Ruminococcus flavefaciens 007C cellulosomes and cellulase consortium



Ruminococcus flavefaciens is among the most important cellulolytic bacterial species in rumen and gastrointestinal tract of monogastric herbivorous animals. Its efficiency in degradation of (hemi)cellulosic substrates is associated with the production of remarkably intricate extracellular multienzyme complexes, named cellulosomes. In the present work we investigated the cellulolytic system of 007C. The bioinformatic analysis of the draft genome sequence revealed identical organization of sca gene cluster as has previously been found in four other strains of R. flavefaciens. The cluster consists of five genes in the following order: scaC-scaA-scaB-cttA-scaE. The cellulases of R. flavefaciens 007C belong to four families of glycoside hydrolases, namely GH48, GH44, GH9 in GH5. Majority of these enzymes are putative endoglucanases, belonging to families GH5 and GH9, whereas only one gene encoding GH44 and GH48 was found. Apart from catalytic domains, most of these proteins also contain dockerins – signature sequences, which indicate their attachement to cellulosomes. On the other hand, carbohydrate-binding modules were only found coupled to GH9 catalytic domains. Zymogram analysis showed that larger endoglucanases were mostly constitutively expressed, wheras smaller enzymes were only detected in later phases of Avicel-grown cultures.


microbiology; molecular genetics; Ruminococcus flavefaciens; cellulosomes; glycoside hydrolases; anaerobic cellulose degradation


Bayer E.A., Lamed R., White B., Flint, H.J. 2008. From cellulosomes to cellulosomics. Chemical record, 8: 364–77, doi:10.1002/tcr.20160

Beckham G.T., Matthews J.F., Peters B., Bomble Y.J., Himmel M.E., Crowley M.F. 2011. Molecular-level origins of biomass recalcitrance: decrystallization free energies for four common cellulose polymorphs. The Journal of Physical Chemistry B, 115: 4118–4127, doi:10.1021/jp1106394

Béguin P., Lemaire M. 1996. The cellulosome: an exocellular, multiprotein complex specialized in cellulose degradation. Critical Reviews in Biochemistry and Molecular Biology, 31: 201–236, doi:10.3109/10409239609106584

Berg Miller M.E. in sod. 2009. Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1. PLoS ONE 4, 8: e6650

Brulc J.M. in sod. 2011. Cellulosomics, a Gene-Centric Approach to Investigating the Intraspecific Diversity and Adaptation of Ruminococcus flavefaciens within the Rumen. PLoS ONE 6: e25329, doi:10.1371/journal.pone.0025329

Bryant M.P., Robinson I.M. 1961. Some Nutritional Requirements of the Genus Ruminococcus. Applied microbiology, 9: 91–5

Bryant M.P. 1972. Commentary on the Hungate technique for culture of anaerobic bacteria. American Journal of Clinical Nutrition: 1324–1328

CAZY. The Carbohydrate Active enZYmes database.

Chandel A.K., Chandrasekhar G., Silva M.B., Da Silva S.S. 2012. The realm of cellulases in biorefinery development. Critical Reviews in Biotechnology, 32/3: 187–202, doi:10.3109/07388551.2011.595385

Chassard C., Delmas E., Robert C., Lawson P.A., Bernalier-Donadille A. 2011. Ruminococcus champanellensis sp. nov., a cellulose-degrading bacteria from the human gut microbiota. International Journal of Systematic and Evolutionary Microbiology, 62: 138–143, doi:10.1099/ijs.0.027375-0

Čater M., Zorec M., Marinšek Logar R. 2014 Methods for improving anaerobic lignocellulosic substrates degradation for enhanced biogas production. Springer science reviews, in press

Ding S.Y. in sod. 2001. Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens. Journal of Bacteriology, 183: 1945–1953, doi:10.1128/JB.183.6.1945-1953.2001

Flint H.J., Bayer E. A, Rincon M.T., Lamed R., White B.A. 2008. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nature reviews: Microbiology, 6: 121–131, doi:10.1038/nrmicro1817

Fontes C.M., Gilbert H.J. 2010. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annual review of biochemistry, 79: 655–681, doi:10.1146/annurev-biochem-091208-085603

Gold N.D., Martin V.J.J. 2007. Global View of the Clostridium thermocellum Cellulosome Revealed by Quantitative Proteomic Analysis. Journal Of Bacteriology, 189: 6787–6795, doi:10.1128/JB.00882-07

Hall T. 2011. BioEdit Software. Informer Technologies Inc,

Hungate R.E., Stack R.J. 1982. Phenylpropanoic Acid: Growth Factor for Ruminococcus albus. Applied and Environmental Microbiology, 44: 79–83

Jeihanipour A., Karimi K., Taherzadeh M.J. 2010. Enhancement of ethanol and biogas production from high-crystalline cellulose by different modes of NMO pretreatment. Biotechnology and Bioengineering, 105: 469–476, doi:10.1002/bit.22558

