Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions

Vered Israeli-Ruimy, Pedro Bule, Sadanari Jindou, Bareket Dassa, Sarah Moraïs, Ilya Borovok, Yoav Barak, Michal Slutzki, Yuval Hamberg, Vânia Cardoso, Victor D Alves, Shabir Najmudin, Bryan A White, Harry J Flint, Harry J Gilbert, Raphael Lamed, Carlos M G A Fontes, Edward A Bayer

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Abstract

Protein-protein interactions play a vital role in cellular processes as exemplified by assembly of the intricate multi-enzyme cellulosome complex. Cellulosomes are assembled by selective high-affinity binding of enzyme-borne dockerin modules to repeated cohesin modules of structural proteins termed scaffoldins. Recent sequencing of the fiber-degrading Ruminococcus flavefaciens FD-1 genome revealed a particularly elaborate cellulosome system. In total, 223 dockerin-bearing ORFs potentially involved in cellulosome assembly and a variety of multi-modular scaffoldins were identified, and the dockerins were classified into six major groups. Here, extensive screening employing three complementary medium- to high-throughput platforms was used to characterize the different cohesin-dockerin specificities. The platforms included (i) cellulose-coated microarray assay, (ii) enzyme-linked immunosorbent assay (ELISA) and (iii) in-vivo co-expression and screening in Escherichia coli. The data revealed a collection of unique cohesin-dockerin interactions and support the functional relevance of dockerin classification into groups. In contrast to observations reported previously, a dual-binding mode is involved in cellulosome cell-surface attachment, whereas single-binding interactions operate for cellulosome integration of enzymes. This sui generis cellulosome model enhances our understanding of the mechanisms governing the remarkable ability of R. flavefaciens to degrade carbohydrates in the bovine rumen and provides a basis for constructing efficient nano-machines applied to biological processes.

Original languageEnglish
Article number42355
JournalScientific Reports
Volume7
DOIs
Publication statusPublished - 10 Feb 2017

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Cellulosomes
Ruminococcus
Proteins
Enzymes
Biological Phenomena
Rumen
FD 1
Cellulose
Open Reading Frames
Enzyme-Linked Immunosorbent Assay
Carbohydrates
Genome
Escherichia coli

Keywords

  • Multienzyme complexes
  • Proteins

Cite this

Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. / Israeli-Ruimy, Vered; Bule, Pedro; Jindou, Sadanari; Dassa, Bareket; Moraïs, Sarah; Borovok, Ilya; Barak, Yoav; Slutzki, Michal; Hamberg, Yuval; Cardoso, Vânia; Alves, Victor D; Najmudin, Shabir; White, Bryan A; Flint, Harry J; Gilbert, Harry J; Lamed, Raphael; Fontes, Carlos M G A; Bayer, Edward A.

In: Scientific Reports, Vol. 7, 42355, 10.02.2017.

Research output: Contribution to journalArticle

Israeli-Ruimy, V, Bule, P, Jindou, S, Dassa, B, Moraïs, S, Borovok, I, Barak, Y, Slutzki, M, Hamberg, Y, Cardoso, V, Alves, VD, Najmudin, S, White, BA, Flint, HJ, Gilbert, HJ, Lamed, R, Fontes, CMGA & Bayer, EA 2017, 'Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions', Scientific Reports, vol. 7, 42355. https://doi.org/10.1038/srep42355
Israeli-Ruimy, Vered ; Bule, Pedro ; Jindou, Sadanari ; Dassa, Bareket ; Moraïs, Sarah ; Borovok, Ilya ; Barak, Yoav ; Slutzki, Michal ; Hamberg, Yuval ; Cardoso, Vânia ; Alves, Victor D ; Najmudin, Shabir ; White, Bryan A ; Flint, Harry J ; Gilbert, Harry J ; Lamed, Raphael ; Fontes, Carlos M G A ; Bayer, Edward A. / Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. In: Scientific Reports. 2017 ; Vol. 7.
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title = "Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions",
abstract = "Protein-protein interactions play a vital role in cellular processes as exemplified by assembly of the intricate multi-enzyme cellulosome complex. Cellulosomes are assembled by selective high-affinity binding of enzyme-borne dockerin modules to repeated cohesin modules of structural proteins termed scaffoldins. Recent sequencing of the fiber-degrading Ruminococcus flavefaciens FD-1 genome revealed a particularly elaborate cellulosome system. In total, 223 dockerin-bearing ORFs potentially involved in cellulosome assembly and a variety of multi-modular scaffoldins were identified, and the dockerins were classified into six major groups. Here, extensive screening employing three complementary medium- to high-throughput platforms was used to characterize the different cohesin-dockerin specificities. The platforms included (i) cellulose-coated microarray assay, (ii) enzyme-linked immunosorbent assay (ELISA) and (iii) in-vivo co-expression and screening in Escherichia coli. The data revealed a collection of unique cohesin-dockerin interactions and support the functional relevance of dockerin classification into groups. In contrast to observations reported previously, a dual-binding mode is involved in cellulosome cell-surface attachment, whereas single-binding interactions operate for cellulosome integration of enzymes. This sui generis cellulosome model enhances our understanding of the mechanisms governing the remarkable ability of R. flavefaciens to degrade carbohydrates in the bovine rumen and provides a basis for constructing efficient nano-machines applied to biological processes.",
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note = "This work was supported in part by the European Union, Area NMP.2013.1.1–2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530, and by the EU Seventh Framework Programme (FP7 2007–2013) under the WallTraC project (Grant Agreement no 263916), and BioStruct-X (grant agreement no 283570). This paper reflects the author’s views only. The European Community is not liable for any use that may be made of the information contained herein. CMGAF is also supported by Funda{\cc}{\~a}o para a Ci{\^e}ncia e a Tecnologia (Lisbon, Portugal) through grants PTDC/BIA-PRO/103980/2008 and EXPL/BIA-MIC/1176/2012. EAB is also funded by a grant (No. 1349/13) from the Israel Science Foundation (ISF), Jerusalem, Israel and by a grant (No. 2013284) from the U.S.-Israel Binational Science Foundation (BSF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry.",
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AU - Israeli-Ruimy, Vered

AU - Bule, Pedro

AU - Jindou, Sadanari

AU - Dassa, Bareket

AU - Moraïs, Sarah

AU - Borovok, Ilya

AU - Barak, Yoav

AU - Slutzki, Michal

AU - Hamberg, Yuval

AU - Cardoso, Vânia

AU - Alves, Victor D

AU - Najmudin, Shabir

AU - White, Bryan A

AU - Flint, Harry J

AU - Gilbert, Harry J

AU - Lamed, Raphael

AU - Fontes, Carlos M G A

AU - Bayer, Edward A

N1 - This work was supported in part by the European Union, Area NMP.2013.1.1–2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530, and by the EU Seventh Framework Programme (FP7 2007–2013) under the WallTraC project (Grant Agreement no 263916), and BioStruct-X (grant agreement no 283570). This paper reflects the author’s views only. The European Community is not liable for any use that may be made of the information contained herein. CMGAF is also supported by Fundação para a Ciência e a Tecnologia (Lisbon, Portugal) through grants PTDC/BIA-PRO/103980/2008 and EXPL/BIA-MIC/1176/2012. EAB is also funded by a grant (No. 1349/13) from the Israel Science Foundation (ISF), Jerusalem, Israel and by a grant (No. 2013284) from the U.S.-Israel Binational Science Foundation (BSF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry.

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KW - Proteins

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