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Aymé L, Hébert A, Henrissat B, Lombard V, Franche N, Perret S, Jourdier E, Heiss-Blanquet S. Characterization of three bacterial glycoside hydrolase family 9 endoglucanases with different modular architectures isolated from a compost metagenome. Biochim Biophys Acta Gen Subj 2021; 1865:129848. [PMID: 33460770 DOI: 10.1016/j.bbagen.2021.129848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Environmental bacteria express a wide diversity of glycoside hydrolases (GH). Screening and characterization of GH from metagenomic sources provides an insight into biomass degradation strategies of non-cultivated prokaryotes. METHODS In the present report, we screened a compost metagenome for lignocellulolytic activities and identified six genes encoding enzymes belonging to family GH9 (GH9a-f). Three of these enzymes (GH9b, GH9d and GH9e) were successfully expressed and characterized. RESULTS A phylogenetic analysis of the catalytic domain of pro- and eukaryotic GH9 enzymes suggested the existence of two major subgroups. Bacterial GH9s displayed a wide variety of modular architectures and those harboring an N-terminal Ig-like domain, such as GH9b and GH9d, segregated from the remainder. We purified and characterized GH9 endoglucanases from both subgroups and examined their stabilities, substrate specificities and product profiles. GH9e exhibited an original hydrolysis pattern, liberating an elevated proportion of oligosaccharides longer than cellobiose. All of the enzymes exhibited processive behavior and a synergistic action on crystalline cellulose. Synergy was also evidenced between GH9d and a GH48 enzyme identified from the same metagenome. CONCLUSIONS The characterized GH9 enzymes displayed different modular architectures and distinct substrate and product profiles. The presence of a cellulose binding domain was shown to be necessary for binding and digestion of insoluble cellulosic substrates, but not for processivity. GENERAL SIGNIFICANCE The identification of six GH9 enzymes from a compost metagenome and the functional variety of three characterized members highlight the importance of this enzyme family in bacterial biomass deconstruction.
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Affiliation(s)
- Laure Aymé
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Agnès Hébert
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France
| | - Nathalie Franche
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Stéphanie Perret
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Etienne Jourdier
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France.
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Bule P, Cameron K, Prates JAM, Ferreira LMA, Smith SP, Gilbert HJ, Bayer EA, Najmudin S, Fontes CMGA, Alves VD. Structure-function analyses generate novel specificities to assemble the components of multienzyme bacterial cellulosome complexes. J Biol Chem 2018; 293:4201-4212. [PMID: 29367338 PMCID: PMC5857977 DOI: 10.1074/jbc.ra117.001241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/11/2018] [Indexed: 02/02/2023] Open
Abstract
The cellulosome is a remarkably intricate multienzyme nanomachine produced by anaerobic bacteria to degrade plant cell wall polysaccharides. Cellulosome assembly is mediated through binding of enzyme-borne dockerin modules to cohesin modules of the primary scaffoldin subunit. The anaerobic bacterium Acetivibrio cellulolyticus produces a highly intricate cellulosome comprising an adaptor scaffoldin, ScaB, whose cohesins interact with the dockerin of the primary scaffoldin (ScaA) that integrates the cellulosomal enzymes. The ScaB dockerin selectively binds to cohesin modules in ScaC that anchors the cellulosome onto the cell surface. Correct cellulosome assembly requires distinct specificities displayed by structurally related type-I cohesin-dockerin pairs that mediate ScaC-ScaB and ScaA-enzyme assemblies. To explore the mechanism by which these two critical protein interactions display their required specificities, we determined the crystal structure of the dockerin of a cellulosomal enzyme in complex with a ScaA cohesin. The data revealed that the enzyme-borne dockerin binds to the ScaA cohesin in two orientations, indicating two identical cohesin-binding sites. Combined mutagenesis experiments served to identify amino acid residues that modulate type-I cohesin-dockerin specificity in A. cellulolyticus Rational design was used to test the hypothesis that the ligand-binding surfaces of ScaA- and ScaB-associated dockerins mediate cohesin recognition, independent of the structural scaffold. Novel specificities could thus be engineered into one, but not both, of the ligand-binding sites of ScaB, whereas attempts at manipulating the specificity of the enzyme-associated dockerin were unsuccessful. These data indicate that dockerin specificity requires critical interplay between the ligand-binding surface and the structural scaffold of these modules.
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Affiliation(s)
- Pedro Bule
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Kate Cameron
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - José A M Prates
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Luís M A Ferreira
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Steven P Smith
- the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Harry J Gilbert
- the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom, and
| | - Edward A Bayer
- the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100 Israel
| | - Shabir Najmudin
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Carlos M G A Fontes
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal,
| | - Victor D Alves
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal,
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The Ruminococci: key symbionts of the gut ecosystem. J Microbiol 2018; 56:199-208. [PMID: 29492877 DOI: 10.1007/s12275-018-8024-4] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/05/2018] [Accepted: 02/12/2018] [Indexed: 12/22/2022]
Abstract
Mammalian gut microbial communities form intricate mutualisms with their hosts, which have profound implications on overall health. One group of important gut microbial mutualists are bacteria in the genus Ruminococcus, which serve to degrade and convert complex polysaccharides into a variety of nutrients for their hosts. Isolated decades ago from the bovine rumen, ruminococci have since been cultured from other ruminant and non-ruminant sources, and next-generation sequencing has further shown their distribution to be widespread in a diversity of animal hosts. While most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic, nonruminant-associated species, such as those found in humans. Furthermore, a mechanistic understanding of the role of Ruminococcus spp. in their respective hosts is still a work in progress. This review highlights the broad work done on species within the genus Ruminococcus with respect to their physiology, phylogenetic relatedness, and their potential impact on host health.
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Verdorfer T, Bernardi RC, Meinhold A, Ott W, Luthey-Schulten Z, Nash MA, Gaub HE. Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics. J Am Chem Soc 2017; 139:17841-17852. [PMID: 29058444 PMCID: PMC5737924 DOI: 10.1021/jacs.7b07574] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cellulosomes are polyprotein machineries that efficiently degrade cellulosic material. Crucial to their function are scaffolds consisting of highly homologous cohesin domains, which serve a dual role by coordinating a multiplicity of enzymes as well as anchoring the microbe to its substrate. Here we combined two approaches to elucidate the mechanical properties of the main scaffold ScaA of Acetivibrio cellulolyticus. A newly developed parallelized one-pot in vitro transcription-translation and protein pull-down protocol enabled high-throughput atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) measurements of all cohesins from ScaA with a single cantilever, thus promising improved relative force comparability. Albeit very similar in sequence, the hanging cohesins showed considerably lower unfolding forces than the bridging cohesins, which are subjected to force when the microbe is anchored to its substrate. Additionally, all-atom steered molecular dynamics (SMD) simulations on homology models offered insight into the process of cohesin unfolding under force. Based on the differences among the individual force propagation pathways and their associated correlation communities, we designed mutants to tune the mechanical stability of the weakest hanging cohesin. The proposed mutants were tested in a second high-throughput AFM SMFS experiment revealing that in one case a single alanine to glycine point mutation suffices to more than double the mechanical stability. In summary, we have successfully characterized the force induced unfolding behavior of all cohesins from the scaffoldin ScaA, as well as revealed how small changes in sequence can have large effects on force resilience in cohesin domains. Our strategy provides an efficient way to test and improve the mechanical integrity of protein domains in general.
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Affiliation(s)
- Tobias Verdorfer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aylin Meinhold
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Wolfgang Ott
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Zaida Luthey-Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael A Nash
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), 4058 Basel, Switzerland
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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Zhivin O, Dassa B, Moraïs S, Utturkar SM, Brown SD, Henrissat B, Lamed R, Bayer EA. Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:211. [PMID: 28912832 PMCID: PMC5590126 DOI: 10.1186/s13068-017-0898-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/29/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND (Pseudo) Bacteroides cellulosolvens is an anaerobic, mesophilic, cellulolytic, cellulosome-producing clostridial bacterium capable of utilizing cellulose and cellobiose as carbon sources. Recently, we sequenced the B. cellulosolvens genome, and subsequent comprehensive bioinformatic analysis, herein reported, revealed an unprecedented number of cellulosome-related components, including 78 cohesin modules scattered among 31 scaffoldins and more than 200 dockerin-bearing ORFs. In terms of numbers, the B. cellulosolvens cellulosome system represents the most intricate, compositionally diverse cellulosome system yet known in nature. RESULTS The organization of the B. cellulosolvens cellulosome is unique compared to previously described cellulosome systems. In contrast to all other known cellulosomes, the cohesin types are reversed for all scaffoldins i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. Many of the type II dockerin-bearing ORFs include X60 modules, which are known to stabilize type II cohesin-dockerin interactions. In the present work, we focused on revealing the architectural arrangement of cellulosome structure in this bacterium by examining numerous interactions between the various cohesin and dockerin modules. In total, we cloned and expressed 43 representative cohesins and 27 dockerins. The results revealed various possible architectures of cell-anchored and cell-free cellulosomes, which serve to assemble distinctive cellulosome types via three distinct cohesin-dockerin specificities: type I, type II, and a novel-type designated R (distinct from type III interactions, predominant in ruminococcal cellulosomes). CONCLUSIONS The results of this study provide novel insight into the architecture and function of the most intricate and extensive cellulosomal system known today, thereby extending significantly our overall knowledge base of cellulosome systems and their components. The robust cellulosome system of B. cellulosolvens, with its unique binding specificities and reversal of cohesin-dockerin types, has served to amend our view of the cellulosome paradigm. Revealing new cellulosomal interactions and arrangements is critical for designing high-efficiency artificial cellulosomes for conversion of plant-derived cellulosic biomass towards improved production of biofuels.
