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Lamote B, da Fonseca MJM, Vanderstraeten J, Meert K, Elias M, Briers Y. Current challenges in designer cellulosome engineering. Appl Microbiol Biotechnol 2023; 107:2755-2770. [PMID: 36941434 DOI: 10.1007/s00253-023-12474-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023]
Abstract
Designer cellulosomes (DCs) are engineered multi-enzyme complexes, comprising carbohydrate-active enzymes attached to a common backbone, the scaffoldin, via high-affinity cohesin-dockerin interactions. The use of DCs in the degradation of renewable biomass polymers is a promising approach for biorefineries. Indeed, DCs have shown significant hydrolytic activities due to the enhanced enzyme-substrate proximity and inter-enzyme synergies, but technical hurdles in DC engineering have hindered further progress towards industrial application. The challenge in DC engineering lies in the large diversity of possible building blocks and architectures, resulting in a multivariate and immense design space. Simultaneously, the precise DC composition affects many relevant parameters such as activity, stability, and manufacturability. Since protein engineers face a lack of high-throughput approaches to explore this vast design space, DC engineering may result in an unsatisfying outcome. This review provides a roadmap to guide researchers through the process of DC engineering. Each step, starting from concept to evaluation, is described and provided with its challenges, along with possible solutions, both for DCs that are assembled in vitro or are displayed on the yeast cell surface. KEY POINTS: • Construction of designer cellulosomes is a multi-step process. • Designer cellulosome research deals with multivariate construction challenges. • Boosting designer cellulosome efficiency requires exploring a vast design space.
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Affiliation(s)
- Babette Lamote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | | | - Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Kenan Meert
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Marte Elias
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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Dorival J, Moraïs S, Labourel A, Rozycki B, Cazade PA, Dabin J, Setter-Lamed E, Mizrahi I, Thompson D, Thureau A, Bayer EA, Czjzek M. Mapping the deformability of natural and designed cellulosomes in solution. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:68. [PMID: 35725490 PMCID: PMC9210761 DOI: 10.1186/s13068-022-02165-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/08/2022] [Indexed: 12/02/2022]
Abstract
Background Natural cellulosome multi-enzyme complexes, their components, and engineered ‘designer cellulosomes’ (DCs) promise an efficient means of breaking down cellulosic substrates into valuable biofuel products. Their broad uptake in biotechnology relies on boosting proximity-based synergy among the resident enzymes, but the modular architecture challenges structure determination and rational design. Results We used small angle X-ray scattering combined with molecular modeling to study the solution structure of cellulosomal components. These include three dockerin-bearing cellulases with distinct substrate specificities, original scaffoldins from the human gut bacterium Ruminococcus champanellensis (ScaA, ScaH and ScaK) and a trivalent cohesin-bearing designer scaffoldin (Scaf20L), followed by cellulosomal complexes comprising these components, and the nonavalent fully loaded Clostridium thermocellum CipA in complex with Cel8A from the same bacterium. The size analysis of Rg and Dmax values deduced from the scattering curves and corresponding molecular models highlight their variable aspects, depending on composition, size and spatial organization of the objects in solution. Conclusions Our data quantifies variability of form and compactness of cellulosomal components in solution and confirms that this native plasticity may well be related to speciation with respect to the substrate that is targeted. By showing that scaffoldins or components display enhanced compactness compared to the free objects, we provide new routes to rationally enhance their stability and performance in their environment of action. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02165-3.
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Abstract
Cellulosomes are elaborate multienzyme complexes capable of efficiently deconstructing lignocellulosic substrates, produced by cellulolytic anaerobic microorganisms, colonizing a large variety of ecological niches. These macromolecular structures have a modular architecture and are composed of two main elements: the cohesin-bearing scaffoldins, which are non-catalytic structural proteins, and the various dockerin-bearing enzymes that tenaciously bind to the scaffoldins. Cellulosome assembly is mediated by strong and highly specific interactions between the cohesin modules, present in the scaffoldins, and the dockerin modules, present in the catalytic units. Cellulosomal architecture and composition varies between species and can even change within the same organism. These differences seem to be largely influenced by external factors, including the nature of the available carbon-source. Even though cellulosome producing organisms are relatively few, the development of new genomic and proteomic technologies has allowed the identification of cellulosomal components in many archea, bacteria and even some primitive eukaryotes. This reflects the importance of this cellulolytic strategy and suggests that cohesin-dockerin interactions could be involved in other non-cellulolytic processes. Due to their building-block nature and highly cellulolytic capabilities, cellulosomes hold many potential biotechnological applications, such as the conversion of lignocellulosic biomass in the production of biofuels or the development of affinity based technologies.
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Affiliation(s)
- Victor D Alves
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Carlos M G A Fontes
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Pedro Bule
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal.
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Galera-Prat A, Vera AM, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. Impact of scaffoldin mechanostability on cellulosomal activity. Biomater Sci 2020; 8:3601-3610. [PMID: 32232253 DOI: 10.1039/c9bm02052g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignocellulose is the most abundant renewable carbon source in the biosphere. However, the main bottleneck in its conversion to produce second generation biofuels is the saccharification step: the hydrolysis of lignocellulosic material into soluble fermentable sugars. Some anaerobic bacteria have developed an extracellular multi-enzyme complex called the cellulosome that efficiently degrades cellulosic substrates. Cellulosome complexes rely on enzyme-integrating scaffoldins that are large non-catalytic scaffolding proteins comprising several cohesin modules and additional functional modules that mediate the anchoring of the complex to the cell surface and the specific binding to its cellulosic substrate. It was proposed that mechanical forces may affect the cohesins positioned between the cell- and cellulose-anchoring points in the so-called connecting region. Consequently, the mechanical resistance of cohesins within the scaffoldin is of great importance, both to understand cellulosome function and as a parameter of industrial interest, to better mimic natural complexes through the use of the established designer cellulosome technology. Here we study how the mechanical stability of cohesins in a scaffoldin affects the enzymatic activity of a cellulosome. We found that when a cohesin of low mechanical stability is positioned in the connecting region of a scaffoldin, the activity of the resulting cellulosome is reduced as opposed to a cohesin of higher mechanical stability. This observation directly relates mechanical stability of the scaffoldin-borne cohesins to cellulosome activity and provides a rationale for the design of artificial cellulosomes for industrial applications, by incorporating mechanical stability as a new industrial parameter in the biotechnology toolbox.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, Department of Molecular, Cellular and Developmental Neurobiology. IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain.
