Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007

Maša Vodovnik; Sylvia H. Duncan; Martin D. Reid; Louise Cantlay; Keith Turner; Julian Parkhill; Raphael Lamed; Carl J. Yeoman; Margret E. Berg. Miller; Bryan A. White; Edward A. Bayer; Romana Marinšek-Logar; Harry J. Flint

doi:10.1371/journal.pone.0065333

Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007

Maša Vodovnik, Sylvia H. Duncan, Martin D. Reid, Louise Cantlay, Keith Turner, Julian Parkhill, Raphael Lamed, Carl J. Yeoman, Margret E. Berg. Miller, Bryan A. White, Edward A. Bayer, Romana Marinšek-Logar, Harry J. Flint

The Rowett Institute of Nutrition and Health

Research output: Contribution to journal › Article › peer-review

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Abstract

Background

Ruminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut. Cellulolytic strains from the bovine rumen have been shown to produce complex cellulosome structures that are associated with the cell surface. R. flavefaciens 007 is a highly cellulolytic strain whose ability to degrade dewaxed cotton, but not Avicel cellulose, was lost following initial isolation in the variant 007S. The ability was recovered after serial subculture to give the cotton-degrading strain 007C. This has allowed us to investigate the factors required for degradation of this particularly recalcitrant form of cellulose.

Methodology/Principal Findings

The major proteins associated with the bacterial cell surface and with the culture supernatant were analyzed for R. flavefaciens 007S and 007C grown with cellobiose, xylan or Avicel cellulose as energy sources. Identification of the proteins was enabled by a draft genome sequence obtained for 007C. Among supernatant proteins a cellulosomal GH48 hydrolase, a rubrerthyrin-like protein and a protein with type IV pili N-terminal domain were the most strongly up-regulated in 007C cultures grown on Avicel compared with cellobiose. Strain 007S also showed substrate-related changes, but supernatant expression of the Pil protein and rubrerythrin in particular were markedly lower in 007S than in 007C during growth on Avicel.

Conclusions/Significance

This study provides new information on the extracellular proteome of R. flavefaciens and its regulation in response to different growth substrates. Furthermore it suggests that the cotton cellulose non-degrading strain (007S) has altered regulation of multiple proteins that may be required for breakdown of cotton cellulose. One of these, the type IV pilus was previously shown to play a role in adhesion to cellulose in R. albus, and a related pilin protein was identified here for the first time as a major extracellular protein in R. flavefaciens.

Original language	English
Article number	e65333
Pages (from-to)	1-11
Number of pages	11
Journal	PloS ONE
Volume	8
Issue number	6
DOIs	https://doi.org/10.1371/journal.pone.0065333
Publication status	Published - 4 Jun 2013

Bibliographical note

Funding: The Rowett Institute receives funding from SG-RESAS (Scottish Government Rural and Environmental Science and Analysis Service). Visit of M.V. was supported by research grants from FEMS and Slovene human resources development and scholarship funds. Parts of this work were funded by grants from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel – BSF Energy Research grant to E.A.B. and B.A.W. and Regular BSF Research grants to R.L. and B.A.W. – and by the Israel Science Foundation (grant nos 966/09 and 159/07 291/08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007
© 2013 Vodovnik et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. https://creativecommons.org/licenses/by/4.0/
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Vodovnik, M., Duncan, S. H., Reid, M. D., Cantlay, L., Turner, K., Parkhill, J., Lamed, R., Yeoman, C. J., Miller, M. E. B., White, B. A., Bayer, E. A., Marinšek-Logar, R., & Flint, H. J. (2013). Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007. PloS ONE, 8(6), 1-11. Article e65333. https://doi.org/10.1371/journal.pone.0065333

Vodovnik, M, Duncan, SH, Reid, MD, Cantlay, L, Turner, K, Parkhill, J, Lamed, R, Yeoman, CJ, Miller, MEB, White, BA, Bayer, EA, Marinšek-Logar, R & Flint, HJ 2013, 'Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007', PloS ONE, vol. 8, no. 6, e65333, pp. 1-11. https://doi.org/10.1371/journal.pone.0065333

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abstract = "BackgroundRuminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut. Cellulolytic strains from the bovine rumen have been shown to produce complex cellulosome structures that are associated with the cell surface. R. flavefaciens 007 is a highly cellulolytic strain whose ability to degrade dewaxed cotton, but not Avicel cellulose, was lost following initial isolation in the variant 007S. The ability was recovered after serial subculture to give the cotton-degrading strain 007C. This has allowed us to investigate the factors required for degradation of this particularly recalcitrant form of cellulose.Methodology/Principal FindingsThe major proteins associated with the bacterial cell surface and with the culture supernatant were analyzed for R. flavefaciens 007S and 007C grown with cellobiose, xylan or Avicel cellulose as energy sources. Identification of the proteins was enabled by a draft genome sequence obtained for 007C. Among supernatant proteins a cellulosomal GH48 hydrolase, a rubrerthyrin-like protein and a protein with type IV pili N-terminal domain were the most strongly up-regulated in 007C cultures grown on Avicel compared with cellobiose. Strain 007S also showed substrate-related changes, but supernatant expression of the Pil protein and rubrerythrin in particular were markedly lower in 007S than in 007C during growth on Avicel.Conclusions/SignificanceThis study provides new information on the extracellular proteome of R. flavefaciens and its regulation in response to different growth substrates. Furthermore it suggests that the cotton cellulose non-degrading strain (007S) has altered regulation of multiple proteins that may be required for breakdown of cotton cellulose. One of these, the type IV pilus was previously shown to play a role in adhesion to cellulose in R. albus, and a related pilin protein was identified here for the first time as a major extracellular protein in R. flavefaciens.",