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Affiliation(s)
- Olga Zhivin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sagar M. Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919 USA
- BioEnergy Science Center, Oak Ridge, TN USA
| | - Steven D. Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919 USA
- BioEnergy Science Center, Oak Ridge, TN USA
- Biosciences Division, Energy and Environment Directorate, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University and CNRS, Marseille, France
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3). Appl Environ Microbiol 2017; 83:AEM.00521-17. [PMID: 28314726 DOI: 10.1128/aem.00521-17] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/11/2017] [Indexed: 01/01/2023] Open
Abstract
We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic data sets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene data sets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic data sets comprising 73,079 proteins. Metabolic reconstruction suggests a prevalent saprophytic lifestyle in all "Latescibacteria" orders, with marked capacities for the degradation of proteins, lipids, and polysaccharides predominant in plant, bacterial, fungal/crustacean, and eukaryotic algal cell walls. As well, extensive transport and central metabolic pathways for the metabolism of imported monomers were identified. Interestingly, genes and domains suggestive of the production of a cellulosome-e.g., protein-coding genes harboring dockerin I domains attached to a glycosyl hydrolase and scaffoldin-encoding genes harboring cohesin I and CBM37 domains-were identified in order PBSIII_9, GN03, and MSB-4E2 fragments recovered from four anoxic aquatic habitats; hence extending the cellulosomal production capabilities in Bacteria beyond the Gram-positive Firmicutes In addition to fermentative pathways, a complete electron transport chain with terminal cytochrome c oxidases Caa3 (for operation under high oxygen tension) and Cbb3 (for operation under low oxygen tension) were identified in PBSIII_9 and GN03 fragments recovered from oxygenated and partially/seasonally oxygenated aquatic habitats. Our metagenomic recruitment effort hence represents a comprehensive pangenomic view of this yet-uncultured phylum and provides insights broader than and complementary to those gained from genome recovery initiatives focusing on a single or few sampled environments.IMPORTANCE Our understanding of the phylogenetic diversity, metabolic capabilities, and ecological roles of yet-uncultured microorganisms is rapidly expanding. However, recent efforts mainly have been focused on recovering genomes of novel microbial lineages from a specific sampling site, rather than from a wide range of environmental habitats. To comprehensively evaluate the genomic landscape, putative metabolic capabilities, and ecological roles of yet-uncultured candidate phyla, efforts that focus on the recovery of genomic fragments from a wide range of habitats and that adequately sample the intraphylum diversity within a specific target lineage are needed. Here, we investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" Our results document the preference of specific "Latescibacteria" orders to specific habitats, the prevalence of plant polysaccharide degradation abilities within all "Latescibacteria" orders, the occurrence of all genes/domains necessary for the production of cellulosomes within three "Latescibacteria" orders (GN03, PBSIII_9, and MSB-4E2) in data sets recovered from anaerobic locations, and the identification of the components of an aerobic respiratory chain, as well as occurrence of multiple O2-dependent metabolic reactions in "Latescibacteria" orders GN03 and PBSIII_9 recovered from oxygenated habitats. The results demonstrate the value of phylocentric pangenomic surveys for understanding the global ecological distribution and panmetabolic abilities of yet-uncultured microbial lineages since they provide broader and more complementary insights than those gained from single-cell genomic and/or metagenomic-enabled genome recovery efforts focusing on a single sampling site.
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Yue Y, Lu YY, Li M, Zhang ZJ, Tan TW, Fan LH. Co-localization of proteins with defined sequential order and controlled stoichiometric ratio on magnetic nanoparticles. NANOSCALE 2017; 9:4397-4400. [PMID: 28319222 DOI: 10.1039/c7nr00557a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Co-immobilization of enzymes used in cascade reactions is important for improving the overall catalytic efficiency. In this work, we employed scaffoldins as a bridge and succeeded in a highly-ordered co-localization of multiple proteins on magnetic nanoparticles with a loading capacity of ∼0.831 μmol g-1 supports.
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Affiliation(s)
- Yi Yue
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. and Beijing Key Laboratory of Bioprocess, Beijing 100029, China
| | - Yang-Yang Lu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. and Beijing Key Laboratory of Bioprocess, Beijing 100029, China
| | - Mei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. and Beijing Key Laboratory of Bioprocess, Beijing 100029, China
| | - Zi-Jian Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. and Beijing Key Laboratory of Bioprocess, Beijing 100029, China
| | - Tian-Wei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. and Beijing Key Laboratory of Bioprocess, Beijing 100029, China
| | - Li-Hai Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. and Beijing Key Laboratory of Bioprocess, Beijing 100029, China
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Artzi L, Bayer EA, Moraïs S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat Rev Microbiol 2017; 15:83-95. [PMID: 27941816 DOI: 10.1038/nrmicro.2016.164] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes are multienzyme complexes that are produced by anaerobic cellulolytic bacteria for the degradation of lignocellulosic biomass. They comprise a complex of scaffoldin, which is the structural subunit, and various enzymatic subunits. The intersubunit interactions in these multienzyme complexes are mediated by cohesin and dockerin modules. Cellulosome-producing bacteria have been isolated from a large variety of environments, which reflects their prevalence and the importance of this microbial enzymatic strategy. In a given species, cellulosomes exhibit intrinsic heterogeneity, and between species there is a broad diversity in the composition and configuration of cellulosomes. With the development of modern technologies, such as genomics and proteomics, the full protein content of cellulosomes and their expression levels can now be assessed and the regulatory mechanisms identified. Owing to their highly efficient organization and hydrolytic activity, cellulosomes hold immense potential for application in the degradation of biomass and are the focus of much effort to engineer an ideal microorganism for the conversion of lignocellulose to valuable products, such as biofuels.
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Affiliation(s)
- Lior Artzi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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Abstract
Designer cellulosomes consist of chimeric cohesin-bearing scaffoldins for the controlled incorporation of recombinant dockerin-containing enzymes. The largest designer cellulosome reported to date is a chimeric scaffoldin that contains 6 cohesins. This scaffoldin represented a technical limit of sorts, since adding another cohesin proved problematic, owing to resultant low expression levels, instability (cleavage) of the scaffoldin polypeptide, and limited numbers of available cohesin-dockerin specificities—the hallmark of designer cellulosomes. Nevertheless, increasing the number of enzymes integrated into designer cellulosomes is critical, in order to further enhance degradation of plant cell wall material. Adaptor scaffoldins comprise an intermediate type of scaffoldin that can both incorporate various enzymes and attach to an additional scaffoldin. Using this strategy, we constructed an efficient form of adaptor scaffoldin that possesses three type I cohesins for enzyme integration, a single type II dockerin for interaction with an additional scaffoldin, and a carbohydrate-binding module for targeting to the cellulosic substrate. In parallel, we designed a hexavalent scaffoldin capable of connecting to the adaptor scaffoldin by the incorporation of an appropriate type II cohesin. The resultant extended designer cellulosome comprised 8 recombinant enzymes—4 xylanases and 4 cellulases—thereby representing a potent enzymatic cocktail for solubilization of natural lignocellulosic substrates. The contribution of the adaptor scaffoldin clearly demonstrated that proximity between the two scaffoldins and their composite set of enzymes is crucial for optimized degradation. After 72 h of incubation, the performance of the extended designer cellulosome was determined to be approximately 70% compared to that of native cellulosomes. Plant cell wall residues represent a major source of renewable biomass for the production of biofuels such as ethanol via breakdown to soluble sugars. The natural microbial degradation process, however, is inefficient for achieving cost-effective processes in the conversion of plant-derived biomass to biofuels, either from dedicated crops or human-generated cellulosic wastes. The accumulation of the latter is considered a major environmental pollutant. The development of designer cellulosome nanodevices for enhanced plant cell wall degradation thus has major impacts in the fields of environmental pollution, bioenergy production, and biotechnology in general. The findings reported in this article comprise a true breakthrough in our capacity to produce extended designer cellulosomes via synthetic biology means, thus enabling the assembly of higher-order complexes that can supersede the number of enzymes included in a single multienzyme complex.
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Cameron K, Najmudin S, Alves VD, Bayer EA, Smith SP, Bule P, Waller H, Ferreira LMA, Gilbert HJ, Fontes CMGA. Cell-surface Attachment of Bacterial Multienzyme Complexes Involves Highly Dynamic Protein-Protein Anchors. J Biol Chem 2015; 290:13578-90. [PMID: 25855788 PMCID: PMC4505603 DOI: 10.1074/jbc.m114.633339] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/31/2015] [Indexed: 11/06/2022] Open
Abstract
Protein-protein interactions play a pivotal role in the assembly of the cellulosome, one of nature's most intricate nanomachines dedicated to the depolymerization of complex carbohydrates. The integration of cellulosomal components usually occurs through the binding of type I dockerin modules located at the C terminus of the enzymes to cohesin modules located in the primary scaffoldin subunit. Cellulosomes are typically recruited to the cell surface via type II cohesin-dockerin interactions established between primary and cell-surface anchoring scaffoldin subunits. In contrast with type II interactions, type I dockerins usually display a dual binding mode that may allow increased conformational flexibility during cellulosome assembly. Acetivibrio cellulolyticus produces a highly complex cellulosome comprising an unusual adaptor scaffoldin, ScaB, which mediates the interaction between the primary scaffoldin, ScaA, through type II cohesin-dockerin interactions and the anchoring scaffoldin, ScaC, via type I cohesin-dockerin interactions. Here, we report the crystal structure of the type I ScaB dockerin in complex with a type I ScaC cohesin in two distinct orientations. The data show that the ScaB dockerin displays structural symmetry, reflected by the presence of two essentially identical binding surfaces. The complex interface is more extensive than those observed in other type I complexes, which results in an ultra-high affinity interaction (Ka ∼10(12) M). A subset of ScaB dockerin residues was also identified as modulating the specificity of type I cohesin-dockerin interactions in A. cellulolyticus. This report reveals that recruitment of cellulosomes onto the cell surface may involve dockerins presenting a dual binding mode to incorporate additional flexibility into the quaternary structure of highly populated multienzyme complexes.