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The Cellulosome Paradigm in An Extreme Alkaline Environment. Microorganisms 2019; 7:microorganisms7090347. [PMID: 31547347 PMCID: PMC6780208 DOI: 10.3390/microorganisms7090347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/01/2019] [Accepted: 09/10/2019] [Indexed: 11/19/2022] Open
Abstract
Rapid decomposition of plant biomass in soda lakes is associated with microbial activity of anaerobic cellulose-degrading communities. The alkaliphilic bacterium, Clostridium alkalicellulosi, is the single known isolate from a soda lake that demonstrates cellulolytic activity. This microorganism secretes cellulolytic enzymes that degrade cellulose under anaerobic and alkaliphilic conditions. A previous study indicated that the protein fraction of cellulose-grown cultures showed similarities in composition and size to known components of the archetypical cellulosome Clostridium thermocellum. Bioinformatic analysis of the C. alkalicellulosi draft genome sequence revealed 44 cohesins, organized into 22 different scaffoldins, and 142 dockerin-containing proteins. The modular organization of the scaffoldins shared similarities to those of C. thermocellum and Acetivibrio cellulolyticus, whereas some exhibited unconventional arrangements containing peptidases and oxidative enzymes. The binding interactions among cohesins and dockerins assessed by ELISA, revealed a complex network of cellulosome assemblies and suggested both cell-associated and cell-free systems. Based on these interactions, C. alkalicellulosi cellulosomal systems have the genetic potential to create elaborate complexes, which could integrate up to 105 enzymatic subunits. The alkalistable C. alkalicellulosi cellulosomal systems and their enzymes would be amenable to biotechnological processes, such as treatment of lignocellulosic biomass following prior alkaline pretreatment.
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Galera-Prat A, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. The cohesin module is a major determinant of cellulosome mechanical stability. J Biol Chem 2018; 293:7139-7147. [PMID: 29567834 PMCID: PMC5950008 DOI: 10.1074/jbc.ra117.000644] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Indexed: 01/20/2023] Open
Abstract
Cellulosomes are bacterial protein complexes that bind and efficiently degrade lignocellulosic substrates. These are formed by multimodular scaffolding proteins known as scaffoldins, which comprise cohesin modules capable of binding dockerin-bearing enzymes and usually a carbohydrate-binding module that anchors the system to a substrate. It has been suggested that cellulosomes bound to the bacterial cell surface might be exposed to significant mechanical forces. Accordingly, the mechanical properties of these anchored cellulosomes may be important to understand and improve cellulosome function. Here we used single-molecule force spectroscopy to study the mechanical properties of selected cohesin modules from scaffoldins of different cellulosomes. We found that cohesins located in the region connecting the cell and the substrate are more robust than those located outside these two anchoring points. This observation applies to cohesins from primary scaffoldins (i.e. those that directly bind dockerin-bearing enzymes) from different cellulosomes despite their sequence differences. Furthermore, we also found that cohesin nanomechanics (specifically, mechanostability and the position of the mechanical clamp of cohesin) are not significantly affected by other cellulosomal components, including linkers between cohesins, multiple cohesin repeats, and dockerin binding. Finally, we also found that cohesins (from both the connecting and external regions) have poor refolding efficiency but similar refolding rates, suggesting that the high mechanostability of connecting cohesins may be an evolutionarily conserved trait selected to minimize the occurrence of cohesin unfolding, which could irreversibly damage the cellulosome. We conclude that cohesin mechanostability is a major determinant of the overall mechanical stability of the cellulosome.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
| | - Sarah Moraïs
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Vazana
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain.
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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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Ben-David Y, Dassa B, Bensoussan L, Bayer EA, Moraïs S. Methods for Discovery of Novel Cellulosomal Cellulases Using Genomics and Biochemical Tools. Methods Mol Biol 2018; 1796:67-84. [PMID: 29856047 DOI: 10.1007/978-1-4939-7877-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Cell wall degradation by cellulases is extensively explored owing to its potential contribution to biofuel production. The cellulosome is an extracellular multienzyme complex that can degrade the plant cell wall very efficiently, and cellulosomal enzymes are therefore of great interest. The cellulosomal cellulases are defined as enzymes that contain a dockerin module, which can interact with a cohesin module contained in multiple copies in a noncatalytic protein, termed scaffoldin. The assembly of the cellulosomal cellulases into the cellulosomal complex occurs via specific protein-protein interactions. Cellulosome systems have been described initially only in several anaerobic cellulolytic bacteria. However, owing to ongoing genome sequencing and metagenomic projects, the discovery of novel cellulosome-producing bacteria and the description of their cellulosomal genes have dramatically increased in the recent years. In this chapter, methods for discovery of novel cellulosomal cellulases from a DNA sequence by bioinformatics and biochemical tools are described. Their biochemical characterization is also described, including both the enzymatic activity of the putative cellulases and their assembly into mature designer cellulosomes.
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Affiliation(s)
- Yonit Ben-David
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Lizi Bensoussan
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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Röder J, Fischer R, Commandeur U. Engineering Potato Virus X Particles for a Covalent Protein Based Attachment of Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1702151. [PMID: 29125698 DOI: 10.1002/smll.201702151] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/25/2017] [Indexed: 05/23/2023]
Abstract
Plant virus nanoparticles are often used to display functional amino acids or small peptides, thus serving as building blocks in application areas as diverse as nanoelectronics, bioimaging, vaccination, drug delivery, and bone differentiation. This is most easily achieved by expressing coat protein fusions, but the assembly of the corresponding virus particles can be hampered by factors such as the fusion protein size, amino acid composition, and post-translational modifications. Size constraints can be overcome by using the Foot and mouth disease virus 2A sequence, but the compositional limitations cannot be avoided without the introduction of time-consuming chemical modifications. SpyTag/SpyCatcher technology is used in the present study to covalently attach the Trichoderma reesei endoglucanase Cel12A to Potato virus X (PVX) nanoparticles. The formation of PVX particles is confirmed by western blot, and the ability of the particles to display Cel12A is demonstrated by enzyme-linked immunosorbent assays and transmission electron microscopy. Enzymatic assays show optimal reaction conditions of 50 °C and pH 6.5, and an increased substrate conversion rate compared to free enzymes. It is concluded that PVX displaying the SpyTag can serve as new scaffold for protein display, most notably for proteins with post-translational modifications.
