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.
authors.affiliation: Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Vered
authors.initials: V
authors.lastname: Israeli-Ruimy
authors.affiliation: CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.
authors.forename: Pedro
authors.initials: P
authors.lastname: Bule
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.
authors.forename: Sadanari
authors.initials: S
authors.lastname: Jindou
authors.affiliation: Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Bareket
authors.initials: B
authors.lastname: Dassa
authors.affiliation: Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Sarah
authors.initials: S
authors.lastname: Moraïs
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.
authors.forename: Ilya
authors.initials: I
authors.lastname: Borovok
authors.affiliation: Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.|Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Yoav
authors.initials: Y
authors.lastname: Barak
authors.affiliation: Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Michal
authors.initials: M
authors.lastname: Slutzki
authors.affiliation: Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Hamberg
authors.affiliation: CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.
authors.forename: Vânia
authors.initials: V
authors.lastname: Cardoso
authors.affiliation: CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.
authors.forename: Victor D
authors.initials: VD
authors.lastname: Alves
authors.affiliation: CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.
authors.forename: Shabir
authors.initials: S
authors.lastname: Najmudin
authors.affiliation: Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.|Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
authors.forename: Bryan A
authors.initials: BA
authors.lastname: White
authors.affiliation: Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, Scotland, UK.
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Flint
authors.affiliation: Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, UK.
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Gilbert
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.
authors.forename: Raphael
authors.initials: R
authors.lastname: Lamed
authors.affiliation: CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.
authors.forename: Carlos M G A
authors.initials: CM
authors.lastname: Fontes
authors.affiliation: Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Edward A
authors.initials: EA
authors.lastname: Bayer
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D018797:Cell Cycle Proteins / Q000378:metabolism; D002482:Cellulose / Q000378:metabolism; D044603:Cellulosomes / Q000378:metabolism*; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism; D008954:Models, Biological; D010802:Phylogeny; D040081:Protein Array Analysis; D060066:Protein Interaction Maps; D045857:Ruminococcus / Q000378:metabolism*; D000097722:Cohesins
chemical_list: D001426:Bacterial Proteins; D018797:Cell Cycle Proteins; D002482:Cellulose; D002868:Chromosomal Proteins, Non-Histone; D000097722:Cohesins