Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1

PLoS ONE

Volumn 5, Issue 8, 2010, Pages

  Rincon, Marco T ^a   Dassa, Bareket ^b   Flint, Harry J ^a   Travis, Anthony J ^a   Jindou, Sadanari ^c   Borovok, Ilya ^c   Lamed, Raphael ^c   Bayer, Edward A ^b   Henrissat, Bernard ^d   Coutinho, Pedro M ^d   Antonopoulos, Dion A ^e   Miller, Margret E Berg ^e   White, Bryan A ^e  

^a ROWETT RESEARCH INSTITUTE   (United Kingdom)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^c TEL AVIV UNIVERSITY   (Israel)

^d AIX MARSEILLE UNIVERSITY   (France)

^e UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CELLULOSOME; COHESIN; DOCKERIN; PEPTIDASE; SCAFFOLD PROTEIN; UNCLASSIFIED DRUG; CELL CYCLE PROTEIN; COHESINS; NONHISTONE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BIOINFORMATICS; CALCIUM BINDING; CARBOHYDRATE ANALYSIS; COMPLEX FORMATION; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DNA FLANKING REGION; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; RUMINOCOCCUS FLAVEFACIENS; CARBOHYDRATE METABOLISM; CHEMISTRY; CLASSIFICATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; RUMINOCOCCUS;

BACTERIA (MICROORGANISMS); RUMINOCOCCUS FLAVEFACIENS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CARBOHYDRATE METABOLISM; CELL CYCLE PROTEINS; CHROMOSOMAL PROTEINS, NON-HISTONE; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; RUMINOCOCCUS;

EID: 77957935787     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012476     Document Type: Article

References (34)