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Affiliation(s)
- Juliane Röder
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Rainer Fischer
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, 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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Brás JLA, Pinheiro BA, Cameron K, Cuskin F, Viegas A, Najmudin S, Bule P, Pires VMR, Romão MJ, Bayer EA, Spencer HL, Smith S, Gilbert HJ, Alves VD, Carvalho AL, Fontes CMGA. Diverse specificity of cellulosome attachment to the bacterial cell surface. Sci Rep 2016; 6:38292. [PMID: 27924829 PMCID: PMC5141474 DOI: 10.1038/srep38292] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/07/2016] [Indexed: 12/02/2022] Open
Abstract
During the course of evolution, the cellulosome, one of Nature's most intricate multi-enzyme complexes, has been continuously fine-tuned to efficiently deconstruct recalcitrant carbohydrates. To facilitate the uptake of released sugars, anaerobic bacteria use highly ordered protein-protein interactions to recruit these nanomachines to the cell surface. Dockerin modules located within a non-catalytic macromolecular scaffold, whose primary role is to assemble cellulosomal enzymatic subunits, bind cohesin modules of cell envelope proteins, thereby anchoring the cellulosome onto the bacterial cell. Here we have elucidated the unique molecular mechanisms used by anaerobic bacteria for cellulosome cellular attachment. The structure and biochemical analysis of five cohesin-dockerin complexes revealed that cell surface dockerins contain two cohesin-binding interfaces, which can present different or identical specificities. In contrast to the current static model, we propose that dockerins utilize multivalent modes of cohesin recognition to recruit cellulosomes to the cell surface, a mechanism that maximises substrate access while facilitating complex assembly.
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Affiliation(s)
- Joana L. A. Brás
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, 1649-038 Lisboa, Portugal
| | - Benedita A. Pinheiro
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Kate Cameron
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Fiona Cuskin
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Aldino Viegas
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Institute of Physical Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Shabir Najmudin
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Pedro Bule
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Virginia M. R. Pires
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Maria João Romão
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Holly L. Spencer
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Steven Smith
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Victor D. Alves
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Ana Luísa Carvalho
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M. G. A. Fontes
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, 1649-038 Lisboa, Portugal
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12
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Cunha ES, Hatem CL, Barrick D. Synergistic enhancement of cellulase pairs linked by consensus ankyrin repeats: Determination of the roles of spacing, orientation, and enzyme identity. Proteins 2016; 84:1043-54. [PMID: 27071357 DOI: 10.1002/prot.25047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 03/09/2016] [Accepted: 03/25/2016] [Indexed: 12/22/2022]
Abstract
Biomass deconstruction to small simple sugars is a potential approach to biofuels production; however, the highly recalcitrant nature of biomass limits the economic viability of this approach. Thus, research on efficient biomass degradation is necessary to achieve large-scale production of biofuels. Enhancement of cellulolytic activity by increasing synergism between cellulase enzymes holds promise in achieving high-yield biofuels production. Here we have inserted cellulase pairs from extremophiles into hyperstable α-helical consensus ankyrin repeat domain scaffolds. Such chimeric constructs allowed us to optimize arrays of enzyme pairs against a variety of cellulolytic substrates. We found that endocellulolytic domains CelA (CA) and Cel12A (C12A) act synergistically in the context of ankyrin repeats, with both three and four repeat spacing. The extent of synergy differs for different substrates. Also, having C12A N-terminal to CA provides greater synergy than the reverse construct, especially against filter paper. In contrast, we do not see synergy for these enzymes in tandem with CelK (CK) catalytic domain, a larger exocellulase, demonstrating the importance of enzyme identity in synergistic enhancement. Furthermore, we found endocellulases CelD and CA with three repeat spacing to act synergistically against filter paper. Importantly, connecting CA and C12A with a disordered linker of similar contour length shows no synergistic enhancement, indicating that synergism results from connecting these domains with folded ankyrin repeats. These results show that ankyrin arrays can be used to vary spacing and orientation between enzymes, helping to design and optimize artificial cellulosomes, providing a novel architecture for synergistic enhancement of enzymatic cellulose degradation. Proteins 2016; 84:1043-1054. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Eva S Cunha
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, Maryland, 21218.,Department of Structural Biology, Max Plank Institute of Biophysics, Max-von-Laue-Str. 3, Frankfurt am Main, D-60438, Germany
| | - Christine L Hatem
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, Maryland, 21218
| | - Doug Barrick
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, Maryland, 21218
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13
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Kim HJ, Lee EJ, Park JS, Sim SJ, Lee J. Reversible and multi-cyclic protein-protein interaction in bacterial cellulosome-mimic system using rod-shaped viral nanostructure. J Biotechnol 2016; 221:101-6. [PMID: 26820321 DOI: 10.1016/j.jbiotec.2016.01.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/19/2016] [Accepted: 01/22/2016] [Indexed: 12/31/2022]
Abstract
The type II cohesin domain and type II dockerin of bacterial cellulosome were cloned from Clostridium thermocellum and expressed with the fusion of tobacco mosaic virus coat protein (TMVcp) and enhanced green fluorescent protein (EGFP), respectively, in Escherichia coli. The TMVcp-cohesin fusion protein was assembled to the stable and rod-shaped nanostructure (TMVcp-Coh rod) under a particular buffer condition, where many active cohesin proteins are biologically and densely displayed around the 3-dimensional surface of TMVcp-Coh rod. Using EGFP-dockerin as a fluorescent reporter, we confirmed that the Ca(2+)-dependent binding and dissociation between native cohesin and dockerin were reproduced with the two recombinant fusion proteins, TMVcp-cohesin and EGFP-dockerin. The multi-cyclic binding-dissociation operation of TMVcp-Coh rod and EGFP-dockerin was successfully performed with maintaining the reversible cohesin-dockerin interaction in every cycle. EGFP that was fused to dockerin as a proof-of-concept here can be switched to other functional proteins/peptides that need to be used in multi-cyclic operation.
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Affiliation(s)
- Hyun Jin Kim
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul 136-713, Republic of Korea
| | - Eun Jung Lee
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul 136-713, Republic of Korea; Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Jin-Seung Park
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul 136-713, Republic of Korea; Research Institute of Biotechnology, CJ CheilJedang, 92 Gayang-Dong, Gangseo-Gu, Seoul 157-801, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul 136-713, Republic of Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Seongbuk-Gu, Seoul 136-713, Republic of Korea.
