Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens

Sadanari Jindou, Jennifer M. Brulc, Maly Levy-Assaraf, Marco T. Rincon, Harry James Flint, Margret E. Berg, Melissa K. Wilson, Bryan A. White, Edward A. Bayer, Raphael Lamed, Ilya Borovok

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

Ruminococcus flavefaciens is a vital cellulosome-producing fibrolytic rumen bacterium. The arrangement of the cellulosomal scaffoldin gene cluster (scaC-scaA-scaB-cttA-scaE) is conserved in two R. flavefaciens strains (17 and FD-1). Sequence analysis revealed a high mosaic conservation of the intergenic regions in the two strains that contrasted sharply with the divergence of the structural sca gene sequences. Based on the conserved intergenic regions, we designed PCR primers in order to examine the sca gene cluster in additional R. flavefaciens strains (C94, B34b, C1a and JM1). Using these conserved and/or degenerate primers, the scaC, scaA and scaB genes were amplified in all six strains, while the entire sca gene cluster and the proximal genes cttA and scaE were successfully amplified in four of the strains (17, FD-1, C94 and JM1). The sequencing of scaA and scaC genes in all the strains yielded additional insight into the variability of the structural genes with regard to the number and type of cohesin modules contained in a conserved molecular skeleton. Moreover, the scaC gene, being short and variable, appears to be a promising functional phylotyping target for metagenomic population studies of R. flavefaciens in the rumen as a function of the individual host animal.

Original languageEnglish
Pages (from-to)188-194
Number of pages7
JournalFEMS Microbiology Letters
Volume285
Issue number2
Early online date28 Jun 2008
DOIs
Publication statusPublished - Aug 2008

Keywords

  • conserved intergenic regions
  • strain variability
  • functional phylotyping
  • scaffoldins
  • cohesins
  • Clostridium cluster IV
  • herbivore gastrointestinal-tract
  • gradient gel-electrophoresis
  • ribosomal-RNA
  • phylogenetic analysis
  • microbial diversity
  • rumen bacteria
  • populations
  • hybridization
  • ecology
  • regions

Cite this

Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens. / Jindou, Sadanari; Brulc, Jennifer M.; Levy-Assaraf, Maly; Rincon, Marco T.; Flint, Harry James; Berg, Margret E.; Wilson, Melissa K.; White, Bryan A.; Bayer, Edward A.; Lamed, Raphael; Borovok, Ilya.

In: FEMS Microbiology Letters, Vol. 285, No. 2, 08.2008, p. 188-194.

Research output: Contribution to journalArticle

Jindou, S, Brulc, JM, Levy-Assaraf, M, Rincon, MT, Flint, HJ, Berg, ME, Wilson, MK, White, BA, Bayer, EA, Lamed, R & Borovok, I 2008, 'Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens', FEMS Microbiology Letters, vol. 285, no. 2, pp. 188-194. https://doi.org/10.1111/j.1574-6968.2008.01234.x
Jindou, Sadanari ; Brulc, Jennifer M. ; Levy-Assaraf, Maly ; Rincon, Marco T. ; Flint, Harry James ; Berg, Margret E. ; Wilson, Melissa K. ; White, Bryan A. ; Bayer, Edward A. ; Lamed, Raphael ; Borovok, Ilya. / Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens. In: FEMS Microbiology Letters. 2008 ; Vol. 285, No. 2. pp. 188-194.
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abstract = "Ruminococcus flavefaciens is a vital cellulosome-producing fibrolytic rumen bacterium. The arrangement of the cellulosomal scaffoldin gene cluster (scaC-scaA-scaB-cttA-scaE) is conserved in two R. flavefaciens strains (17 and FD-1). Sequence analysis revealed a high mosaic conservation of the intergenic regions in the two strains that contrasted sharply with the divergence of the structural sca gene sequences. Based on the conserved intergenic regions, we designed PCR primers in order to examine the sca gene cluster in additional R. flavefaciens strains (C94, B34b, C1a and JM1). Using these conserved and/or degenerate primers, the scaC, scaA and scaB genes were amplified in all six strains, while the entire sca gene cluster and the proximal genes cttA and scaE were successfully amplified in four of the strains (17, FD-1, C94 and JM1). The sequencing of scaA and scaC genes in all the strains yielded additional insight into the variability of the structural genes with regard to the number and type of cohesin modules contained in a conserved molecular skeleton. Moreover, the scaC gene, being short and variable, appears to be a promising functional phylotyping target for metagenomic population studies of R. flavefaciens in the rumen as a function of the individual host animal.",
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AU - Jindou, Sadanari

