.
5. Bateman, A. 1999. The SIS domain: a phosphosugar-binding domain. Trends Biochem. Sci. 24:94-95.
6. Bentley, S. D., K. F. Chater, A. M. Cerdeno-Tarraga, G. L. Challis, N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, et al. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147.
7. Black, G. W., J. E. Rixon, J. H. Clarke, G. P. Hazlewood, M. K. Theodorou, P. Morris, and H. J. Gilbert. 1996. Evidence that linker sequences and cellulose-binding domains enhance the activity of hemicellulases against complex substrates. Biochem. J. 319:515-520.
8. Brown, I. E., M. H. Mallen, S. J. Charnock, G. J. Davies, and G. W. Black. 2001. Pectate lyase 10A from Pseudomonas cellulosa is a modular enzyme containing a family 2a carbohydrate-binding module. Biochem. J. 355:155-165.
9. Connell, T., D. Metzger, J. Lynch, and J. Folster. 1998. Endochitinase is transported to the extracellular milieu by the eps-encoded general secretory pathway of Vibrio cholerae. J. Bacteriol. 180:5591-5600.
10. DelVecchio, V. G., V. Kapatral, R. J. Redkar, G. Patra, C. Mujer, T. Los, N. Ivanova, I. Anderson, A. Bhattacharyya, A. Lykidis, et al. 2002. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl. Acad. Sci. USA 99:443-448.
11. Ensor, L., S. Stosz, and R. Weiner. 1999. Expression of multiple complex polysaccharide-degrading enzyme systems by marine bacterium strain 2-40. J. Ind. Microbiol. Biotechnol. 21:123-126.
12. Folders, J., J. Algra, M. Roelofs, L. Loon, J. Tommassen, and W. Bitter. 2001. Characterization of Pseudomonas aeruginosa chitinase, a gradually secreted protein. J. Bacteriol. 183:7044-7052.
13. Gilkes, N. R., R. A. Warren, R. C. Miller, Jr., and D. G. Kilburn. 1988. Precise excision of the cellulose binding domains from two Cellulomonasfimi cellulases by a homologous protease and the effect on catalysis. J. Biol. Chem. 263:10401-10407.
14. Gonzalez, J., and R. Weiner. 2000. Phylogenetic characterization of a marine bacterium strain 2-40, a degrader of complex polysaccharides. Int. J. Syst. Bacteriol. 8:831-834.
15. Gooday, G. 1994. Physiology of microbial degradation of chitin and chitosan. p. 279-312. In C. Ratledge (ed.), Biochemistry of microbial degradation. Kluwer, Dordrecht, The Netherlands.
16. Hall, J., G. W. Black, L. M. Ferreira, S. J. Millward-Sadler, B. R. Ali, G. P. Hazlewood, and H. J. Gilbert. 1995. The non-catalytic cellulose-binding domain of a novel cellulase from Pseudomonas fluorescens subsp. cellulosa is important for the efficient hydrolysis of Avicel. Biochem. J. 309:749-756.
17. Hall, J., G. P. Hazlewood, N. S. Huskisson, A. J. Durrant, and H. J. Gilbert. 1989. Conserved serine-rich sequences in xylanase and cellulase from Pseudomonas fluorescens subspecies cellulosa: internal signal sequence and unusual protein processing. Mol. Microbiol. 3:1211-1219.
18. Heidelberg, J. F., J. A. Eisen, W. C. Nelson, R. A. Clayton, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, L. Umayam, et al. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477-483.
19. Henikoff, S., G. Haughn, J. Calvo, and J. Wallace. 1988. A large family of bacterial activator proteins. Proc. Natl. Acad. Sci. USA 85:6602-6606.
20. Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266:383-402.
21. Keyhani, N., X. Li, and S. Roseman. 2000. Identification and molecular cloning of a chitoporin. J. Biol. Chem. 275:33068-33076.
22. Keyhani, N., and S. Roseman. 1996. The chitin catabolic cascade in the marine bacterium Vibrio furnissii. Molecular cloning, isolation, and characterization of a periplasmic chitodextrinase. J. Biol. Chem. 271:33414-33424.
23. Keyhani, N., and S. Roseman. 1996. The chitin catabolic cascade in the marine bacterium Vibrio furnissii. Molecular cloning, isolation, and characterization of a periplasmic beta-N-acetylglucosaminidase. J. Biol. Chem. 271:33425-33432.
24. Keyhani, N., L. Wang, Y. Lee, and S. Roseman. 1996. Characterization of an N,N′-diacetylchitobiose transport system. J. Biol. Chem. 271:33409-33413.
25. Keyhani, N., L. Wang, Y. Lee, and S. Roseman. 2000. The chitin disaccharide, N,N′-diacetylchitobiose, is catabolized by E. coli and is transported/phosphorylated by the phosphoenolpyruvate:glycose phosphotransferase system. J. Biol. Chem. 275:33084-33090.
26. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
27. Letunic, I., L. Goodstadt, N. J. Dickens, T. Doerks, J. Schultz, R. Mott, F. Ciccarelli, R. R. Copley, C. P. Ponting, and P. Bork. 2002. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30:242-244.
28. Matsuo, Y., M. Kurita, J. K. Park, K. Tanaka, T. Nakagawa, M. Kawamukai, and H. Matsuda. 1999. Purification, characterization and gene analysis of N-acetylglucosaminidase from Enterobacter sp. G-1. Biosci. Biotechnol. Biochem. 63:1261-1268.