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14
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Sand A, Holwerda EK, Ruppertsberger NM, Maloney M, Olson DG, Nataf Y, Borovok I, Sonenshein AL, Bayer EA, Lamed R, Lynd LR, Shoham Y. Three cellulosomal xylanase genes inClostridium thermocellumare regulated by both vegetative SigA (σA) and alternative SigI6 (σI6) factors. FEBS Lett 2015; 589:3133-40. [DOI: 10.1016/j.febslet.2015.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/10/2015] [Accepted: 08/14/2015] [Indexed: 11/29/2022]
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15
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Cameron K, Weinstein JY, Zhivin O, Bule P, Fleishman SJ, Alves VD, Gilbert HJ, Ferreira LMA, Fontes CMGA, Bayer EA, Najmudin S. Combined Crystal Structure of a Type I Cohesin: MUTATION AND AFFINITY BINDING STUDIES REVEAL STRUCTURAL DETERMINANTS OF COHESIN-DOCKERIN SPECIFICITIES. J Biol Chem 2015; 290:16215-25. [PMID: 25934389 PMCID: PMC4481221 DOI: 10.1074/jbc.m115.653303] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/24/2015] [Indexed: 11/06/2022] Open
Abstract
Cohesin-dockerin interactions orchestrate the assembly of one of nature's most elaborate multienzyme complexes, the cellulosome. Cellulosomes are produced exclusively by anaerobic microbes and mediate highly efficient hydrolysis of plant structural polysaccharides, such as cellulose and hemicellulose. In the canonical model of cellulosome assembly, type I dockerin modules of the enzymes bind to reiterated type I cohesin modules of a primary scaffoldin. Each type I dockerin contains two highly conserved cohesin-binding sites, which confer quaternary flexibility to the multienzyme complex. The scaffoldin also bears a type II dockerin that anchors the entire complex to the cell surface by binding type II cohesins of anchoring scaffoldins. In Bacteroides cellulosolvens, however, the organization of the cohesin-dockerin types is reversed, whereby type II cohesin-dockerin pairs integrate the enzymes into the primary scaffoldin, and type I modules mediate cellulosome attachment to an anchoring scaffoldin. Here, we report the crystal structure of a type I cohesin from B. cellulosolvens anchoring scaffoldin ScaB to 1.84-Å resolution. The structure resembles other type I cohesins, and the putative dockerin-binding site, centered at β-strands 3, 5, and 6, is likely to be conserved in other B. cellulosolvens type I cohesins. Combined computational modeling, mutagenesis, and affinity-based binding studies revealed similar hydrogen-bonding networks between putative Ser/Asp recognition residues in the dockerin at positions 11/12 and 45/46, suggesting that a dual-binding mode is not exclusive to the integration of enzymes into primary cellulosomes but can also characterize polycellulosome assembly and cell-surface attachment. This general approach may provide valuable structural information of the cohesin-dockerin interface, in lieu of a definitive crystal structure.
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Affiliation(s)
- Kate Cameron
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Jonathan Y Weinstein
- the Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel, and
| | - Olga Zhivin
- the Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel, and
| | - Pedro Bule
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sarel J Fleishman
- the Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel, and
| | - Victor D Alves
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Harry J Gilbert
- the Institute of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Luís M A Ferreira
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Carlos M G A Fontes
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Edward A Bayer
- the Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel, and
| | - Shabir Najmudin
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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16
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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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17
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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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18
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Hong W, Zhang J, Feng Y, Mohr G, Lambowitz AM, Cui GZ, Liu YJ, Cui Q. The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:80. [PMID: 24955112 PMCID: PMC4045903 DOI: 10.1186/1754-6834-7-80] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 05/13/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium thermocellum is a thermophilic anaerobic bacterium that degrades cellulose by using a highly effective cellulosome, a macromolecular complex consisting of multiple cellulose degrading enzymes organized and attached to the cell surface by non-catalytic scaffoldins. However, due largely to lack of efficient methods for genetic manipulation of C. thermocellum, it is still unclear how the different scaffoldins and their functional modules contribute to cellulose hydrolysis. RESULTS We constructed C. thermocellum mutants with the primary scaffoldin CipA (cellulosome-integrating protein A) truncated at different positions or lacking four different secondary scaffoldins by using a newly developed thermotargetron system, and we analyzed cellulose hydrolysis, cellulosome formation, and cellulose binding of the mutants. A CipA truncation that deletes six type I cohesin modules, which bind cellulolytic enzymes, decreased cellulose hydrolysis rates by 46%, and slightly longer truncations that also delete the carbohydrate binding module decreased rates by 89 to 92%, indicating strong cellulosome-substrate synergy. By contrast, a small CipA truncation that deletes only the C-terminal type II dockerin (XDocII) module detached cellulosomes from the cells, but decreased cellulose hydrolysis rates by only 9%, suggesting a relatively small contribution of cellulosome-cell synergy. Disruptants lacking any of four different secondary scaffoldins (OlpB, 7CohII, Orf2p, or SdbA) showed moderately decreased cellulose hydrolysis rates, suggesting additive contributions. Surprisingly, the CipA-ΔXDocII mutant, which lacks cell-associated polycellulosomes, adheres to cellulose almost as strongly as wild-type cells, revealing an alternate, previously unknown cellulose-binding mechanism. CONCLUSIONS Our results emphasize the important role of cellulosome-substrate synergy in cellulose degradation, demonstrate a contribution of secondary scaffoldins, and suggest a previously unknown, non-cellulosomal system for binding insoluble cellulose. Our findings provide new insights into cellulosome function and impact genetic engineering of microorganisms to enhance bioconversions of cellulose substrates.
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Affiliation(s)
- Wei Hong
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Jie Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Georg Mohr
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Gu-Zhen Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
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19
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Zhao G, Li H, Wamalwa B, Sakka M, Kimura T, Sakka K. Different Binding Specificities of S-Layer Homology Modules fromClostridium thermocellumAncA, Slp1, and Slp2. Biosci Biotechnol Biochem 2014; 70:1636-41. [PMID: 16861798 DOI: 10.1271/bbb.50699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
S-layer homology (SLH) module polypeptides were derived from Clostridium thermocellum S-layer proteins Slp1 and Slp2 and cellulosome anchoring protein AncA as rSlp1-SLH, rSlp2-SLH, and rAncA-SLH respectively. Their binding specificities were investigated using C. thermocellum cell-wall preparations. rAncA-SLH associated with native peptidoglycan-containing sacculi from C. thermocellum, including both peptidoglycan and secondary cell wall polymers (SCWP), but not to hydrofluoric acid-extracted peptidoglycan-containing sacculi (HF-EPCS) lacking SCWPs, suggesting that SCWPs are responsible for binding with SLH modules of AncA. On the other hand, rSlp1-SLH and rSlp2-SLH associated with HF-EPCS, suggesting that these polypeptides had an affinity for peptidoglycan. A binding assay using a peptidoglycan fraction prepared from Escherichia coli cells definitely confirmed that rSlp1-SLH and rSlp2-SLH specifically interacted with peptidoglycan but not with SCWP.