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Affiliation(s)
- Kate Cameron
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal,
| | - Victor D Alves
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Edward A Bayer
- the Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Steven P Smith
- the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada, and
| | - Pedro Bule
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Helen Waller
- the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Luís M A Ferreira
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Harry J Gilbert
- the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Carlos M G A Fontes
- From the CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal,
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Abstract
Clostridium clariflavum is an anaerobic, cellulosome-forming thermophile, containing in its genome genes for a large number of cellulosomal enzyme and a complex scaffoldin system. Previously, we described the major cohesin-dockerin interactions of the cellulosome components, and on this basis a model of diverse cellulosome assemblies was derived. In this work, we cultivated C. clariflavum on cellobiose-, microcrystalline cellulose-, and switchgrass-containing media and isolated cell-free cellulosome complexes from each culture. Gel filtration separation of the cellulosome samples revealed two major fractions, which were analyzed by label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) in order to identify the key players of the cellulosome assemblies therein. From the 13 scaffoldins present in the C. clariflavum genome, 11 were identified, and a variety of enzymes from different glycoside hydrolase and carbohydrate esterase families were identified, including the glycoside hydrolase families GH48, GH9, GH5, GH30, GH11, and GH10. The expression level of the cellulosomal proteins varied as a function of the carbon source used for cultivation of the bacterium. In addition, the catalytic activity of each cellulosome was examined on different cellulosic substrates, xylan and switchgrass. The cellulosome isolated from the microcrystalline cellulose-containing medium was the most active of all the cellulosomes that were tested. The results suggest that the expression of the cellulosome proteins is regulated by the type of substrate in the growth medium. Moreover, both cell-free and cell-bound cellulosome complexes were produced which together may degrade the substrate in a synergistic manner. These observations are compatible with our previously published model of cellulosome assemblies in this bacterium. Because the reservoir of unsustainable fossil fuels, such as coal, petroleum, and natural gas, is overutilized and continues to contribute to environmental pollution and CO2 emission, the need for appropriate alternative energy sources becomes more crucial. Bioethanol produced from dedicated crops and cellulosic waste can provide a partial answer, yet a cost-effective production method must be developed. The cellulosome system of the anaerobic thermophile C. clariflavum comprises a large number of cellulolytic and hemicellulolytic enzymes, which self-assemble in a number of different cellulosome architectures for enhanced cellulosic biomass degradation. Identification of the major cellulosomal components expressed during growth of the bacterium and their influence on its catalytic capabilities provide insight into the performance of the remarkable cellulosome of this intriguing bacterium. The findings, together with the thermophilic characteristics of the proteins, render C. clariflavum of great interest for future use in industrial cellulose conversion processes.
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Hamberg Y, Ruimy-Israeli V, Dassa B, Barak Y, Lamed R, Cameron K, Fontes CMGA, Bayer EA, Fried DB. Elaborate cellulosome architecture of Acetivibrio cellulolyticus revealed by selective screening of cohesin-dockerin interactions. PeerJ 2014; 2:e636. [PMID: 25374780 PMCID: PMC4217186 DOI: 10.7717/peerj.636] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/02/2014] [Indexed: 11/20/2022] Open
Abstract
Cellulosic waste represents a significant and underutilized carbon source for the biofuel industry. Owing to the recalcitrance of crystalline cellulose to enzymatic degradation, it is necessary to design economical methods of liberating the fermentable sugars required for bioethanol production. One route towards unlocking the potential of cellulosic waste lies in a highly complex class of molecular machines, the cellulosomes. Secreted mainly by anaerobic bacteria, cellulosomes are structurally diverse, cell surface-bound protein assemblies that can contain dozens of catalytic components. The key feature of the cellulosome is its modularity, facilitated by the ultra-high affinity cohesin-dockerin interaction. Due to the enormous number of cohesin and dockerin modules found in a typical cellulolytic organism, a major bottleneck in understanding the biology of cellulosomics is the purification of each cohesin- and dockerin-containing component, prior to analyses of their interaction. As opposed to previous approaches, the present study utilized proteins contained in unpurified whole-cell extracts. This strategy was made possible due to an experimental design that allowed for the relevant proteins to be "purified" via targeted affinity interactions as a function of the binding assay. The approach thus represents a new strategy, appropriate for future medium- to high-throughput screening of whole genomes, to determine the interactions between cohesins and dockerins. We have selected the cellulosome of Acetivibrio cellulolyticus for this work due to its exceptionally complex cellulosome systems and intriguing diversity of its cellulosomal modular components. Containing 41 cohesins and 143 dockerins, A. cellulolyticus has one of the largest number of potential cohesin-dockerin interactions of any organism, and contains unusual and novel cellulosomal features. We have surveyed a representative library of cohesin and dockerin modules spanning the cellulosome's total cohesin and dockerin sequence diversity, emphasizing the testing of unusual and previously-unknown protein modules. The screen revealed several novel cell-bound cellulosome architectures, thus expanding on those previously known, as well as soluble cellulose systems that are not bound to the bacterial cell surface. This study sets the stage for screening the entire complement of cellulosomal components from A. cellulolyticus and other organisms with large cellulosome systems. The knowledge gained by such efforts brings us closer to understanding the exceptional catalytic abilities of cellulosomes and will allow the use of novel cellulosomal components in artificial assemblies and in enzyme cocktails for sustainable energy-related research programs.
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Affiliation(s)
- Yuval Hamberg
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot , Israel
| | - Vered Ruimy-Israeli
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot , Israel
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot , Israel
| | - Yoav Barak
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot , Israel ; Chemical Research Support, The Weizmann Institute of Science , Rehovot , Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University , Ramat Aviv , Israel
| | - Kate Cameron
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa , Avenida da Universidade Técnica, Lisboa , Portugal
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa , Avenida da Universidade Técnica, Lisboa , Portugal
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot , Israel
| | - Daniel B Fried
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot , Israel
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Artzi L, Dassa B, Borovok I, Shamshoum M, Lamed R, Bayer EA. Cellulosomics of the cellulolytic thermophile Clostridium clariflavum. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:100. [PMID: 26413154 PMCID: PMC4582956 DOI: 10.1186/1754-6834-7-100] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium clariflavum is an anaerobic, thermophilic, Gram-positive bacterium, capable of growth on crystalline cellulose as a single carbon source. The genome of C. clariflavum has been sequenced to completion, and numerous cellulosomal genes were identified, including putative scaffoldin and enzyme subunits. RESULTS Bioinformatic analysis of the C. clariflavum genome revealed 49 cohesin modules distributed on 13 different scaffoldins and 79 dockerin-containing proteins, suggesting an abundance of putative cellulosome assemblies. The 13-scaffoldin system of C. clariflavum is highly reminiscent of the proposed cellulosome system of Acetivibrio cellulolyticus. Analysis of the C. clariflavum type I dockerin sequences indicated a very high level of conservation, wherein the putative recognition residues are remarkably similar to those of A. cellulolyticus. The numerous interactions among the cellulosomal components were elucidated using a standardized affinity ELISA-based fusion-protein system. The results revealed a rather simplistic recognition pattern of cohesin-dockerin interaction, whereby the type I and type II cohesins generally recognized the dockerins of the same type. The anticipated exception to this rule was the type I dockerin of the ScaB adaptor scaffoldin which bound selectively to the type I cohesins of ScaC and ScaJ. CONCLUSIONS The findings reveal an intricate picture of predicted cellulosome assemblies in C. clariflavum. The network of cohesin-dockerin pairs provides a thermophilic alternative to those of C. thermocellum and a basis for subsequent utilization of the C. clariflavum cellulosomal system for biotechnological application.
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Affiliation(s)
- Lior Artzi
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Melina Shamshoum
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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15
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Vazana Y, Barak Y, Unger T, Peleg Y, Shamshoum M, Ben-Yehezkel T, Mazor Y, Shapiro E, Lamed R, Bayer EA. A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:182. [PMID: 24341331 PMCID: PMC3878649 DOI: 10.1186/1754-6834-6-182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/27/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Select cellulolytic bacteria produce multi-enzymatic cellulosome complexes that bind to the plant cell wall and catalyze its efficient degradation. The multi-modular interconnecting cellulosomal subunits comprise dockerin-containing enzymes that bind cohesively to cohesin-containing scaffoldins. The organization of the modules into functional polypeptides is achieved by intermodular linkers of different lengths and composition, which provide flexibility to the complex and determine its overall architecture. RESULTS Using a synthetic biology approach, we systematically investigated the spatial organization of the scaffoldin subunit and its effect on cellulose hydrolysis by designing a combinatorial library of recombinant trivalent designer scaffoldins, which contain a carbohydrate-binding module (CBM) and 3 divergent cohesin modules. The positions of the individual modules were shuffled into 24 different arrangements of chimaeric scaffoldins. This basic set was further extended into three sub-sets for each arrangement with intermodular linkers ranging from zero (no linkers), 5 (short linkers) and native linkers of 27-35 amino acids (long linkers). Of the 72 possible scaffoldins, 56 were successfully cloned and 45 of them expressed, representing 14 full sets of chimaeric scaffoldins. The resultant 42-component scaffoldin library was used to assemble designer cellulosomes, comprising three model C. thermocellum cellulases. Activities were examined using Avicel as a pure microcrystalline cellulose substrate and pretreated cellulose-enriched wheat straw as a model substrate derived from a native source. All scaffoldin combinations yielded active trivalent designer cellulosome assemblies on both substrates that exceeded the levels of the free enzyme systems. A preferred modular arrangement for the trivalent designer scaffoldin was not observed for the three enzymes used in this study, indicating that they could be integrated at any position in the designer cellulosome without significant effect on cellulose-degrading activity. Designer cellulosomes assembled with the long-linker scaffoldins achieved higher levels of activity, compared to those assembled with short-and no-linker scaffoldins. CONCLUSIONS The results demonstrate the robustness of the cellulosome system. Long intermodular scaffoldin linkers are preferable, thus leading to enhanced degradation of cellulosic substrates, presumably due to the increased flexibility and spatial positioning of the attached enzymes in the complex. These findings provide a general basis for improved designer cellulosome systems as a platform for bioethanol production.