1. Bryant MP, Small N, Bouma C, Robinson IM (1958) Characteristics of ruminal anaerobic cellulolytic cocci and Cilliobacterium cellulosolvens n. sp. J Bacteriol 76: 529-537.
2. Dehority BA, Scott HW (1967) Extent of cellulose and hemicellulose digestion in various forages by pure cultures of cellulolytic rumen bacteria. J Dairy Sci 50: 1136-1141.
3. Sijpesteijn AK (1951) On Ruminococcus flavefaciens, a cellulose-decomposing bacterium from the rumen of sheep and cattle. J Gen Microbiol 5(5Suppl.): 869-879.
4. Flint HJ, Bayer EA (2008) Plant cell wall breakdown by anaerobic bacteria from the mammalian digestive tract. Ann NY Acad Sci 1125: 280-288.
5. Flint HJ, Bayer EA, Lamed R, White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nature Rev Microbiol 6: 121-131.
6. Doerner KC, White BA (1990) Assessment of the endo-1,4-b-glucanase components of Ruminococcus flavefaciens FD-1. Appl Environ Microbiol 56: 1844-1850.
7. Flint HJ, Martin J, McPherson CA, Daniel AS, Zhang JX (1993) A bifunctional enzyme, with separate xylanase and b(1,3-1,4)-glucanase domains, encoded by the xynD gene of Ruminococcus flavefaciens. J Bacteriol 175: 2943-2951.
8. Flint HJ, McPherson CA, Bisset J (1989) Molecular cloning of genes from Ruminococcus flavefaciens encoding xylanase and b(1-3,1-4)glucanase activities. Appl Environ Microbiol 55: 1230-1233.
9. Gardner RM, Doerner KC, White BA (1987) Purification and characterization of an exo-beta-1,4-glucanase from Ruminococcus flavefaciens FD-1. J Bacteriol 169: 4581-4588.
10. Pettipher GL, Latham MJ (1979) Characteristics of enzymes produced by Ruminococcus flavefaciens that degrade plant cell walls. J Gen Microbiol 110: 21-27.
11. Wood TM, Wilson CA, Stewart CS (1982) Preparation of the cellulase from the cellulolytic anaerobic rumen bacterium Ruminococcus albus and its release from the bacterial cell wall. Biochem J 205: 129-137.
12. Lamed R, Naimark J, Morgenstern E, Bayer EA (1987) Specialized cell surface structures in cellulolytic bacteria. J Bacteriol 169: 3792-3800.
13. Rasmussen MA, Hespell RB, White BA, Bothast RJ (1988) Inhibitory effects of methylcellulose on cellulose degradation by Ruminococcus flavefaciens. Appl Environ Microbiol 54: 890-897.
14. Aurilia V, Martin JC, McCrae SI, Scott KP, Rincon MT, et al. (2000) Three multidomain esterases from the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17 that carry divergent dockerin sequences. Microbiology 146: 1391-1397.
15. Aurilia V, Martin JC, Munro CA, Mercer DK, Flint HJ (2000) Organisation and strain distribution of genes responsible for the utilization of xylans by the rumen cellulolytic bacterium Ruminococcus flavefaciens. Anaerobe 6: 333-340.
16. Kirby J, Martin JC, Daniel AS, Flint HJ (1997) Dockerin-like sequences in cellulases and xylanases from the rumen cellulolytic bacterium Ruminococcus flavefaciens. FEMS Microbiol Lett 149: 213-219.
17. Rincon MT, McCrae SI, Kirby J, Scott KP, Flint HJ (2001) EndB, a multidomain family 44 cellulase from Ruminococcus flavefaciens 17, binds to cellulose via a novel cellulose-binding module and to another R. flavefaciens protein via a dockerin domain. Appl Environ Microbiol 67: 4426-4431.
18. Ding S-Y, Rincon MT, Lamed R, Martin JC, McCrae SI, et al. (2001) Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens. J Bacteriol 183: 1945-1953.
19. Rincon MT, Ding S-Y, McCrae SI, Martin JC, Aurilia V, et al. (2003) Novel organization and divergent dockerin specificities in the cellulosome system of Ruminococcus flavefaciens. J Bacteriol 185: 703-713.
20. Jindou S, Borovok I, Rincon MT, Flint HJ, Antonopoulos DA, et al. (2006) Conservation and divergence in cellulosome architecture between two strains of Ruminococcus flavefaciens. J Bacteriol 188: 7971-7976.
21. Bayer EA, Belaich J-P, Shoham Y, Lamed R (2004) The cellulosomes: Multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 58: 521-554.
22. Bayer EA, Lamed R, White BA, Flint HJ (2008) From cellulosomes to cellulosomics. Chem Rec 8: 364-377.
23. Doi RH, Kosugi A (2004) Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat Rev Microbiol 2: 541-551.
24. Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, et al. (2009) Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS ONE 4: e6650.
25. Jindou S, Levy-Assaraf M, Rincon MT, Flint HJ, Berg ME, et al. (2008) Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens. FEMS Microbiol Lett 285: 188-194.
26. Rincon MT, Martin JC, Aurilia V, McCrae SI, Rucklidge G, et al. (2004) ScaC, an adaptor protein carrying a novel cohesin that expands the dockerin-binding repertoire of the Ruminococcus flavefaciens 17 cellulosome. J Bacteriol 186: 2576-2585.
27. Rincon MT, Cepeljnik T, Martin JC, Lamed R, Barak Y, et al. (2005) Unconventional mode of attachment of the Ruminococcus flavefaciens cellulosome to the cell surface. J Bacteriol 187: 7569-7578.
28. Rincon MT, Cepeljnik T, Martin JC, Barak Y, Lamed R, et al. (2007) A novel cell surface-anchored cellulose-binding protein encoded by the sca gene cluster of Ruminococcus flavefaciens. J Bacteriol 189: 4774-7283.
29. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389-3402.
30. Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
31. Morgenstern B (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211-218.
32. Pagès S, Belaich A, Belaich J-P, Morag E, Lamed R, et al. (1997) Speciesspecificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: Prediction of specificity determinants of the dockerin domain. Proteins 29: 517-527.
33. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, et al. (2009) The Carbohydrate-Active Enzymes database (CAZy): an expert resource for glycogenomics. Nucl Acids Res 37: D233-238.
34. Peer A, Smith SP, Bayer EA, Lamed R, Borovok I (2009) Non-cellulosomal cohesin and dockerin-like modules in the three domains of life. FEMS Microbiol Lett 291: 1-16.