author = "Ma{\v s}a Vodovnik and Duncan, {Sylvia H.} and Reid, {Martin D.} and Louise Cantlay and Keith Turner and Julian Parkhill and Raphael Lamed and Yeoman, {Carl J.} and Miller, {Margret E. Berg.} and White, {Bryan A.} and Bayer, {Edward A.} and Romana Marin{\v s}ek-Logar and Flint, {Harry J.}",

note = "Funding: The Rowett Institute receives funding from SG-RESAS (Scottish Government Rural and Environmental Science and Analysis Service). Visit of M.V. was supported by research grants from FEMS and Slovene human resources development and scholarship funds. Parts of this work were funded by grants from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel – BSF Energy Research grant to E.A.B. and B.A.W. and Regular BSF Research grants to R.L. and B.A.W. – and by the Israel Science Foundation (grant nos 966/09 and 159/07 291/08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.",

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T1 - Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007

AU - Vodovnik, Maša

AU - Duncan, Sylvia H.

AU - Reid, Martin D.

AU - Cantlay, Louise

AU - Turner, Keith

AU - Parkhill, Julian

AU - Lamed, Raphael

AU - Yeoman, Carl J.

AU - Miller, Margret E. Berg.

AU - White, Bryan A.

AU - Bayer, Edward A.

AU - Marinšek-Logar, Romana

AU - Flint, Harry J.

N1 - Funding: The Rowett Institute receives funding from SG-RESAS (Scottish Government Rural and Environmental Science and Analysis Service). Visit of M.V. was supported by research grants from FEMS and Slovene human resources development and scholarship funds. Parts of this work were funded by grants from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel – BSF Energy Research grant to E.A.B. and B.A.W. and Regular BSF Research grants to R.L. and B.A.W. – and by the Israel Science Foundation (grant nos 966/09 and 159/07 291/08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Y1 - 2013/6/4

N2 - BackgroundRuminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut. Cellulolytic strains from the bovine rumen have been shown to produce complex cellulosome structures that are associated with the cell surface. R. flavefaciens 007 is a highly cellulolytic strain whose ability to degrade dewaxed cotton, but not Avicel cellulose, was lost following initial isolation in the variant 007S. The ability was recovered after serial subculture to give the cotton-degrading strain 007C. This has allowed us to investigate the factors required for degradation of this particularly recalcitrant form of cellulose.Methodology/Principal FindingsThe major proteins associated with the bacterial cell surface and with the culture supernatant were analyzed for R. flavefaciens 007S and 007C grown with cellobiose, xylan or Avicel cellulose as energy sources. Identification of the proteins was enabled by a draft genome sequence obtained for 007C. Among supernatant proteins a cellulosomal GH48 hydrolase, a rubrerthyrin-like protein and a protein with type IV pili N-terminal domain were the most strongly up-regulated in 007C cultures grown on Avicel compared with cellobiose. Strain 007S also showed substrate-related changes, but supernatant expression of the Pil protein and rubrerythrin in particular were markedly lower in 007S than in 007C during growth on Avicel.Conclusions/SignificanceThis study provides new information on the extracellular proteome of R. flavefaciens and its regulation in response to different growth substrates. Furthermore it suggests that the cotton cellulose non-degrading strain (007S) has altered regulation of multiple proteins that may be required for breakdown of cotton cellulose. One of these, the type IV pilus was previously shown to play a role in adhesion to cellulose in R. albus, and a related pilin protein was identified here for the first time as a major extracellular protein in R. flavefaciens.

AB - BackgroundRuminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut. Cellulolytic strains from the bovine rumen have been shown to produce complex cellulosome structures that are associated with the cell surface. R. flavefaciens 007 is a highly cellulolytic strain whose ability to degrade dewaxed cotton, but not Avicel cellulose, was lost following initial isolation in the variant 007S. The ability was recovered after serial subculture to give the cotton-degrading strain 007C. This has allowed us to investigate the factors required for degradation of this particularly recalcitrant form of cellulose.Methodology/Principal FindingsThe major proteins associated with the bacterial cell surface and with the culture supernatant were analyzed for R. flavefaciens 007S and 007C grown with cellobiose, xylan or Avicel cellulose as energy sources. Identification of the proteins was enabled by a draft genome sequence obtained for 007C. Among supernatant proteins a cellulosomal GH48 hydrolase, a rubrerthyrin-like protein and a protein with type IV pili N-terminal domain were the most strongly up-regulated in 007C cultures grown on Avicel compared with cellobiose. Strain 007S also showed substrate-related changes, but supernatant expression of the Pil protein and rubrerythrin in particular were markedly lower in 007S than in 007C during growth on Avicel.Conclusions/SignificanceThis study provides new information on the extracellular proteome of R. flavefaciens and its regulation in response to different growth substrates. Furthermore it suggests that the cotton cellulose non-degrading strain (007S) has altered regulation of multiple proteins that may be required for breakdown of cotton cellulose. One of these, the type IV pilus was previously shown to play a role in adhesion to cellulose in R. albus, and a related pilin protein was identified here for the first time as a major extracellular protein in R. flavefaciens.

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Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007

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