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Affiliation(s)
- Yael Vazana
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Barak
- Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Unger
- Structural Proteomics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Peleg
- Structural Proteomics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Melina Shamshoum
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tuval Ben-Yehezkel
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yair Mazor
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ehud Shapiro
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Yaniv O, Petkun S, Shimon LJW, Bayer EA, Lamed R, Frolow F. A single mutation reforms the binding activity of an adhesion-deficient family 3 carbohydrate-binding module. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:819-28. [PMID: 22751667 DOI: 10.1107/s0907444912013133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 03/26/2012] [Indexed: 11/10/2022]
Abstract
The crystal structure of the family 3b carbohydrate-binding module (CBM3b) of the cellulosomal multimodular hydrolytic enzyme cellobiohydrolase 9A (Cbh9A) from Clostridium thermocellum has been determined. Cbh9A CBM3b crystallized in space group P4(1) with four molecules in the asymmetric unit and diffracted to a resolution of 2.20 Å using synchrotron radiation. The structure was determined by molecular replacement using C. thermocellum Cel9V CBM3b' (PDB entry 2wnx) as a model. The C. thermocellum Cbh9A CBM3b molecule forms a nine-stranded antiparallel β-sandwich similar to other family 3 carbohydrate-binding modules (CBMs). It has a short planar array of two aromatic residues that are assumed to bind cellulose, yet it lacks the ability to bind cellulose. The molecule contains a shallow groove of unknown function that characterizes other family 3 CBMs with high sequence homology. In addition, it contains a calcium-binding site formed by a group of amino-acid residues that are highly conserved in similar structures. After determination of the three-dimensional structure of Cbh9A CBM3b, the site-specific N126W mutant was produced with the intention of enhancing the cellulose-binding ability of the CBM. Cbh9A CBM3b(N126W) crystallized in space group P4(1)2(1)2, with one molecule in the asymmetric unit. The crystals diffracted to 1.04 Å resolution using synchrotron radiation. The structure of Cbh9A CBM3b(N126W) revealed incorporation of the mutated Trp126 into the putative cellulose-binding strip of residues. Cellulose-binding experiments demonstrated the ability of Cbh9A CBM3b(N126W) to bind cellulose owing to the mutation. This is the first report of the engineered conversion of a non-cellulose-binding CBM3 to a binding CBM3 by site-directed mutagenesis. The three-dimensional structure of Cbh9A CBM3b(N126W) provided a structural correlation with cellulose-binding ability, revealing a longer planar array of definitive cellulose-binding residues.
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Affiliation(s)
- Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
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17
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Dassa B, Borovok I, Lamed R, Henrissat B, Coutinho P, Hemme CL, Huang Y, Zhou J, Bayer EA. Genome-wide analysis of acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. BMC Genomics 2012; 13:210. [PMID: 22646801 PMCID: PMC3413522 DOI: 10.1186/1471-2164-13-210] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/30/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth. In order to process heterogeneous plant-derived biomass, specialized anaerobic bacteria use an elaborate multi-enzyme cellulosome complex to synergistically deconstruct cellulosic substrates. The cellulosome was first discovered in the cellulolytic thermophile, Clostridium thermocellum, and much of our knowledge of this intriguing type of protein composite is based on the cellulosome of this environmentally and biotechnologically important bacterium. The recently sequenced genome of the cellulolytic mesophile, Acetivibrio cellulolyticus, allows detailed comparison of the cellulosomes of these two select cellulosome-producing bacteria. RESULTS Comprehensive analysis of the A. cellulolyticus draft genome sequence revealed a very sophisticated cellulosome system. Compared to C. thermocellum, the cellulosomal architecture of A. cellulolyticus is much more extensive, whereby the genome encodes for twice the number of cohesin- and dockerin-containing proteins. The A. cellulolyticus genome has thus evolved an inflated number of 143 dockerin-containing genes, coding for multimodular proteins with distinctive catalytic and carbohydrate-binding modules that play critical roles in biomass degradation. Additionally, 41 putative cohesin modules distributed in 16 different scaffoldin proteins were identified in the genome, representing a broader diversity and modularity than those of Clostridium thermocellum. Although many of the A. cellulolyticus scaffoldins appear in unconventional modular combinations, elements of the basic structural scaffoldins are maintained in both species. In addition, both species exhibit similarly elaborate cell-anchoring and cellulosome-related gene- regulatory elements. CONCLUSIONS This work portrays a particularly intricate, cell-surface cellulosome system in A. cellulolyticus and provides a blueprint for examining the specific roles of the various cellulosomal components in the degradation of complex carbohydrate substrates of the plant cell wall by the bacterium.
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Affiliation(s)
- Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Bernard Henrissat
- Architecture et Fonction des Macromolecules Biologiques, CNRS and Universite Aix- Marseilles I & II, Marseilles, France
| | - Pedro Coutinho
- Architecture et Fonction des Macromolecules Biologiques, CNRS and Universite Aix- Marseilles I & II, Marseilles, France
| | - Christopher L Hemme
- Department of Botany and Microbiology, and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yue Huang
- Department of Botany and Microbiology, and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Department of Botany and Microbiology, and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Pinheiro BA, Brás JLA, Najmudin S, Carvalho AL, Ferreira LMA, Prates JAM, Fontes CMGA. Flexibility and specificity of the cohesin–dockerin interaction: implications for cellulosome assembly and functionality. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.681854] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Yaniv O, Halfon Y, Shimon LJW, Bayer EA, Lamed R, Frolow F. Structure of CBM3b of the major cellulosomal scaffoldin subunit ScaA from Acetivibrio cellulolyticus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:8-13. [PMID: 22232162 PMCID: PMC3253825 DOI: 10.1107/s174430911104807x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/11/2011] [Indexed: 11/10/2022]
Abstract
The carbohydrate-binding module (CBM) of the major scaffoldin subunit ScaA of the cellulosome of Acetivibrio cellulolyticus is classified as a family 3b CBM and binds strongly to cellulose. The CBM3b was overexpressed, purified and crystallized, and its three-dimensional structure was determined. The structure contained a nickel-binding site located at the N-terminal region in addition to a 'classical' CBM3b calcium-binding site. The structure was also determined independently by the SAD method using data collected at the Ni-absorption wavelength of 1.48395 Å and even at a wavelength of 0.97625 Å in a favourable case. The new scaffoldin-borne CBM3 structure reported here provides clear evidence for the proposition that a family 3b CBM may be accommodated in scaffoldin subunits and functions as the major substrate-binding entity of the cellulosome assembly.
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Affiliation(s)
- Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
- Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Yehuda Halfon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
- Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
- Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
- Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978 Tel Aviv, Israel
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20
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Yaniv O, Shimon LJW, Bayer EA, Lamed R, Frolow F. Scaffoldin-borne family 3b carbohydrate-binding module from the cellulosome of Bacteroides cellulosolvens: structural diversity and significance of calcium for carbohydrate binding. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:506-15. [PMID: 21636890 DOI: 10.1107/s0907444911011322] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 03/27/2011] [Indexed: 11/10/2022]
Abstract
The potent cellulose-binding modules of cellulosomal scaffoldin subunits belong to the greater family of carbohydrate-binding modules (CBMs). They have generally been classified as belonging to family 3a on the basis of sequence similarity. They form nine-stranded β-sandwich structures with jelly-roll topology. The members of this family possess on their surface a planar array of aromatic amino-acid residues (known as the linear strip) that form stacking interactions with the glucose rings of cellulose chains and have a conserved Ca(2+)-binding site. Intriguingly, the CBM3 from scaffoldin A (ScaA) of Bacteroides cellulosolvens exhibits alterations in sequence that make it more similar to the CBMs of free cellulolytic enzymes, which are classified into CBM family 3b. X-ray structural analysis was undertaken in order to examine the structural consequences of the sequence changes and the consequent family affiliation. The CBM3 crystallized in space group I4(1)22 with one molecule in the asymmetric unit, yielding diffraction to a resolution of 1.83 Å using X-ray synchrotron radiation. Compared with the known structures of other scaffoldin-borne CBMs, a sequence insertion and deletion appear to compensate for each other as both contained an aromatic residue that is capable of contributing to cellulose binding; hence, even though there are alterations in the composition and localization of the aromatic residues in the linear strip its binding ability was not compromised. Interestingly, no Ca(2+) ions were detected in the conserved calcium-binding site, although the module was properly folded; this suggests that the structural role of Ca(2+) is less important than originally supposed. These observations indicate that despite their conserved function the scaffoldin-borne CBMs are more diverse in their sequences and structures than previously assumed.
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Affiliation(s)
- Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
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21
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Synergy, Structure and Conformational Flexibility of Hybrid Cellulosomes Displaying Various Inter-cohesins Linkers. J Mol Biol 2011; 405:143-57. [DOI: 10.1016/j.jmb.2010.10.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 10/07/2010] [Accepted: 10/12/2010] [Indexed: 11/17/2022]
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Petkun S, Jindou S, Shimon LJW, Rosenheck S, Bayer EA, Lamed R, Frolow F. Structure of a family 3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum: structural diversity and implications for carbohydrate binding. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 66:33-43. [PMID: 20057047 DOI: 10.1107/s0907444909043030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 10/19/2009] [Indexed: 11/10/2022]
Abstract
Family 3 carbohydrate-binding modules (CBM3s) are associated with both cellulosomal scaffoldins and family 9 glycoside hydrolases (GH9s), which are multi-modular enzymes that act on cellulosic substrates. CBM3s bind cellulose. X-ray crystal structures of these modules have established an accepted cellulose-binding mechanism based on stacking interactions between the sugar rings of cellulose and a planar array of aromatic residues located on the CBM3 surface. These planar-strip residues are generally highly conserved, although some CBM3 sequences lack one or more of these residues. In particular, CBM3b' from Clostridium thermocellum Cel9V exhibits such sequence changes and fails to bind cellulosic substrates. A crystallographic investigation of CBM3b' has been initiated in order to understand the structural reason(s) for this inability. CBM3b' crystallized in space group C222(1) (diffraction was obtained to 2.0 A resolution in-house) with three independent molecules in the asymmetric unit and in space group P4(1)2(1)2 (diffraction was obtained to 1.79 A resolution in-house and to 1.30 A resolution at a synchrotron) with one molecule in the asymmetric unit. The molecular structure of Cel9V CBM3b' revealed that in addition to the loss of several cellulose-binding residues in the planar strip, changes in the backbone create a surface 'hump' which could interfere with the formation of cellulose-protein surface interactions and thus prevent binding to crystalline cellulose.