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Affiliation(s)
- Guangshan Zhao
- Faculty of Bioresources, Mie University, Tsu 514-8507, Japan
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20
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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21
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Currie DH, Herring CD, Guss AM, Olson DG, Hogsett DA, Lynd LR. Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:32. [PMID: 23448319 PMCID: PMC3598777 DOI: 10.1186/1754-6834-6-32] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/08/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cellulose is highly recalcitrant and thus requires a specialized suite of enzymes to solubilize it into fermentable sugars. In C. thermocellum, these extracellular enzymes are present as a highly active multi-component system known as the cellulosome. This study explores the expression of a critical C. thermocellum cellulosomal component in T. saccharolyticum as a step toward creating a thermophilic bacterium capable of consolidated bioprocessing by employing heterologously expressed cellulosomes. RESULTS We developed an inducible promoter system based on the native T. saccharolyticum xynA promoter, which was shown to be induced by xylan and xylose. The promoter was used to express the cellulosomal component cipA*, an engineered form of the wild-type cipA from C. thermocellum. Expression and localization to the supernatant were both verified for CipA*. When a ΔcipA mutant C. thermocellum strain was cultured with a CipA*-expressing T. saccharolyticum strain, hydrolysis and fermentation of 10 grams per liter SigmaCell 101, a highly crystalline cellulose, were observed. This trans-species complementation of a cipA deletion demonstrated the ability for CipA* to assemble a functional cellulosome. CONCLUSION This study is the first example of an engineered thermophile heterologously expressing a structural component of a cellulosome. To achieve this goal we developed and tested an inducible promoter for controlled expression in T. saccharolyticum as well as a synthetic cipA. In addition, we demonstrate a high degree of hydrolysis (up to 93%) on microcrystalline cellulose.
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Affiliation(s)
- Devin H Currie
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Mascoma Corporation, Lebanon, NH 03766, USA
| | | | - Adam M Guss
- Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Mascoma Corporation, Lebanon, NH 03766, USA
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22
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Brás JLA, Alves VD, Carvalho AL, Najmudin S, Prates JAM, Ferreira LMA, Bolam DN, Romão MJ, Gilbert HJ, Fontes CMGA. Novel Clostridium thermocellum type I cohesin-dockerin complexes reveal a single binding mode. J Biol Chem 2012; 287:44394-405. [PMID: 23118225 PMCID: PMC3531753 DOI: 10.1074/jbc.m112.407700] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 10/25/2012] [Indexed: 11/06/2022] Open
Abstract
Protein-protein interactions play a pivotal role in a large number of biological processes exemplified by the assembly of the cellulosome. Integration of cellulosomal components occurs through the binding of type I cohesin modules located in a non-catalytic molecular scaffold to type I dockerin modules located at the C terminus of cellulosomal enzymes. The majority of type I dockerins display internal symmetry reflected by the presence of two essentially identical cohesin-binding surfaces. Here we report the crystal structures of two novel Clostridium thermocellum type I cohesin-dockerin complexes (CohOlpC-Doc124A and CohOlpA-Doc918). The data revealed that the two dockerins, Doc918 and Doc124A, are unusual because they lack the structural symmetry required to support a dual binding mode. Thus, in both cases, cohesin recognition is dominated by residues located at positions 11, 12, and 19 of one of the dockerin binding surfaces. The alternative binding mode is not possible (Doc918) or highly limited (Doc124A) because residues that assume the critical interacting positions, when dockerins are reoriented by 180°, make steric clashes with the cohesin. In common with a third dockerin (Doc258) that also presents a single binding mode, Doc124A directs the appended cellulase, Cel124A, to the surface of C. thermocellum and not to cellulosomes because it binds preferentially to type I cohesins located at the cell envelope. Although there are a few exceptions, such as Doc918 described here, these data suggest that there is considerable selective pressure for the evolution of a dual binding mode in type I dockerins that direct enzymes into cellulosomes.
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Affiliation(s)
- Joana L. A. Brás
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Victor D. Alves
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Ana Luísa Carvalho
- the REQUIMTE/CQFB, Departamento de Química, FCT-UNL, 2829–516 Caparica, Portugal, and
| | - Shabir Najmudin
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - José A. M. Prates
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Luís M. A. Ferreira
- From the Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - David N. Bolam
- the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Maria João Romão
- the REQUIMTE/CQFB, Departamento de Química, FCT-UNL, 2829–516 Caparica, Portugal, and
| | - 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 Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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Wieczorek AS, Martin VJJ. Effects of synthetic cohesin-containing scaffold protein architecture on binding dockerin-enzyme fusions on the surface of Lactococcus lactis. Microb Cell Fact 2012; 11:160. [PMID: 23241215 PMCID: PMC3542058 DOI: 10.1186/1475-2859-11-160] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The microbial synthesis of fuels, commodity chemicals, and bioactive compounds necessitates the assemblage of multiple enzyme activities to carry out sequential chemical reactions, often via substrate channeling by means of multi-domain or multi-enzyme complexes. Engineering the controlled incorporation of enzymes in recombinant protein complexes is therefore of interest. The cellulosome of Clostridium thermocellum is an extracellular enzyme complex that efficiently hydrolyzes crystalline cellulose. Enzymes interact with protein scaffolds via type 1 dockerin/cohesin interactions, while scaffolds in turn bind surface anchor proteins by means of type 2 dockerin/cohesin interactions, which demonstrate a different binding specificity than their type 1 counterparts. Recombinant chimeric scaffold proteins containing cohesins of different specificity allow binding of multiple enzymes to specific sites within an engineered complex. RESULTS We report the successful display of engineered chimeric scaffold proteins containing both type 1 and type 2 cohesins on the surface of Lactococcus lactis cells. The chimeric scaffold proteins were able to form complexes with the Escherichia coli β-glucuronidase fused to either type 1 or type 2 dockerin, and differences in binding efficiencies were correlated with scaffold architecture. We used E. coli β-galactosidase, also fused to type 1 or type 2 dockerins, to demonstrate the targeted incorporation of two enzymes into the complexes. The simultaneous binding of enzyme pairs each containing a different dockerin resulted in bi-enzymatic complexes tethered to the cell surface. The sequential binding of the two enzymes yielded insights into parameters affecting assembly of the complex such as protein size and position within the scaffold. CONCLUSIONS The spatial organization of enzymes into complexes is an important strategy for increasing the efficiency of biochemical pathways. In this study, chimeric protein scaffolds consisting of type 1 and type 2 cohesins anchored on the surface of L. lactis allowed for the controlled positioning of dockerin-fused reporter enzymes onto the scaffolds. By binding single enzymes or enzyme pairs to the scaffolds, our data also suggest that the size and relative positions of enzymes can affect the catalytic profiles of the resulting complexes. These insights will be of great value as we engineer more advanced scaffold-guided protein complexes to optimize biochemical pathways.