29. McClelland, M., K. E. Sanderson, J. Spieth, S. W. Clifton, P. Latreille, L. Courtney, S. Porwollik, J. Ali, M. Dante, F. Du, S. Hou, et al. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-856.
30. Muzzarelli, R. 1999. Native, industrial, and fossil chitins, p. 1-5. In R. A. Muzzarelli and P. Jooaes (ed.), Chitin and chitinases. Birkhauser, Basel, Switzerland.
31. Nielsen, H., J. Englebrecht, S. Brunak, and G. von Heijne. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
32. Nierman, W. C., T. V. Feldblyum, M. T. Laub, I. T. Paulsen, K. E. Nelson, J. A. Eisen, J. F. Heidelberg, M. R. Alley, N. Ohta, J. R. Maddock, et al. 2001. Complete genome sequence of Caulobacter crescentus. Proc. Natl. Acad. Sci. USA 98:4136-4141.
33. Peri, K. G., H. Goldie, and E. B. Waygood. 1990. Cloning and characterization of the N-acetylglucosamine operon of Escherichia coli. Biochem. Cell Biol. 68:123-137.
34. Plumbridge, J. 2001. Regulation of PTS gene expression by the homologous transcriptional regulators, Mlc and NagC, in Escherichia coli (or how two similar repressors can behave differently). J. Mol. Microbiol. Biotechnol. 3:371-380.
35. Plumbridge, J., and A. Kolb. 1991. CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli. J. Mol. Biol. 217:661-679.
36. Plumbridge, J. A. 1989. Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon. Mol. Microbiol. 3:505-515.
37. Riemann, L., and F. Azam. 2002. Widespread N-acetyl-D-glucosamine uptake among pelagic marine bacteria and its ecological implications. Appl. Environ. Microbiol. 68:5554-5562.
38. Sambrook, J., and D. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
39. Schultz, J., R. R. Copley, T. Doerks, C. P. Ponting, and P. Bork. 2000. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28:231-234.
40. Shen, H., M. Schmuck, I. Pilz, N. R. Gilkes, D. G. Kilburn, R. C. Miller, Jr., and R. A. Warren. 1991. Deletion of the linker connecting the catalytic and cellulose-binding domains of endoglucanase A (CenA) of Cellulomonas fimi alters its conformation and catalytic activity. J. Biol. Chem. 266:11335-11340.
41. Simpson, A. J., F. C. Reinach, P. Arruda, F. A. Abreu, M. Acencio, R. Alvarenga, L. M. Alves, J. E. Araya, G. S. Baia, C. S. Baptista, M. H. Barros, E. D. Bonaccorsi, S. Bordin, J. M. Bove, et al. 2000. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406:151-157.
42. Somerville, C. C., and R. R. Colwell. 1993. Sequence analysis of the beta-N-acetylhexosaminidase gene of Vibrio vulnificus: evidence for a common evolutionary origin of hexosaminidases. Proc. Natl. Acad. Sci. USA 90:6751-6755.
43. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. Brinkman, W. O. Hufnagle, D. J. Kowalik, M. Lagrou, et al. 2000. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959-964.
44. Techkarnjanaruk, S., and A. Goodman. 1999. Multiple genes involved in chitin degradation from the marine bacterium Pseudoaltermonas sp. strain S91. Microbiology 145:925-934.
45. Trudel, J., and A. Asselin. 1990. Detection of chitin deacetylase activity after polyacrylamide gel electrophoresis. Anal. Biochem. 189:249-253.
46. Tsujibo, H., H. Orikoshi, K. Shiotani, M. Hayashi, J. Umeda, K. Miyamoto, C. Imada, Y. Okami, and Y. Inamori. 1998. Characterization of chitinase C from a marine bacterium, Alteromonas sp. strain O-7, and its corresponding gene and domain structure. Appl. Environ. Microbiol. 64:472-478.
47. Tsujibo, H., H. Orikoshi, N. Baba, M. Miyahara, K. Miyamoto, M. Yasuda, and Y. Inamori. 2002. Identification and characterization of the gene cluster involved in chitin degradation in a marine bacterium, Alteromonas sp. strain O-7. Appl. Environ. Microbiol. 68:263-270.
48. Vetrivel, K. S., S. K. Pandian, U. Chaudhary, and K. Dharmalingam. 2001. Purification, cloning, and DNA sequence analysis of a chitinase from an overproducing mutant of Streptomyces peucetius defective in daunorubicin biosynthesis. Can. J. Microbiol. 47:179-187.
49. Wang, L., N. Keyhani, S. Roseman, and Y. Lee. 1997. 4-Methylumbelliferyl glycosides of N-acetyl 4-thiochito-oligosaccharides as fluorogenic substrates for chitodextrinase from Vibrio furnissii. Glycobiology 7:855-860.
50. Watanabe, T., K. Kimura, T. Sumiya, N. Nikaidou, K. Suzuki, M. Suzuki, M. Taiyoji, S. Ferrer, and M. Regue. 1997. Genetic analysis of the chitinase system of Serratia marcescens 2170. J. Bacteriol. 179:7111-7117.
51. Weiner, R., L. Taylor, N. Ekborg, and L. Whitehead. 2001. Degradosomes: potential importance in the ocean's carbon cycle and in aquaculture and algal culture, p. 259-268. In N. Seaxena (ed.), Recent advances in marine science and technology, 2000. Pacon International, New York, N.Y.
52. Zobell, C., and S. Rittenberg. 1937. The occurrence and characteristics of chitinoclastic bacteria in the sea. J. Bacteriol. 35:275-287.