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Affiliation(s)
- Svetlana Petkun
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
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Noach I, Frolow F, Alber O, Lamed R, Shimon LJW, Bayer EA. Intermodular linker flexibility revealed from crystal structures of adjacent cellulosomal cohesins of Acetivibrio cellulolyticus. J Mol Biol 2009; 391:86-97. [PMID: 19501595 DOI: 10.1016/j.jmb.2009.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/25/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
Cellulosome complexes comprise an intercalated set of multimodular dockerin-containing enzymatic subunits connected to cohesin-containing nonenzymatic subunits called scaffoldins. The adjoining modules in each cellulosomal subunit are interconnected by a variety of linker segments of different lengths and composition. The exact role of the cellulosomal linkers has yet to be described, although it is assumed that they contribute to the architecture and action of the cellulosome by providing the protein subunits with flexibility and by providing spacers between the enzymatic modules that could enhance interactions with the cellulose substrate. Here we present four crystal structures of Acetivibrio cellulolyticus cellulosomal type II cohesins with linker extensions. Two of the structures represent two different crystal forms (trigonal and orthorhombic) of the same N-terminal cohesin module (CohB1) together with its full (6-residue) native C-terminal linker, derived from scaffoldin B. The other two structures belong to the adjacent (second) cohesin module (CohB2), each of which was crystallized with the same 6-residue linker segment, but now positioned at the N-terminus and with either a truncated (5-residue) or a full-length (45-residue) C-terminal linker, respectively. Comparison between the two CohB1 structures revealed significant differences in the conformation of their equivalent C-terminal linker segment. In one crystal form a helical conformation was observed, as opposed to an extended conformation in the other. The CohB2 structures also displayed diverse conformations in their linker segments. In these structures, different linker conformations were observed in the individual molecules within the asymmetric unit of each structure. This conformational diversity implies that the linkers may adopt alternative conformations in their natural environment, consistent with varying environmental conditions. The findings suggest that linkers can play an important role in the assembly, dynamics and function of the cellulosomal components.
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Affiliation(s)
- Ilit Noach
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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24
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Pason P, Kosugi A, Waeonukul R, Tachaapaikoon C, Ratanakhanokchai K, Arai T, Murata Y, Nakajima J, Mori Y. Purification and characterization of a multienzyme complex produced by Paenibacillus curdlanolyticus B-6. Appl Microbiol Biotechnol 2009; 85:573-80. [DOI: 10.1007/s00253-009-2117-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/27/2009] [Accepted: 06/28/2009] [Indexed: 10/20/2022]
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25
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A Novel Endoglucanase (Cel9P) From a Marine Bacterium Paenibacillus sp. BME-14. Appl Biochem Biotechnol 2009; 160:1627-36. [DOI: 10.1007/s12010-009-8648-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Accepted: 04/12/2009] [Indexed: 11/27/2022]
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26
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Abstract
Cellulosomes are intricate multienzyme systems produced by several cellulolytic bacteria, the first example of which was discovered in the anaerobic thermophilic bacterium, Clostridium thermocellum. Cellulosomes are designed for efficient degradation of plant cell wall polysaccharides, notably cellulose--the most abundant renewable polymer on earth. The component parts of the multicomponent complex are integrated by virtue of a unique family of integrating modules, the cohesins and the dockerins, whose distribution and specificity dictate the overall cellulosome architecture. A full generation of research has elapsed since the original publications that documented the cellulosome concept. In this review, we provide a personal account on the discovery process, while describing how divergent cellulosome systems were identified and investigated, culminating in the collaboration of several labs worldwide to tackle together the challenging field of cellulosome genomics and metagenomics.
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Affiliation(s)
- Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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27
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Peer A, Smith SP, Bayer EA, Lamed R, Borovok I. Noncellulosomal cohesin- and dockerin-like modules in the three domains of life. FEMS Microbiol Lett 2008; 291:1-16. [PMID: 19025568 DOI: 10.1111/j.1574-6968.2008.01420.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. Until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. Widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing proteins in Bacteria, Archaea, and in primitive eukaryotes. The newly identified modules appear to serve diverse functions that are clearly distinct from the classical cellulosome archetype, and the vast majority of parent proteins are not predicted glycoside hydrolases. In most cases, only a few such genes have been identified in a given microorganism, which encode proteins containing but a single cohesin and/or dockerin. In some cases, one or the other module appears to be missing from a given species, and in other cases both modules occur within the same protein. This review provides a bioinformatics-based survey of the current status of cohesin- and dockerin-like sequences in species from the Bacteria, Archaea, and Eukarya. Surprisingly, many identified modules and their parent proteins are clearly unrelated to cellulosomes. The cellulosome paradigm may thus be the exception rather than the rule for bacterial, archaeal, and eukaryotic employment of cohesin and dockerin modules.
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Affiliation(s)
- Ayelet Peer
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
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28
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Ding SY, Xu Q, Crowley M, Zeng Y, Nimlos M, Lamed R, Bayer EA, Himmel ME. A biophysical perspective on the cellulosome: new opportunities for biomass conversion. Curr Opin Biotechnol 2008; 19:218-27. [PMID: 18513939 DOI: 10.1016/j.copbio.2008.04.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 04/28/2008] [Accepted: 04/29/2008] [Indexed: 11/28/2022]
Abstract
The cellulosome is a multiprotein complex, produced primarily by anaerobic microorganisms, which functions to degrade lignocellulosic materials. An important topic of current debate is whether cellulosomal systems display greater ability to deconstruct complex biomass materials (e.g. plant cell walls) than nonaggregated enzymes, and in so doing would be appropriate for improved, commercial bioconversion processes. To sufficiently understand the complex macromolecular processes between plant cell wall polymers, cellulolytic microbes, and their secreted enzymes, a highly concerted research approach is required. Adaptation of existing biophysical techniques and development of new science tools must be applied to this system. This review focuses on strategies likely to permit improved understanding of the bacterial cellulosome using biophysical approaches, with emphasis on advanced imaging and computational techniques.
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Affiliation(s)
- Shi-You Ding
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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29
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Haimovitz R, Barak Y, Morag E, Voronov-Goldman M, Shoham Y, Lamed R, Bayer EA. Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules. Proteomics 2008; 8:968-79. [PMID: 18219699 DOI: 10.1002/pmic.200700486] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Indexed: 11/10/2022]
Abstract
The cellulosome is an intricate multienzyme complex, designed for efficient degradation of plant cell wall polysaccharides, notably cellulose. The supramolecular cellulosome architecture in different bacteria is the consequence of the types and specificities of the interacting cohesin and dockerin modules, borne by the different cellulosomal subunits. In this study, we describe a microarray system for determining cohesin-dockerin specificity, which allows global comparison among the interactions between various members of these two complementary families of interacting protein modules. Matching recombinant fusion proteins were prepared that contained one of the interacting modules: cohesins were joined to an appropriate cellulose-binding module (CBM) and the dockerins were fused to a thermostable xylanase that served to enhance expression and proper folding. The CBM-fused cohesins were immobilized on cellulose-coated glass slides, to which xylanase-fused dockerin samples were applied. Knowledge of the specificity characteristics of native and mutated members of the cohesin and dockerin families provides insight into the architecture of the parent cellulosome and allows selection of suitable cohesin-dockein pairs for biotechnological and nanotechnological application. Using this approach, extensive cross-species interaction among type-II cohesins and dockerins is shown for the first time. Selective intraspecies binding of an archaeal dockerin to two complementary cohesins is also demonstrated.
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Affiliation(s)
- Rachel Haimovitz
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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30
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Karpol A, Barak Y, Lamed R, Shoham Y, Bayer EA. Functional asymmetry in cohesin binding belies inherent symmetry of the dockerin module: insight into cellulosome assembly revealed by systematic mutagenesis. Biochem J 2008; 410:331-8. [PMID: 18021074 DOI: 10.1042/bj20071193] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The cellulosome is an intricate multi-enzyme complex, known for its efficient degradation of recalcitrant cellulosic substrates. Its supramolecular architecture is determined by the high-affinity intermodular cohesin-dockerin interaction. The dockerin module comprises a calcium-binding, duplicated 'F-hand' loop-helix motif that bears striking similarity to the EF-hand loop-helix-loop motif of eukaryotic calcium-binding proteins. In the present study, we demonstrate by progressive truncation and alanine scanning of a representative type-I dockerin module from Clostridium thermocellum, that only one of the repeated motifs is critical for high-affinity cohesin binding. The results suggest that the near-symmetry in sequence and structure of the repeated elements of the dockerin is not essential to cohesin binding. The first calcium-binding loop can be deleted entirely, with almost full retention of binding. Likewise, significant deletion of the second repeated segment can be achieved, provided that its calcium-binding loop remains intact. Essentially the same conclusion was verified by systematically mutating the highly conserved residues in the calcium-binding loop. Mutations in one of the calcium-binding loops failed to disrupt cohesin recognition and binding, whereas a single mutation in both loops served to reduce the affinity significantly. The results are mutually compatible with recent crystal structures of the type-I cohesin-dockerin heterodimer, which demonstrate that the dockerin can bind in an equivalent manner to its cohesin counterpart through either its first or second repeated motif. The observed plasticity in cohesin-dockerin binding may facilitate cellulosome assembly in vivo or, alternatively, provide a conformational switch that promotes access of the tethered cellulosomal enzymes to their polysaccharide substrates.