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Affiliation(s)
- Andrew S Wieczorek
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Vincent JJ Martin
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec, H4B 1R6, Canada
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Self-surface assembly of cellulosomes with two miniscaffoldins on Saccharomyces cerevisiae for cellulosic ethanol production. Proc Natl Acad Sci U S A 2012; 109:13260-5. [PMID: 22853950 DOI: 10.1073/pnas.1209856109] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Yeast to directly convert cellulose and, especially, the microcrystalline cellulose into bioethanol, was engineered through display of minicellulosomes on the cell surface of Saccharomyces cerevisiae. The construction and cell surface attachment of cellulosomes were accomplished with two individual miniscaffoldins to increase the display level. All of the cellulases including a celCCA (endoglucanase), a celCCE (cellobiohydrolase), and a Ccel_2454 (β-glucosidase) were cloned from Clostridium cellulolyticum, ensuring the thermal compatibility between cellulose hydrolysis and yeast fermentation. Cellulases and one of miniscaffoldins were secreted by α-factor; thus, the assembly and attachment to anchoring miniscaffoldin were accomplished extracellularly. Immunofluorescence microscopy, flow cytometric analysis (FACS), and cellulosic ethanol fermentation confirmed the successful display of such complex on the yeast surface. Enzyme-enzyme synergy, enzyme-proximity synergy, and cellulose-enzyme-cell synergy were analyzed, and the length of anchoring miniscaffoldin was optimized. The engineered S. cerevisiae was applied in fermentation of carboxymethyl cellulose (CMC), phosphoric acid-swollen cellulose (PASC), or Avicel. It showed a significant hydrolytic activity toward microcrystalline cellulose, with an ethanol titer of 1,412 mg/L. This indicates that simultaneous saccharification and fermentation of crystalline cellulose to ethanol can be accomplished by the yeast, engineered with minicellulosome.
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25
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Gefen G, Anbar M, Morag E, Lamed R, Bayer EA. Enhanced cellulose degradation by targeted integration of a cohesin-fused β-glucosidase into the Clostridium thermocellum cellulosome. Proc Natl Acad Sci U S A 2012; 109:10298-303. [PMID: 22689961 PMCID: PMC3387075 DOI: 10.1073/pnas.1202747109] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The conversion of recalcitrant plant-derived cellulosic biomass into biofuels is dependent on highly efficient cellulase systems that produce near-quantitative levels of soluble saccharides. Similar to other fungal and bacterial cellulase systems, the multienzyme cellulosome system of the anaerobic, cellulolytic bacterium Clostridium thermocellum is strongly inhibited by the major end product cellobiose. Cellobiose-induced inhibition can be relieved via its cleavage to noninhibitory glucose by the addition of exogenous noncellulosomal enzyme β-glucosidase; however, because the cellulosome is adsorbed to the insoluble substrate only a fraction of β-glucosidase would be available to the cellulosome. Towards this end, we designed a chimeric cohesin-fused β-glucosidase (BglA-CohII) that binds directly to the cellulosome through an unoccupied dockerin module of its major scaffoldin subunit. The β-glucosidase activity is thus focused at the immediate site of cellobiose production by the cellulosomal enzymes. BglA-CohII was shown to retain cellobiase activity and was readily incorporated into the native cellulosome complex. Surprisingly, it was found that the native C. thermocellum cellulosome exists as a homooligomer and the high-affinity interaction of BglA-CohII with the scaffoldin moiety appears to dissociate the oligomeric state of the cellulosome. Complexation of the cellulosome and BglA-CohII resulted in higher overall degradation of microcrystalline cellulose and pretreated switchgrass compared to the native cellulosome alone or in combination with wild-type BglA in solution. These results demonstrate the effect of enzyme targeting and its potential for enhanced degradation of cellulosic biomass.
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Affiliation(s)
- Gilad Gefen
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael Anbar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ely Morag
- Designer Energy Ltd., 2 Bergman Street, Rehovot, Israel; and
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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26
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Currie MA, Adams JJ, Faucher F, Bayer EA, Jia Z, Smith SP. Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome. J Biol Chem 2012; 287:26953-61. [PMID: 22707718 DOI: 10.1074/jbc.m112.343897] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulosomes are multienzyme complexes responsible for efficient degradation of plant cell wall polysaccharides. The nonenzymatic scaffoldin subunit provides a platform for cellulolytic enzyme binding that enhances the overall activity of the bound enzymes. Understanding the unique quaternary structural elements responsible for the enzymatic synergy of the cellulosome is hindered by the large size and inherent flexibility of these multiprotein complexes. Herein, we have used x-ray crystallography and small angle x-ray scattering to structurally characterize a ternary protein complex from the Clostridium thermocellum cellulosome that comprises a C-terminal trimodular fragment of the CipA scaffoldin bound to the SdbA type II cohesin module and the type I dockerin module from the Cel9D glycoside hydrolase. This complex represents the largest fragment of the cellulosome solved by x-ray crystallography to date and reveals two rigid domains formed by the type I cohesin·dockerin complex and by the X module-type II cohesin·dockerin complex, which are separated by a 13-residue linker in an extended conformation. The type I dockerin modules of the four structural models found in the asymmetric unit are in an alternate orientation to that previously observed that provides further direct support for the dual mode of binding. Conserved intermolecular contacts between symmetry-related complexes were also observed and may play a role in higher order cellulosome structure. SAXS analysis of the ternary complex revealed that the 13-residue intermodular linker of the scaffoldin subunit is highly dynamic in solution. These studies provide fundamental insights into modular positioning, linker flexibility, and higher order organization of the cellulosome.
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Affiliation(s)
- Mark A Currie
- Department of Biomedical and Molecular Sciences, University, Kingston, Ontario K7L 3N6, Canada
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27
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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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28
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Brás JLA, Carvalho AL, Viegas A, Najmudin S, Alves VD, Prates JAM, Ferreira LMA, Romão MJ, Gilbert HJ, Fontes CMGA. Escherichia coli expression, purification, crystallization, and structure determination of bacterial cohesin-dockerin complexes. Methods Enzymol 2012; 510:395-415. [PMID: 22608738 DOI: 10.1016/b978-0-12-415931-0.00021-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Cellulosomes are highly efficient nanomachines that play a fundamental role during the anaerobic deconstruction of complex plant cell wall carbohydrates. The assembly of these complex nanomachines results from the very tight binding of repetitive cohesin modules, located in a noncatalytic molecular scaffold, and dockerin domains located at the C-terminus of the enzyme components of the cellulosome. The number of enzymes found in a cellulosome varies but may reach more than 100 catalytic subunits if cellulosomes are further organized in polycellulosomes, through a second type of cohesin-dockerin interaction. Structural studies have revealed how the cohesin-dockerin interaction mediates cellulosome assembly and cell-surface attachment, while retaining the flexibility required to potentiate catalytic synergy within the complex. Methods that might be applied for the production, purification, and structure determination of cohesin-dockerin complexes are described here.
