1887

Abstract

Selected butyrate-producing bacteria from the human colon that are related to spp. and showed a good ability to utilize a variety of starches for growth when compared with the Gram-negative amylolytic anaerobe . A major cell-associated amylase of high molecular mass (140–210 kDa) was detected in each strain by SDS-PAGE zymogram analysis, and genes corresponding to these enzymes were analysed for two representative strains. Amy13B from 16/4 is a multi-domain enzyme of 144.6 kDa that includes a family 13 glycoside hydrolase domain, and duplicated family 26 carbohydrate-binding modules. Amy13A (182.4 kDa), from A2-194, also includes a family 13 domain, which is preceded by two repeat units of ∼116 aa rich in aromatic residues, an isoamylase N-terminal domain, a pullulanase-associated domain, and an additional unidentified domain. Both Amy13A and Amy13B have N-terminal signal peptides and C-terminal cell-wall sorting signals, including a modified LPXTG motif similar to that involved in interactions with the cell surface in other Gram-positive bacteria, a hydrophobic transmembrane segment, and a basic C terminus. The overexpressed family 13 domains showed an absolute requirement for Mg or Ca for activity, and functioned as 1,4--glucanohydrolases (-amylases; EC 3.2.1.1). These major starch-degrading enzymes thus appear to be anchored to the cell wall in this important group of human gut bacteria.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.29233-0
2006-11-01
2020-10-22
Loading full text...

Full text loading...

/deliver/fulltext/micro/152/11/3281.html?itemId=/content/journal/micro/10.1099/mic.0.29233-0&mimeType=html&fmt=ahah