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Affiliation(s)
- Alon Karpol
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel
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31
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Noach I, Alber O, Bayer EA, Lamed R, Levy-Assaraf M, Shimon LJW, Frolow F. Crystallization and preliminary X-ray analysis of Acetivibrio cellulolyticus cellulosomal type II cohesin module: two versions having different linker lengths. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:58-61. [PMID: 18097105 PMCID: PMC2373993 DOI: 10.1107/s1744309107066821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 12/13/2007] [Indexed: 11/10/2022]
Abstract
The second type II cohesin module of the cellulosomal scaffoldin polypeptide ScaB from Acetivibrio cellulolyticus (CohB2) was cloned into two constructs: one containing a short (five-residue) C-terminal linker (CohB2_S) and the second incorporating the full native 45-residue linker (CohB2_L). Both constructs encode proteins that also include the full native six-residue N-terminal linker. The CohB2_S and CohB2_L proteins were expressed, purified and crystallized in the orthorhombic crystal system, but with different unit cells and symmetries: space group P2(1)2(1)2(1) with unit-cell parameters a = 90.36, b = 68.65, c = 111.29 A for CohB2_S and space group P2(1)2(1)2 with unit-cell parameters a = 68.76, b = 159.22, c = 44.21 A for CohB2_L. The crystals diffracted to 2.0 and 2.9 A resolution, respectively. The asymmetric unit of CohB2_S contains three cohesin molecules, while that of CohB2_L contains two molecules.
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Affiliation(s)
- Ilit Noach
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Orly Alber
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Maly Levy-Assaraf
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv 69978, Israel
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32
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Doi RH. Cellulases of mesophilic microorganisms: cellulosome and noncellulosome producers. Ann N Y Acad Sci 2007; 1125:267-79. [PMID: 18096849 DOI: 10.1196/annals.1419.002] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The cellulolytic activity of mesophilic bacteria and fungi is described, with special emphasis on the large extracellular enzyme complex called the cellulosome. The cellulosome is composed of a scaffolding protein, which is attached to various cellulolytic and hemicellulolytic enzymes, and this complex allows the organisms to degrade plant cell walls very efficently. The enzymes include a variety of cellulases, hemicellulases, and pectinases that work synergistically to degrade complex cell-wall molecules.
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Affiliation(s)
- Roy H Doi
- Section of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA.
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33
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Mingardon F, Chanal A, Tardif C, Bayer EA, Fierobe HP. Exploration of new geometries in cellulosome-like chimeras. Appl Environ Microbiol 2007; 73:7138-49. [PMID: 17905885 PMCID: PMC2168198 DOI: 10.1128/aem.01306-07] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 09/15/2007] [Indexed: 11/20/2022] Open
Abstract
In this study, novel cellulosome chimeras exhibiting atypical geometries and binding modes, wherein the targeting and proximity functions were directly incorporated as integral parts of the enzyme components, were designed. Two pivotal cellulosomal enzymes (family 48 and 9 cellulases) were thus appended with an efficient cellulose-binding module (CBM) and an optional cohesin and/or dockerin. Compared to the parental enzymes, the chimeric cellulases exhibited improved activity on crystalline cellulose as opposed to their reduced activity on amorphous cellulose. Nevertheless, the various complexes assembled using these engineered enzymes were somewhat less active on crystalline cellulose than the conventional designer cellulosomes containing the parental enzymes. The diminished activity appeared to reflect the number of protein-protein interactions within a given complex, which presumably impeded the mobility of their catalytic modules. The presence of numerous CBMs in a given complex, however, also reduced their performance. Furthermore, a "covalent cellulosome" that combines in a single polypeptide chain a CBM, together with family 48 and family 9 catalytic modules, also exhibited reduced activity. This study also revealed that the cohesin-dockerin interaction may be reversible under specific conditions. Taken together, the data demonstrate that cellulosome components can be used to generate higher-order functional composites and suggest that enzyme mobility is a critical parameter for cellulosome efficiency.
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Affiliation(s)
- Florence Mingardon
- Department of Bioénergétique et Ingénierie des Protéines, CNRS, IBSM, 13402 Marseille, France
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34
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Ai X, Xu Q, Jones M, Song Q, Ding SY, Ellingson RJ, Himmel M, Rumbles G. Photophysics of (CdSe)ZnS colloidal quantum dots in an aqueous environment stabilized with amino acids and genetically-modified proteins. Photochem Photobiol Sci 2007; 6:1027-33. [PMID: 17721603 DOI: 10.1039/b706471c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a combination of two amino acids, histidine and N-acetyl-cysteine, to replace the original organic capping groups of (CdSe)ZnS quantum dots, water-soluble and highly luminescent (CdSe)ZnS quantum dots have been successfully prepared at pH 8. Characterization by steady-state and time-resolved photoluminescence spectroscopy, and transient absorption spectroscopy, demonstrate that the electronic properties of these quantum dots exceed those of the original as-synthesized samples dissolved in a more-conventional organic solvent. Furthermore, these amino acid-stabilized quantum dots have been assembled onto a cellulose substrate via cellulose binding proteins that specifically bind to cellulose and was genetically engineered to harbor dual hexahistidine tags at the N- and C-termini to confer binding with the zinc(II) on the quantum dot surface. The spectroscopic measurements show that the protein-bound quantum dots continue to retain their desirable electronic properties when bound on the substrate. Meanwhile, the specific and very selective binding properties of the proteins have remained effective.
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Affiliation(s)
- Xin Ai
- National Renewable Energy Laboratory, 1617 Cole Blvd, Golden, CO 80401-3393, USA
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35
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Barak Y, Handelsman T, Nakar D, Mechaly A, Lamed R, Shoham Y, Bayer EA. Matching fusion protein systems for affinity analysis of two interacting families of proteins: the cohesin-dockerin interaction. J Mol Recognit 2005; 18:491-501. [PMID: 16167300 DOI: 10.1002/jmr.749] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Cellulosomes are multi-enzyme complexes that orchestrate the efficient degradation of cellulose and related plant cell wall polysaccharides. The complex is maintained by the high-affinity protein-protein interaction between two complementary modules: the cohesin and the dockerin. In order to characterize the interaction between different cohesins and dockerins, we have developed matching fusion-protein systems, which harbor either the cohesin or the dockerin component. For this purpose, corresponding plasmid cassettes were designed, which encoded for the following carrier proteins: (i) a thermostable xylanase with an appended His-tag; and (ii) a highly stable cellulose-binding module (CBM). The resultant xylanase-dockerin and CBM-cohesin fusion products exhibited high expression levels of soluble protein. The expressed, affinity-purified proteins were extremely stable, and the functionality of the cohesin or dockerin component was retained. The fusion protein system was used to establish a sensitive and reliable, semi-quantitative enzyme-linked affinity assay for determining multiple samples of cohesin-dockerin interactions in microtiter plates. A variety of cohesin-dockerin systems, which had been examined previously using other methodologies, were revisited applying the affinity-based enzyme assay, the results of which served to verify the validity of the approach.
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Affiliation(s)
- Yoav Barak
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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36
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Rincon MT, Cepeljnik T, Martin JC, Lamed R, Barak Y, Bayer EA, Flint HJ. Unconventional mode of attachment of the Ruminococcus flavefaciens cellulosome to the cell surface. J Bacteriol 2005; 187:7569-78. [PMID: 16267281 PMCID: PMC1280307 DOI: 10.1128/jb.187.22.7569-7578.2005] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Accepted: 08/24/2005] [Indexed: 11/20/2022] Open
Abstract
Sequence extension of the scaffoldin gene cluster from Ruminococcus flavefaciens revealed a new gene (scaE) that encodes a protein with an N-terminal cohesin domain and a C terminus with a typical gram-positive anchoring signal for sortase-mediated attachment to the bacterial cell wall. The recombinant cohesin of ScaE was recovered after expression in Escherichia coli and was shown to bind to the C-terminal domain of the cellulosomal structural protein ScaB, as well as to three unknown polypeptides derived from native cellulose-bound Ruminococcus flavefaciens protein extracts. The ScaB C terminus includes a cryptic dockerin domain that is unusual in its sequence, and considerably larger than conventional dockerins. The ScaB dockerin binds to ScaE, suggesting that this interaction occurs through a novel cohesin-dockerin pairing. The novel ScaB dockerin was expressed as a xylanase fusion protein, which was shown to bind tenaciously and selectively to a recombinant form of the ScaE cohesin. Thus, ScaE appears to play a role in anchoring the cellulosomal complex to the bacterial cell envelope via its interaction with ScaB. This sortase-mediated mechanism for covalent cell-wall anchoring of the cellulosome in R. flavefaciens differs from those reported thus far for any other cellulosome system.
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Affiliation(s)
- Marco T Rincon
- Microbial Ecology Group, Rowett Research Institute, Aberdeen, UK.
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37
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Abstract
Biomass conversion to ethanol as a liquid fuel by the thermophilic and anaerobic clostridia offers a potential partial solution to the problem of the world's dependence on petroleum for energy. Coculture of a cellulolytic strain and a saccharolytic strain of Clostridium on agricultural resources, as well as on urban and industrial cellulosic wastes, is a promising approach to an alternate energy source from an economic viewpoint. This review discusses the need for such a process, the cellulases of clostridia, their presence in extracellular complexes or organelles (the cellulosomes), the binding of the cellulosomes to cellulose and to the cell surface, cellulase genetics, regulation of their synthesis, cocultures, ethanol tolerance, and metabolic pathway engineering for maximizing ethanol yield.
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Affiliation(s)
- Arnold L Demain
- Charles A. Dana Research Institute for Scientists Emeriti, HS-330, Drew University, Madison, NJ 07940, USA.