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Affiliation(s)
- Joana L A Brás
- CIISA-Faculdade de Medicina Veterinária, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
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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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30
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Newcomb M, Millen J, Chen CY, Wu JHD. Co-transcription of the celC gene cluster in Clostridium thermocellum. Appl Microbiol Biotechnol 2011; 90:625-34. [DOI: 10.1007/s00253-011-3121-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/04/2011] [Accepted: 01/06/2011] [Indexed: 10/18/2022]
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31
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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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Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors. Proc Natl Acad Sci U S A 2010; 107:18646-51. [PMID: 20937888 DOI: 10.1073/pnas.1012175107] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clostridium thermocellum produces a highly efficient cellulolytic extracellular complex, termed the cellulosome, for hydrolyzing plant cell wall biomass. The composition of the cellulosome is affected by the presence of extracellular polysaccharides; however, the regulatory mechanism is unknown. Recently, we have identified in C. thermocellum a set of putative σ and anti-σ factors that include extracellular polysaccharide-sensing components [Kahel-Raifer et al. (2010) FEMS Microbiol Lett 308:84-93]. These factor-encoding genes are homologous to the Bacillus subtilis bicistronic operon sigI-rsgI, which encodes for an alternative σ(I) factor and its cognate anti-σ(I) regulator RsgI that is functionally regulated by an extracytoplasmic signal. In this study, the binding of C. thermocellum putative anti-σ(I) factors to their corresponding σ factors was measured, demonstrating binding specificity and dissociation constants in the range of 0.02 to 1 μM. Quantitative real-time RT-PCR measurements revealed three- to 30-fold up-expression of the alternative σ factor genes in the presence of cellulose and xylan, thus connecting their expression to direct detection of their extracellular polysaccharide substrates. Cellulosomal genes that are putatively regulated by two of these σ factors, σ(I1) or σ(I6), were identified based on the sequence similarity of their promoters. The ability of σ(I1) to direct transcription from the sigI1 promoter and from the promoter of celS (encodes the family 48 cellulase) was demonstrated in vitro by runoff transcription assays. Taken together, the results reveal a regulatory mechanism in which alternative σ factors are involved in regulating the cellulosomal genes via an external carbohydrate-sensing mechanism.
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33
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Wieczorek AS, Martin VJJ. Engineering the cell surface display of cohesins for assembly of cellulosome-inspired enzyme complexes on Lactococcus lactis. Microb Cell Fact 2010; 9:69. [PMID: 20840763 PMCID: PMC2949795 DOI: 10.1186/1475-2859-9-69] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 09/14/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The assembly and spatial organization of enzymes in naturally occurring multi-protein complexes is of paramount importance for the efficient degradation of complex polymers and biosynthesis of valuable products. The degradation of cellulose into fermentable sugars by Clostridium thermocellum is achieved by means of a multi-protein "cellulosome" complex. Assembled via dockerin-cohesin interactions, the cellulosome is associated with the cell surface during cellulose hydrolysis, forming ternary cellulose-enzyme-microbe complexes for enhanced activity and synergy. The assembly of recombinant cell surface displayed cellulosome-inspired complexes in surrogate microbes is highly desirable. The model organism Lactococcus lactis is of particular interest as it has been metabolically engineered to produce a variety of commodity chemicals including lactic acid and bioactive compounds, and can efficiently secrete an array of recombinant proteins and enzymes of varying sizes. RESULTS Fragments of the scaffoldin protein CipA were functionally displayed on the cell surface of Lactococcus lactis. Scaffolds were engineered to contain a single cohesin module, two cohesin modules, one cohesin and a cellulose-binding module, or only a cellulose-binding module. Cell toxicity from over-expression of the proteins was circumvented by use of the nisA inducible promoter, and incorporation of the C-terminal anchor motif of the streptococcal M6 protein resulted in the successful surface-display of the scaffolds. The facilitated detection of successfully secreted scaffolds was achieved by fusion with the export-specific reporter staphylococcal nuclease (NucA). Scaffolds retained their ability to associate in vivo with an engineered hybrid reporter enzyme, E. coli β-glucuronidase fused to the type 1 dockerin motif of the cellulosomal enzyme CelS. Surface-anchored complexes exhibited dual enzyme activities (nuclease and β-glucuronidase), and were displayed with efficiencies approaching 104 complexes/cell. CONCLUSIONS We report the successful display of cellulosome-inspired recombinant complexes on the surface of Lactococcus lactis. Significant differences in display efficiency among constructs were observed and attributed to their structural characteristics including protein conformation and solubility, scaffold size, and the inclusion and exclusion of non-cohesin modules. The surface-display of functional scaffold proteins described here represents a key step in the development of recombinant microorganisms capable of carrying out a variety of metabolic processes including the direct conversion of cellulosic substrates into fuels and chemicals.
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Affiliation(s)
- Andrew S Wieczorek
- Department of Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Vincent JJ Martin
- Department of Biology, Concordia University, Montréal, Québec, H4B 1R6, Canada
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34
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Adams JJ, Currie MA, Ali S, Bayer EA, Jia Z, Smith SP. Insights into higher-order organization of the cellulosome revealed by a dissect-and-build approach: crystal structure of interacting Clostridium thermocellum multimodular components. J Mol Biol 2010; 396:833-9. [PMID: 20070943 DOI: 10.1016/j.jmb.2010.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 01/05/2010] [Accepted: 01/06/2010] [Indexed: 10/20/2022]
Abstract
Cellulosomes are large, multienzyme, plant cell wall-degrading protein complexes found affixed to the surface of a variety of anaerobic microbes. The core of the cellulosome is a noncatalytic scaffoldin protein, which contains several type-I cohesin modules that bind type-I dockerin-containing enzymatic subunits, a cellulose-binding module, an X module, and a type-II dockerin that interacts with type-II cohesin-containing cell surface proteins. The unique arrangement of the enzymatic subunits in the cellulosome complex, made possible by the scaffoldin subunit, promotes enhanced substrate degradation relative to the enzymes free in solution. Despite representative high-resolution structures of all of the individual modules of the cellulosome, this mechanism of enzymatic synergy remains poorly understood. Consequently, a model of the entire cellulosome and a detailed picture of intermodular contacts will provide more detailed insight into cellulosome activity. Toward this goal, we have solved the structure of a multimodular heterodimeric complex from Clostridium thermocellum composed of the type-II cohesin module of the cell surface protein SdbA bound to a trimodular C-terminal fragment of the scaffoldin subunit CipA to a resolution of 1.95 A. The linker that connects the ninth type-I cohesin module and the X module has elevated temperature factors, reflecting an inherent flexibility within this region. Interestingly, a novel dimer interface was observed between CipA and a second, symmetry-related CipA molecule within the crystal structure, mediated by contacts between a type-I cohesin and an X module of a symmetry mate, resulting in two intertwined scaffoldins. Sedimentation velocity experiments confirmed that dimerization also occurs in solution. These observations support the intriguing possibility that individual cellulosomes can associate with one another via inter-scaffoldin interactions, which may play a role in the mechanism of action of the complex.