References

  1. Abrams S. A, Griffin I. J, Hawthorne K. M, Liang L, Gunn S. K, Darlington G, Ellis K. J. 2005; A combination of prebiotic short- and long-chain inulin-type fructans enhances calcium absorption and bone mineralization in young adolescents. Am J Clin Nutr82:471–476
    [Google Scholar]
  2. Anderson K. L, Salyers A. A. 1989; Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J Bacteriol171:3192–3198
    [Google Scholar]
  3. Archer S. Y, Meng S. F, Sheh A, Hodin R. A. 1998; p21(WAF1) is required for butyrate mediated growth inhibition of human colon cancer cells. Proc Natl Acad Sci U S A95:6791–6796[CrossRef]
    [Google Scholar]
  4. Barcenilla A, Pryde S. E, Martin J. C, Duncan S. H, Stewart C. S, Flint H. J. 2000; Phylogenetic relationships of dominant butyrate producing bacteria from the human gut. Appl Environ Microbiol66:1654–1661[CrossRef]
    [Google Scholar]
  5. Bendtsen J. D, Nielsen H, Brunak S, von Heijne G. 2004; Improved prediction of signal peptides: SignalP 3.0. J Mol Biol340:783–795[CrossRef]
    [Google Scholar]
  6. Boraston A. B, Bolam D. N, Gilbert H. J, Davies G. J. 2004; Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J382:769–781[CrossRef]
    [Google Scholar]
  7. Boraston A. B, Healey M, Klassen J, Ficko-Blean E, Law V, van Bueren A. L. 2006; A structural and functional analysis of α -glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. J Biol Chem281:587–598[CrossRef]
    [Google Scholar]
  8. Cho H. Y, Kim Y. W, Kim T. J, Lee H. S, Kim D. Y, Kim J. W, Lee Y. W, Leed S, Park K. H. 2000; Molecular characterization of a dimeric intracellular maltogenic amylase of Bacillus subtilis SUH4-2. Biochim Biophys Acta1478:333–340[CrossRef]
    [Google Scholar]
  9. Cho K. H, Cho D, Wang G.-R, Salyers A. A. 2001; New regulatory gene that contributes to control of Bacteroides thetaiotaomicron starch utilization genes. J Bacteriol183:7198–7205[CrossRef]
    [Google Scholar]
  10. D'Elia J. N, Salyers A. A. 1996; Contribution of a neopullulanase, a pullulanase, and an α -glucosidase to growth of Bacteroides thetaiotaomicron on starch. J Bacteriol178:7173–7179
    [Google Scholar]
  11. Devereux J, Haeberli P, Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res12:386–395
    [Google Scholar]
  12. Ding S. Y, Rincon M. T, Lamed R, Martin J. C, McCrae S. I, Aurilia V, Shoham Y, Bayer E. A, Flint H. J. 2001; Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens . J Bacteriol183:1945–1953[CrossRef]
    [Google Scholar]
  13. Duncan S. H, Hold G. L, Barcenilla A, Stewart C. S, Flint H. J. 2002; Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int J Syst Evol Microbiol52:1615–1620[CrossRef]
    [Google Scholar]
  14. Duncan S. H, Scott K. P, Ramsay A. G, Harmsen H. J, Welling G. W, Stewart C. S, Flint H. J. 2003; Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system. Appl Environ Microbiol69:1136–1142[CrossRef]
    [Google Scholar]
  15. Duncan S. H, Aminov R. I, Scott K. P, Louis P, Stanton T. B, Flint H. J. 2006; Proposal of Roseburia faecis sp.nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces. Int J Syst Evol Microbiol56:2437–2441[CrossRef]
    [Google Scholar]
  16. Eckburg P. B, Bik E. M, Bernstein C. N, Purdom E, Dethlefsen L, Sargent M, Gill S. R, Nelson K. E, Relman D. A. 2005; Diversity of the human intestinal microbial flora. Science308:1635–1638[CrossRef]
    [Google Scholar]
  17. Englyst H. N, Kingman S. M, Cummings J. H. 1992; Classification and measurement of nutritionally important starch fractions. Eur J Clin Nutr46:S33–S50
    [Google Scholar]
  18. Erra-Pujada M, Debeire P, Duchiron F, O'Donohue M. J. 1999; The type II pullulanase of Thermococcus hydrothermalis : molecular characterisation of the gene and expression of the catalytic domain. J Bacteriol181:3284–3287
    [Google Scholar]
  19. Flint H. J, McPherson C. A, Martin J. 1991; Expression of two xylanase genes from the rumen cellulolytic bacterium Ruminococcus flavefaciens 17 cloned in pUC13. J Gen Microbiol137:123–129[CrossRef]
    [Google Scholar]
  20. Franks A. H, Harmsen H. J, Raangs G. C, Jansen G. J, Schut F, Welling G. W. 1998; Variations of bacterial populations in human faeces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol64:3336–3345
    [Google Scholar]
  21. Giraud E, Cuny G. 1997; Molecular characterization of the α -amylase genes of Lactobacillus plantarum A6 and Lactobacillus amylovorus reveals an unusual 3′-end structure with direct tandem repeats and suggests a common evolutionary origin. Gene198:149–157[CrossRef]
    [Google Scholar]
  22. Hogg D, Pell G, Dupree P, Goubet F, Martin-Orue S. M, Armand S, Gilbert H. J. 2003; The modular architecture of Cellvibrio japonicus mannanases in glycoside hydrolase families 5 and 26 points to differences in their role in mannan degradation. Biochem J371:1027–1043[CrossRef]
    [Google Scholar]
  23. Hold G. L, Pryde S. E, Russell V. J, Furrie E, Flint H. J. 2002; Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol39:33–39[CrossRef]
    [Google Scholar]
  24. Jenkins D. J, Vuksan V, Kendall C. W.7 other authors 1998; Physiological effects of resistant starches on fecal bulk, short chain fatty acids, blood lipids and glycemic index. J Am Coll Nutr17:609–616[CrossRef]
    [Google Scholar]
  25. Kumar S, Tamura K, Nei M. 2004; mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform5:150–163[CrossRef]
    [Google Scholar]
  26. Le Blay G, Michel C, Blottiere H. M, Cherbut C. 1999; Enhancement of butyrate production in the rat caecocolonic tract by long-term ingestion of resistant potato starch. Brit J Nutr82:419–426
    [Google Scholar]
  27. Lever M. 1977; Carbohydrate determination with 4-hydroxybenzoic acid hydrazide (PAHBAH): effect of bismuth on the reaction. Anal Biochem81:21–27[CrossRef]
    [Google Scholar]