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38
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Noach I, Frolow F, Jakoby H, Rosenheck S, Shimon LW, Lamed R, Bayer EA. Crystal structure of a type-II cohesin module from the Bacteroides cellulosolvens cellulosome reveals novel and distinctive secondary structural elements. J Mol Biol 2005; 348:1-12. [PMID: 15808849 DOI: 10.1016/j.jmb.2005.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Revised: 02/01/2005] [Accepted: 02/07/2005] [Indexed: 10/25/2022]
Abstract
The incorporation of enzymes into the multi-enzyme cellulosome complex and its anchoring to the bacterial cell surface are dictated by a set of binding interactions between two complementary protein modules: the cohesin and the dockerin. In this work, the X-ray crystal structure of a type-II cohesin from scaffoldin A of Bacteroides cellulosolvens has been determined to a resolution of 1.6 angstroms using molecular replacement. The type-II B. cellulosolvens cohesin (Bc-cohesin-II) is the first detailed description of a crystal structure for a type-II cohesin, and its features were compared with the known type-I cohesins from Clostridium thermocellum and Clostridium cellulolyticum (Ct-cohesin-I and Cc-cohesin-I, respectively). The overall jelly-roll topology of the type-II Bc-cohesin is very similar to that observed for the type-I cohesins with three additional secondary structures: an alpha-helix and two "beta-flaps" that disrupt the normal course of a beta-strand. In addition, beta-strand 5 is elevated by approximately 4 angstroms on the surface of the molecule, relative to the type-I Ct and Cc-cohesins. Like its type-I analogue, the hydrophobic/aromatic core of Bc-cohesin-II comprises an upper and lower core, but an additional aromatic patch and conserved tryptophan at the crown of the molecule serves to stabilize the alpha-helix of the type-II cohesin. Comparison of Bc-cohesin-II with the known type-I cohesin-dockerin heterodimer suggests that each of the additional secondary structural elements assumes a flanking position relative to the putative dockerin-binding surface. The raised ridge formed by beta-strand 5 confers additional distinctive topographic features to the proposed binding interface that collectively distinguish between the type-II and type-I cohesins.
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Affiliation(s)
- Ilit Noach
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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39
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Adams JJ, Jang CJ, Spencer HL, Elliott M, Smith SP. Expression, purification and structural characterization of the scaffoldin hydrophilic X-module from the cellulosome of Clostridium thermocellum. Protein Expr Purif 2005; 38:258-63. [PMID: 15555941 DOI: 10.1016/j.pep.2004.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Indexed: 11/28/2022]
Abstract
The cellulosome is a membrane-bound, extracellular multi-subunit complex responsible for the degradation of crystalline cellulose by a number of organisms including anaerobic bacteria and fungi. The hydrophilic X-module (CipA-X) from the modular scaffoldin subunit of Clostridium thermocellum cellulosome has been proposed to play various roles in cellulosomal function, including thermal and structural stability. Towards elucidating the function of CipA-X using structural and biophysical studies, the region comprising residues 1692-1785 from the C. thermocellum CipA cDNA encoding CipA-X was cloned into a pET21b expression vector. When expressed in Escherichia coli, the C-terminal His-tagged protein accumulated in the insoluble fraction. Cell fractionation experiments showed that the recombinant protein was localized to inclusion bodies. Refolding and purification involved denaturation of the whole cell lysate by addition of urea, followed by a nickel-Sepharose chromatography step and dialysis into native conditions (25 mM Tris-HCl, pH 7.4, 50 mM NaCl, and 10 mM EDTA). A final gel filtration step purified the protein to homogeneity, yielding 40 mg/L. The two-dimensional 1H-15N correlation spectrum of uniformly 15N-labelled CipA-X showed the characteristics of a well-folded protein comprising significant beta-structure, which is in agreement with the circular dichroism data.
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Affiliation(s)
- Jarrett J Adams
- Department of Biochemistry, Queen's University, Kingston, Ont., Canada
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40
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Xu Q, Barak Y, Kenig R, Shoham Y, Bayer EA, Lamed R. A novel Acetivibrio cellulolyticus anchoring scaffoldin that bears divergent cohesins. J Bacteriol 2004; 186:5782-9. [PMID: 15317783 PMCID: PMC516847 DOI: 10.1128/jb.186.17.5782-5789.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 06/02/2004] [Indexed: 11/20/2022] Open
Abstract
Sequencing of a cellulosome-integrating gene cluster in Acetivibrio cellulolyticus was completed. The cluster contains four tandem scaffoldin genes (scaA, scaB, scaC, and scaD) bounded upstream and downstream, respectively, by a presumed cellobiose phosphorylase and a nucleotide methylase. The sequences and properties of scaA, scaB, and scaC were reported previously, and those of scaD are reported here. The scaD gene encodes an 852-residue polypeptide that includes a signal peptide, three cohesins, and a C-terminal S-layer homology (SLH) module. The calculated molecular weight of the mature ScaD is 88,960; a 67-residue linker segment separates cohesins 1 and 2, and two approximately 30-residue linkers separate cohesin 2 from 3 and cohesin 3 from the SLH module. The presence of an SLH module in ScaD indicates its role as an anchoring protein. The first two ScaD cohesins can be classified as type II, similar to the four cohesins of ScaB. Surprisingly, the third ScaD cohesin belongs to the type I cohesins, like the seven ScaA cohesins. ScaD is the first scaffoldin to be described that contains divergent types of cohesins as integral parts of the polypeptide chain. The recognition properties among selected recombinant cohesins and dockerins from the different scaffoldins of the gene cluster were investigated by affinity blotting. The results indicated that the divergent types of ScaD cohesins also differ in their preference of dockerins. ScaD thus plays a dual role, both as a primary scaffoldin, capable of direct incorporation of a single dockerin-borne enzyme, and as a secondary scaffoldin that anchors the major primary scaffoldin, ScaA and its complement of enzymes to the cell surface.
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Affiliation(s)
- Qi Xu
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Ramat Aviv, Israel
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41
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Ding SY, Lamed R, Bayer EA, Himmel ME. The bacterial scaffoldin: structure, function and potential applications in the nanosciences. GENETIC ENGINEERING 2004; 25:209-25. [PMID: 15260240 DOI: 10.1007/978-1-4615-0073-5_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Natural protein complexes may provide the best templates for nanometer-scale technology and new biomaterials. The bacterial cellulosome is becoming a well-understood multi-protein complex found in cellulolytic microorganisms. The scaffoldin subunits of the bacterial cellulosome function to organize and position other protein subunits into the complex. The scaffoldins can also serve as an attachment device for harnessing the cellulosome onto the cell surface and/or for its targeting to substrate. Biochemical and molecular biological evidence have identified a receptor/adaptor type of protein domain pair, called "cohesin and dockerin," which is responsible for cellulosome self-assembly. The recognition between cohesin and dockerin is generally type and/or species specific. More than 80 cohesin and 100 dockerin sequences have been found, mostly from anaerobic bacteria. X-ray crystallography and NMR have been used to determine the three-dimensional structures of representative cohesin and dockerin domains, respectively. The cohesin peptide is about 140 amino acids in length and highly conserved in sequence and domain structure. The dockerin domain comprises about 70 amino acids and contains two 22 amino acid duplicated regions, each of which includes an "F-hand" modification of the EF-hand calcium-binding motif. Biochemical evidence and site-directed mutagenesis have confirmed that the two F-hand motifs are required for function and calcium dependence; at least two amino acids from each motif are critical for cohesin-dockerin recognition. In this report, we review the structure and function of the scaffoldin of the bacterial cellulosome and emphasize a detailed sequence analysis of the cohesin and dockerin domains. We also speculate about potential applications in nanoscience that may be based on cohesin-dockerin recognition.
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Affiliation(s)
- Shi-You Ding
- National Bioenergy Center, National Renewable Energy Laboratory, 1617 Cole Blvd. Golden, CO 80401, USA
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42
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Xu Q, Morrison M, Nelson KE, Bayer EA, Atamna N, Lamed R. A novel family of carbohydrate-binding modules identified with Ruminococcus albus proteins. FEBS Lett 2004; 566:11-6. [PMID: 15147860 DOI: 10.1016/j.febslet.2004.04.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 03/24/2004] [Accepted: 04/01/2004] [Indexed: 11/24/2022]
Abstract
We recently showed that some of the enzymes underpinning cellulose solubilization by Ruminococcus albus 8 lack the conventional type of dockerin module characteristic of cellulosomal proteins and instead, bear an "X" domain of unknown function at their C-termini. We have now subcloned and expressed six X domains and showed that five of them bind to xylan, chitin, microcrystalline and phosphoric-acid swollen cellulose, as well as more heterogenous substrates such as alfalfa cell walls, banana stem and wheat straw. The X domain that did not bind to these substrates was derived from a family-5 glycoside hydrolase (Cel5G), which possesses two X domains in tandem. Whereas the internal X domain failed to bind to the substrates, the recombinant dyad exhibited markedly enhanced binding relative to that observed for the C-terminal X domain alone. The evidence supports a distinctive carbohydrate-binding role of broad specificity for this type of domain, and we propose a novel family (designated family 37) of carbohydrate-binding modules that appear to be peculiar to R. albus.
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Affiliation(s)
- Qi Xu
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Ramat Aviv, Israel
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43
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Affiliation(s)
- Roy H Doi
- Section of Molecular & Cellular Biology, University of California, Davis, California, USA.
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44
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Rincón MT, Martin JC, Aurilia V, McCrae SI, Rucklidge GJ, Reid MD, Bayer EA, Lamed R, Flint HJ. ScaC, an adaptor protein carrying a novel cohesin that expands the dockerin-binding repertoire of the Ruminococcus flavefaciens 17 cellulosome. J Bacteriol 2004; 186:2576-85. [PMID: 15090497 PMCID: PMC387807 DOI: 10.1128/jb.186.9.2576-2585.2004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new gene, designated scaC and encoding a protein carrying a single cohesin, was identified in the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17 as part of a gene cluster that also codes for the cellulosome structural components ScaA and ScaB. Phylogenetic analysis showed that the sequence of the ScaC cohesin is distinct from the sequences of other cohesins, including the sequences of R. flavefaciens ScaA and ScaB. The scaC gene product also includes at its C terminus a dockerin module that closely resembles those found in R. flavefaciens enzymes that bind to the cohesins of the primary ScaA scaffoldin. The putative cohesin domain and the C-terminal dockerin module were cloned and overexpressed in Escherichia coli as His(6)-tagged products (ScaC-Coh and ScaC-Doc, respectively). Affinity probing of protein extracts of R. flavefaciens 17 separated in one-dimensional and two-dimensional gels with recombinant cohesins from ScaC and ScaA revealed that two distinct subsets of native proteins interact with ScaC-Coh and ScaA-Coh. Furthermore, ScaC-Coh failed to interact with the recombinant dockerin module from the enzyme EndB that is recognized by ScaA cohesins. On the other hand, ScaC-Doc was shown to interact specifically with the recombinant cohesin domain from ScaA, and the ScaA-Coh probe was shown to interact with a native 29-kDa protein spot identified as ScaC by matrix-assisted laser desorption ionization-time of flight mass spectrometry. These results suggest that ScaC plays the role of an adaptor scaffoldin that is bound to ScaA via the ScaC dockerin module, which, via the distinctive ScaC cohesin, expands the range of proteins that can bind to the ScaA-based enzyme complex.