AU - Brulc, Jennifer M.

AU - Levy-Assaraf, Maly

AU - Rincon, Marco T.

AU - Flint, Harry James

AU - Berg, Margret E.

AU - Wilson, Melissa K.

AU - White, Bryan A.

AU - Bayer, Edward A.

AU - Lamed, Raphael

AU - Borovok, Ilya

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N2 - Ruminococcus flavefaciens is a vital cellulosome-producing fibrolytic rumen bacterium. The arrangement of the cellulosomal scaffoldin gene cluster (scaC-scaA-scaB-cttA-scaE) is conserved in two R. flavefaciens strains (17 and FD-1). Sequence analysis revealed a high mosaic conservation of the intergenic regions in the two strains that contrasted sharply with the divergence of the structural sca gene sequences. Based on the conserved intergenic regions, we designed PCR primers in order to examine the sca gene cluster in additional R. flavefaciens strains (C94, B34b, C1a and JM1). Using these conserved and/or degenerate primers, the scaC, scaA and scaB genes were amplified in all six strains, while the entire sca gene cluster and the proximal genes cttA and scaE were successfully amplified in four of the strains (17, FD-1, C94 and JM1). The sequencing of scaA and scaC genes in all the strains yielded additional insight into the variability of the structural genes with regard to the number and type of cohesin modules contained in a conserved molecular skeleton. Moreover, the scaC gene, being short and variable, appears to be a promising functional phylotyping target for metagenomic population studies of R. flavefaciens in the rumen as a function of the individual host animal.

AB - Ruminococcus flavefaciens is a vital cellulosome-producing fibrolytic rumen bacterium. The arrangement of the cellulosomal scaffoldin gene cluster (scaC-scaA-scaB-cttA-scaE) is conserved in two R. flavefaciens strains (17 and FD-1). Sequence analysis revealed a high mosaic conservation of the intergenic regions in the two strains that contrasted sharply with the divergence of the structural sca gene sequences. Based on the conserved intergenic regions, we designed PCR primers in order to examine the sca gene cluster in additional R. flavefaciens strains (C94, B34b, C1a and JM1). Using these conserved and/or degenerate primers, the scaC, scaA and scaB genes were amplified in all six strains, while the entire sca gene cluster and the proximal genes cttA and scaE were successfully amplified in four of the strains (17, FD-1, C94 and JM1). The sequencing of scaA and scaC genes in all the strains yielded additional insight into the variability of the structural genes with regard to the number and type of cohesin modules contained in a conserved molecular skeleton. Moreover, the scaC gene, being short and variable, appears to be a promising functional phylotyping target for metagenomic population studies of R. flavefaciens in the rumen as a function of the individual host animal.

KW - conserved intergenic regions

KW - strain variability

KW - functional phylotyping

KW - scaffoldins

KW - cohesins

KW - Clostridium cluster IV

KW - herbivore gastrointestinal-tract

KW - gradient gel-electrophoresis

KW - ribosomal-RNA

KW - phylogenetic analysis

KW - microbial diversity

KW - rumen bacteria

KW - populations

KW - hybridization

KW - ecology

KW - regions

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DO - 10.1111/j.1574-6968.2008.01234.x

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VL - 285

SP - 188

EP - 194

JO - FEMS Microbiology Letters

JF - FEMS Microbiology Letters

SN - 0378-1097

IS - 2

ER -