Jindou S. in sod. 2008. Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens. FEMS microbiology letters, 285: 188–194, doi:10.1111/j.1574-6968.2008.01234.x

Julliand V., De Vaux A., Millet L., Fonty G. 1999. Identification of Ruminococcus flavefaciens as the predominant cellulolytic bacterial species of the equine cecum. Applied and Environmental Microbiology, 65: 3738–3741

Laemmli U.K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227: 680–685, doi:10.1038/227680a0

Lütke-Eversloh T., Bahl H. 2011. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Current Opinion in Biotechnology, 22: 1–14, doi:10.1016/j.copbio.2011.01.011

Matsui H. in sod. 2010. Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species. Anaerobe, 16: 83–93, doi:10.1016/j.anaerobe.2009.07.005

Petersen T.N., Brunak S., Von Heijne G., Nielsen H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods, 8: 785–786, doi:10.1038/nmeth.1701

Rincon M.T. in sod. 2003. Novel organization and divergent dockerin specificities in the cellulosome system of Ruminococcus flavefaciens. Journal of Bacteriology, 185: 703–713, doi:10.1128/JB.185.3.703-713.2003

Rincon M.T. in sod. 2004. ScaC, an Adaptor Protein Carrying a Novel Cohesin That Expands the Dockerin-Binding Repertoire of the Ruminococcus flavefaciens 17 Cellulosome. Journal of Bacteriology 186: 2576–2585, doi:10.1128/JB.186.9.2576-2585.2004

Rincon M.T. in sod. 2005. Unconventional mode of attachment of the Ruminococcus flavefaciens cellulosome to the cell surface. Journal of bacteriology, 187, 7569–7578, doi:10.1128/JB.187.22.7569-7578.2005

Rincon M.T. in sod. 2007. A novel cell surface-anchored cellulose-binding protein encoded by the sca gene cluster of Ruminococcus flavefaciens. Journal of bacteriology, 189: 4774–83, doi:10.1128/JB.00143-07

Rincon M.T. in sod. 2010. Abundance and Diversity of Dockerin-Containing Proteins in the Fiber-Degrading Rumen Bacterium, Ruminococcus flavefaciens FD-1. PLoS ONE, 5/8: e12476–e12476, doi:10.1371/journal.pone.0012476

Rincon M.T., McCrae S.I., Kirby J., Scott K.P., Flint H.J. 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. Applied and Environmental Microbiology, 67: 4426–4431, doi:10.1128/AEM.67.10.4426-4431.2001

Saul D.J. in sod. 1990. celB, a gene coding for a bifunctional cellulase from the extreme thermophile “Caldocellum saccharolyticum”. Applied and Environmental Microbiology, 56: 3117–3124

Stewart C., Duncan S., McPherson C.A., Richardson A., Flint H.J. 1990. The implications of the loss and regain of cotton-degrading activity for the degradation of straw by Ruminococcus flavefaciens strain 007. Journal of Applied Microbiology, 68: 349–356

Stewart C.S., Duncan H.S., Flint H.J. 1990. The properties of forms of Ruminococcus flavefaciens which differ in their ability to degrade cotton cellulose. FEMS Microbiology Letters, 1–2: 47–50, doi:10.1111/j.1574-6968.1990.tb03859.x

Stewart C.S., Paniagua C., Dinsdale D., Cheng K.J., Garrow S.H. 1981. Selective isolation and characteristics of Bacteriodes succinogenes from the rumen of a cow. Applied and Environmental Microbiology, 41: 504–510

Vercoe P.E., Kocherginskaya, S.A., White B.A. 2003. Differential protein phosphorylation-dephosphorylation in response to carbon source in Ruminococcus flavefaciens FD-1. Journal of applied microbiology, 94: 974–980, doi:10.1046/j.1365-2672.2003.01929.x

Vodovnik M., Marinšek Logar R. 2012. Expression patterns of Ruminococcus flavefaciens revealed by zymogram approach. Folia microbiologica, 57, 4: 367–370, doi:10.1007/s12223-012-0144-3

Vodovnik M. in sod. 2013. Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007. PLOS ONE, 8, 6: 1–11, doi:10.1371/journal.pone.0065333

Wilkesman J., Kurz L. 2009. Protease analysis by zymography: a review on techniques and patents. Recent patents on biotechnology, 3/3: 175–184, doi:10.2174/187220809789389162

Zhang Y.-H.P., Lynd L.R. 2005. Regulation of Cellulase Synthesis in Batch and Continuous Cultures of Clostridium thermocellum. Journal Of Bacteriology, 187: 99–106, doi:10.1128/JB.187.1.99-106.2005

Zorec M., Vodovnik M., Marinšek Logar R. 2014. Cellulose and hemicellulose degradation by rumen bacteria. Food Technology and Biotechnology, 52/2: 210–221



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