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Affiliation(s)
- Marco T Rincón
- Microbial Genetics Group, The Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, United Kingdom.
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45
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Xu Q, Bayer EA, Goldman M, Kenig R, Shoham Y, Lamed R. Architecture of the Bacteroides cellulosolvens cellulosome: description of a cell surface-anchoring scaffoldin and a family 48 cellulase. J Bacteriol 2004; 186:968-77. [PMID: 14761991 PMCID: PMC344227 DOI: 10.1128/jb.186.4.968-977.2004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large gene downstream of the primary Bacteroides cellulosolvens cellulosomal scaffoldin (cipBc, now renamed scaA) was sequenced. The gene, termed scaB, contained an N-terminal leader peptide followed by 10 type I cohesins, an "X" domain of unknown structure and function, and a C-terminal S-layer homology (SLH) surface-anchoring module. In addition, a previously identified gene in a different part of the genome, encoding for a dockerin-borne family 48 cellulosomal glycoside hydrolase (Cel48), was sequenced completely, and a putative cellulosome-related family 9 glycosyl hydrolase was detected. Recombinant fusion proteins, comprising dockerins derived from either the ScaA scaffoldin or Cel48, were overexpressed. Their interaction with ScaA and ScaB cohesins was examined by immunoassay. The results indicated that the ScaB type I cohesin of the new anchoring protein binds selectively to the ScaA dockerin, whereas the Cel48 dockerin binds specifically to the type II ScaA cohesin 5. Thus, by virtue of the 11 type II ScaA cohesins and the 10 type I ScaB cohesins, the relatively simple two-component cellulosome-integrating complex would potentially incorporate 110 enzyme molecules onto the cell surface via the ScaB SLH module. Compared to previously described cellulosome systems, the apparent roles of the B. cellulosolvens cohesins are reversed, in that the type II cohesins are located on the enzyme-binding primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldin. The results underscore the extensive diversity in the supramolecular architecture of cellulosome systems in nature.
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Affiliation(s)
- Qi Xu
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
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46
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Devillard E, Goodheart DB, Karnati SKR, Bayer EA, Lamed R, Miron J, Nelson KE, Morrison M. Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Cel48A and Cel9B, both of which possess a novel modular architecture. J Bacteriol 2004; 186:136-45. [PMID: 14679233 PMCID: PMC303442 DOI: 10.1128/jb.186.1.136-145.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cellulolytic bacterium Ruminococcus albus 8 adheres tightly to cellulose, but the molecular biology underpinning this process is not well characterized. Subtractive enrichment procedures were used to isolate mutants of R. albus 8 that are defective in adhesion to cellulose. Adhesion of the mutant strains was reduced 50% compared to that observed with the wild-type strain, and cellulose solubilization was also shown to be slower in these mutant strains, suggesting that bacterial adhesion and cellulose solubilization are inextricably linked. Two-dimensional polyacrylamide gel electrophoresis showed that all three mutants studied were impaired in the production of two high-molecular-mass, cell-bound polypeptides when they were cultured with either cellobiose or cellulose. The identities of these proteins were determined by a combination of mass spectrometry methods and genome sequence data for R. albus 8. One of the polypeptides is a family 9 glycoside hydrolase (Cel9B), and the other is a family 48 glycoside hydrolase (Cel48A). Both Cel9B and Cel48A possess a modular architecture, Cel9B possesses features characteristic of the B(2) (or theme D) group of family 9 glycoside hydrolases, and Cel48A is structurally similar to the processive endocellulases CelF and CelS from Clostridium cellulolyticum and Clostridium thermocellum, respectively. Both Cel9B and Cel48A could be recovered by cellulose affinity procedures, but neither Cel9B nor Cel48A contains a dockerin, suggesting that these polypeptides are retained on the bacterial cell surface, and recovery by cellulose affinity procedures did not involve a clostridium-like cellulosome complex. Instead, both proteins possess a single copy of a novel X module with an unknown function at the C terminus. Such X modules are also present in several other R. albus glycoside hydrolases and are phylogentically distinct from the fibronectin III-like and X modules identified so far in other cellulolytic bacteria.
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Affiliation(s)
- Estelle Devillard
- The MAPLE Research Initiative, Department of Animal Sciences, The Ohio State University, Columbus 43210, USA
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47
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Schwarz WH, Zverlov VV, Bahl H. Extracellular Glycosyl Hydrolases from Clostridia. ADVANCES IN APPLIED MICROBIOLOGY 2004; 56:215-61. [PMID: 15566981 DOI: 10.1016/s0065-2164(04)56007-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Wolfgang H Schwarz
- Technical University of Munich Institute of Microbiology, D-85350 Freising, Germany
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48
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Bayer EA, Belaich JP, Shoham Y, Lamed R. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 2004; 58:521-54. [PMID: 15487947 DOI: 10.1146/annurev.micro.57.030502.091022] [Citation(s) in RCA: 597] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discrete multicomponent, multienzyme cellulosome complex of anaerobic cellulolytic bacteria provides enhanced synergistic activity among the different resident enzymes to efficiently hydrolyze intractable cellulosic and hemicellulosic substrates of the plant cell wall. A pivotal noncatalytic subunit called scaffoldin secures the various enzymatic subunits into the complex via the cohesin-dockerin interaction. The specificity characteristics and tenacious binding between the scaffoldin-based cohesin modules and the enzyme-borne dockerin domains dictate the supramolecular architecture of the cellulosome. The diversity in cellulosome architecture among the known cellulosome-producing bacteria is manifest in the arrangement of their genes in either multiple-scaffoldin or enzyme-linked clusters on the genome. The recently described three-dimensional crystal structure of the cohesin-dockerin heterodimer sheds light on the critical amino acids that contribute to this high-affinity protein-protein interaction. In addition, new information regarding the regulation of cellulosome-related genes, budding genetic tools, and emerging genomics of cellulosome-producing bacteria promises new insight into the assembly and consequences of the multienzyme complex.
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Affiliation(s)
- Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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49
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Affiliation(s)
- Roy H Doi
- Section of Molecular & Cellular Biology, University of California, Davis, California 95616, USA.
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50
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Xu Q, Gao W, Ding SY, Kenig R, Shoham Y, Bayer EA, Lamed R. The cellulosome system of Acetivibrio cellulolyticus includes a novel type of adaptor protein and a cell surface anchoring protein. J Bacteriol 2003; 185:4548-57. [PMID: 12867464 PMCID: PMC165778 DOI: 10.1128/jb.185.15.4548-4557.2003] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2003] [Accepted: 05/02/2003] [Indexed: 11/20/2022] Open
Abstract
A scaffoldin gene cluster was identified in the mesophilic cellulolytic anaerobe Acetivibrio cellulolyticus. The previously described scaffoldin gene, cipV, encodes an N-terminal family 9 glycoside hydrolase, a family 3b cellulose-binding domain, seven cohesin domains, and a C-terminal dockerin. The gene immediately downstream of cipV was sequenced and designated scaB. The protein encoded by this gene has 942 amino acid residues and a calculated molecular weight of 100,358 and includes an N-terminal signal peptide, four type II cohesions, and a C-terminal dockerin. ScaB cohesins 1 and 2 are very closely linked. Similar, but not identical, 39-residue Thr-rich linker segments separate cohesin 2 from cohesin 3 and cohesin 3 from cohesin 4, and an 84-residue Thr-rich linker connects the fourth cohesin to a C-terminal dockerin. The scaC gene downstream of scaB codes for a 1,237-residue polypeptide that includes a signal peptide, three cohesins, and a C-terminal S-layer homology (SLH) module. A long, ca. 550-residue linker separates the third cohesin and the SLH module of ScaC and is characterized by an 18-residue Pro-Thr-Ala-Ser-rich segment that is repeated 27 times. The calculated molecular weight of the mature ScaC polypeptide (excluding the signal peptide) is 124,162. The presence of the cohesins and the conserved SLH module implies that ScaC acts as an anchoring protein. The ScaC cohesins are on a separate branch of the phylogenetic tree that is close to, but distinct from, the type I cohesins. Affinity blotting with representative recombinant probes revealed the following specific intermodular interactions: (i) an expressed CipV cohesin binds selectively to an enzyme-borne dockerin, (ii) a representative ScaB cohesin binds to the CipV band of the cell-free supernatant fraction, and (iii) a ScaC cohesin binds to the ScaB dockerin. The experimental evidence thus indicates that CipV acts as a primary (enzyme-recognizing) scaffoldin, and the protein was also designated ScaA. In addition, ScaB is thought to assume the role of an adaptor protein, which connects the primary scaffoldin (ScaA) to the cohesin-containing anchoring scaffoldin (ScaC). The cellulosome system of A. cellulolyticus thus appears to exhibit a special type of organization that reflects the function of the ScaB adaptor protein. The intercalation of three multiple cohesin-containing scaffoldins results in marked amplification of the number of enzyme subunits per cellulosome unit. At least 96 enzymes can apparently be incorporated into an individual A. cellulolyticus cellulosome. The role of such amplified enzyme incorporation and the resultant proximity of the enzymes within the cellulosome complex presumably contribute to the enhanced synergistic action and overall efficient digestion of recalcitrant forms of cellulose. Comparison of the emerging organization of the A. cellulolyticus cellulosome with the organizations in other cellulolytic bacteria revealed the diversity of the supramolecular architecture.
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Affiliation(s)
- Qi Xu
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Ramat Aviv, Israel
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