  28. Macfarlane G. T, Englyst H. N. 1986; Starch utilization by the human large intestinal microflora. J Appl Bacteriol60:195–201[CrossRef]
    [Google Scholar]
  29. MacGregor E. A, Janeck S, Svensson B. 2001; Relationship of sequence and structure to specificity in the α -amylase family of enzymes. Biochim Biophys Acta 1546;1–20[CrossRef]
    [Google Scholar]
  30. Marraffini L. A, Ton-That H, Zong Y, Naravana S. V, Schneewind O. 2004; Anchoring of surface proteins to the cell wall of Staphylococcus aureus . A conserved arginine residue is required for efficient catalysis of sortase A. J Biol Chem279:37763–37770[CrossRef]
    [Google Scholar]
  31. Mathupala S, Saha B. C, Zeikus J. G. 1990; Substrate competition and specificity at the active site of amylopullulanase from Clostridium thermohydrosulfuricum . Biochem Biophys Res Commun166:126–132[CrossRef]
    [Google Scholar]
  32. McIntyre A, Gibson P. R, Young G. P. 1993; Butyrate production from dietary fiber and protection against large bowel cancer in a rat model. Gut34:386–391[CrossRef]
    [Google Scholar]
  33. Miyazaki K, Martin J. C, Marinsek-Logar R, Flint H. J. 1997; Degradation and utilization of xylans by the rumen anaerobe Prevotella bryantii (formerly P. ruminicola subsp. brevis) B[sub]1[/sub]4. Anaerobe3:373–381[CrossRef]
    [Google Scholar]
  34. Navarre W. W, Schneewind O. 1999; Surface proteins of Gram-positive bacteria and mechanisms of their targeting to the cell wall envelope. Microbiol Mol Biol Rev63:174–229
    [Google Scholar]
  35. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. 1997; Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng10:1–6[CrossRef]
    [Google Scholar]
  36. Pallen M. J, Lam A. C, Antonio M, Dunbar K. 2001; An embarrassment of sortases – a richness of substrates?. Trends Microbiol9:97–101[CrossRef]
    [Google Scholar]
  37. Reeves A. R, Wang G.-R, Salyers A. A. 1997; Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron . J Bacteriol179:643–649
    [Google Scholar]
  38. Rodriguez S. R, Morlon-Guyot J, Jore J, Pintado J, Juge N, Guyot J. P. 2000; Comparative characterization of complete and truncated forms of Lactobacillus amylovorus alpha-amylase and role of the C-terminal direct repeats in raw-starch binding. Appl Environ Microbiol66:3350–3356[CrossRef]
    [Google Scholar]
  39. Rumbak E, Rawlings D. E, Lindsey G. G, Woods D. R. 1991; Cloning, nucleotide sequence, and enzymatic characterization of an α-amylase from the ruminal bacterium Butyrivibrio fibrisolvens H17c. J Bacteriol173:4203–4211
    [Google Scholar]
  40. Rumney C. J, Duncan S. H, Henderson C, Stewart C. S. 1995; Isolation and characteristics of a wheatbran-degrading Butyrivibrio from human faeces. Lett Appl Microbiol20:232–236[CrossRef]
    [Google Scholar]
  41. Sambrook J, Fritsch E. F, Maniatis T. 1989; Molecular Cloning: a Laboratory Manual, 2nd edn.. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  42. Sara M, Egelseer E. M, Dekitsch C, Sleytr U. B. 1998; Identification of two binding domains, one for peptidoglycan and another for a secondary cell wall polymer, on the N-terminal part of the S-layer protein SbsB from Bacillus stearothermophilus PV72/p2. J Bacteriol180:6780–6783
    [Google Scholar]
  43. Satoh E, Uchimura T, Kudo T, Komagata K. 1997; Purification, characterization, and nucleotide sequence of an intracellular maltotriose-producing α-amylase from Streptococcus bovis 148. Appl Environ Microbiol63:4941–4944
    [Google Scholar]
  44. Saul D. J, Williams L. C, Love D. R, Chamley L. W, Bergquist P. L. 1989; Nucleotide sequencing of a gene from Caldocellum saccharolyticum encoding for an exocellulase and endocellulase activity. Nucleic Acids Res17:439–444[CrossRef]
    [Google Scholar]
  45. Schwiertz A, Lehmann U, Jacobasch G, Blaut M. 2002; Influence of resistant starch on the SCFA production and cell counts of butyrate-producing Eubacterium spp. in the human intestine. J Appl Microbiol93:157–162[CrossRef]
    [Google Scholar]
  46. Shipman J. A, Cho K. H, Siegel H. A, Salyers A. A. 1999; Physiological characterization of SusG, an outer membrane protein essential for starch utilization by Bacteroides thetaiotaomicron . J Bacteriol181:7206–7211
    [Google Scholar]
  47. Silvi S, Rumney C. J, Cresci A, Rowland I. R. 1999; Resistant starch modifies gut microflora and microbial metabolism in human flora-associated rats inoculated with faeces from Italian and UK donors. J Appl Microbiol86:521–530[CrossRef]
    [Google Scholar]
  48. Suau A, Bonnet R, Sutren M, Godon J.-J, Gibson G. R, Collins M. D, Doré J. 1999; Direct analysis of genes encoding 16S rRNA from complex communities reveals many molecular species within the human gut. Appl Environ Microbiol65:4799–4807
    [Google Scholar]
  49. Thompson J. D, Gibson T. J, Plewniak F, Jeanmougin F, Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res25:4876–4882[CrossRef]
    [Google Scholar]
  50. Ton-That H, Marraffini L. A, Schneewind O. 2004; Protein sorting to the cell wall envelope of Gram-positive bacteria. Biochim Biophys Acta 1694;269–278[CrossRef]
    [Google Scholar]
  51. van Munster I. P, Tangerman A, Nagengast F. M. 1994; Effect of resistant starch on colonic fermentation, bile acid metabolism, and mucosal proliferation. Dig Dis Sci39:834–842[CrossRef]
    [Google Scholar]
  52. Wachtershauser A, Stein J. 2000; Rationale for the luminal provision of butyrate in intestinal disease. Eur J Nutr39:164–171[CrossRef]
    [Google Scholar]
  53. Walker A. W, Duncan S. H, McWilliam Leitch E. C, Child M. W, Flint H. J. 2005; pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microbiol71:3692–3700[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.29233-0
Loading
/content/journal/micro/10.1099/mic.0.29233-0
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error