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Affiliation(s)
- Jarrett J Adams
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
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35
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Currie MA, Adams JJ, Ali S, Smith SP, Jia Z. Purification and crystallization of a multimodular heterotrimeric complex containing both type I and type II cohesin-dockerin interactions from the cellulosome of Clostridium thermocellum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:327-9. [PMID: 20208173 PMCID: PMC2833049 DOI: 10.1107/s1744309110001375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 01/12/2010] [Indexed: 11/11/2022]
Abstract
The multimodular scaffoldin subunit CipA is the central component of the cellulosome, a multienzyme plant cell-wall-degrading complex, from Clostridium thermocellum. It captures secreted cellulases and hemicellulases and anchors the entire complex to the cell surface via high-affinity calcium-dependent interactions between cohesin and dockerin modules termed type I and type II interactions. The crystallization of a heterotrimeric complex comprising the type II cohesin module from the cell-surface protein SdbA, a trimodular C-terminal fragment of the scaffoldin CipA and the type I dockerin module from the CelD cellulase is reported. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 119.37, b = 186.31, c = 191.17 A. The crystals diffracted to 2.7 A resolution with four or eight molecules of the ternary protein complex in the asymmetric unit.
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Affiliation(s)
- Mark A. Currie
- Department of Biochemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Jarrett J. Adams
- Department of Biochemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Sabrina Ali
- Department of Biochemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Steven P. Smith
- Department of Biochemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
- Protein Function Discovery Group, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Zongchao Jia
- Department of Biochemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
- Protein Function Discovery Group, Queen’s University, Kingston, ON K7L 3N6, Canada
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36
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Fontes CMGA, Gilbert HJ. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annu Rev Biochem 2010; 79:655-81. [PMID: 20373916 DOI: 10.1146/annurev-biochem-091208-085603] [Citation(s) in RCA: 361] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes can be described as one of nature's most elaborate and highly efficient nanomachines. These cell bound multienzyme complexes orchestrate the deconstruction of cellulose and hemicellulose, two of the most abundant polymers on Earth, and thus play a major role in carbon turnover. Integration of cellulosomal components occurs via highly ordered protein:protein interactions between cohesins and dockerins, whose specificity allows the incorporation of cellulases and hemicellulases onto a molecular scaffold. Cellulosome assembly promotes the exploitation of enzyme synergism because of spatial proximity and enzyme-substrate targeting. Recent structural and functional studies have revealed how cohesin-dockerin interactions mediate both cellulosome assembly and cell-surface attachment, while retaining the spatial flexibility required to optimize the catalytic synergy within the enzyme complex. These emerging advances in our knowledge of cellulosome function are reviewed here.
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Affiliation(s)
- Carlos M G A Fontes
- CIISA, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, 1300-477 Lisboa, Portugal.
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Alber O, Noach I, Rincon MT, Flint HJ, Shimon LJW, Lamed R, Frolow F, Bayer EA. Cohesin diversity revealed by the crystal structure of the anchoring cohesin from Ruminococcus flavefaciens. Proteins 2009; 77:699-709. [PMID: 19544570 DOI: 10.1002/prot.22483] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cellulosome is an intriguing multienzyme complex found in cellulolytic bacteria that plays a key role in the degradation of plant cell-wall polysaccharides. In Ruminococcus flavefaciens, a predominant fiber-degrading bacterium found in ruminants, the cellulosome is anchored to the bacterial cell wall through a relatively short ScaE scaffoldin. Determination of the crystal structure of the lone type-III ScaE cohesin from R. flavefaciens (Rf-CohE) was initiated as a part of a structural effort to define cellulosome assembly. The structure was determined at 1.95 A resolution by single-wavelength anomalous diffraction. This is the first detailed description of a crystal structure for a type-III cohesin, and its features were compared with those of the known type-I and type-II cohesin structures. The Rf-CohE module folds into a nine-stranded beta-sandwich with jellyroll topology, typically observed for cohesins, and includes two beta-flaps in the midst of beta-strands 4 and 8, similar to the type-II cohesin structures. However, the presence in Rf-CohE of an additional 13-residue alpha-helix located between beta-strands 8 and 9 represents a dramatic divergence from other known cohesin structures. The prominent alpha-helix is enveloped by an extensive N-terminal loop, not observed in any other known cohesin, which embraces the helix presumably enhancing its stability. A planar surface at the upper portion of the front face of the molecule, bordered by beta-flap 8, exhibits plausible dimensions and exposed amino acid residues to accommodate the dockerin-binding site.
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Affiliation(s)
- Orly Alber
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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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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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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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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41
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Alber O, Noach I, Lamed R, Shimon LJW, Bayer EA, Frolow F. Preliminary X-ray characterization of a novel type of anchoring cohesin from the cellulosome of Ruminococcus flavefaciens. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:77-80. [PMID: 18259053 PMCID: PMC2374186 DOI: 10.1107/s1744309107067437] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 12/17/2007] [Indexed: 11/10/2022]
Abstract
Ruminococcus flavefaciens is an anaerobic bacterium that resides in the gastrointestinal tract of ruminants. It produces a highly organized multi-enzyme cellulosome complex that plays a key role in the degradation of plant cell walls. ScaE is one of the critical structural components of its cellulosome that serves to anchor the complex to the cell wall. The seleno-L-methionine-labelled derivative of the ScaE cohesin module has been cloned, expressed, purified and crystallized. The crystals belong to space group C2, with unit-cell parameters a = 155.6, b = 69.3, c = 93.0 A, beta = 123.4 degrees, and contain four molecules in the asymmetric unit. Diffraction data were phased to 1.95 A using the anomalous signal from the Se atoms.
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Affiliation(s)
- Orly Alber
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilit Noach
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology, Tel Aviv University, Tel Aviv 69978, Israel
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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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43
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Abstract
The assembly of proteins that display complementary activities into supramolecular intra- and extracellular complexes is central to cellular function. One such nanomachine of considerable biological and industrial significance is the plant cell wall degrading apparatus of anaerobic bacteria termed the cellulosome. The Clostridium thermocellum cellulosome assembles through the interaction of a type I dockerin module in the catalytic entities with one of several type I cohesin modules in the non-catalytic scaffolding protein. Recent structural studies have provided the molecular details of how dockerin-cohesin interactions mediate both cellulosome assembly and the retention of the protein complex on the bacterial cell surface. The type I dockerin, which displays near-perfect sequence and structural symmetry, interacts with its cohesin partner through a dual binding mode in which either the N- or C-terminal helix dominate heterodimer formation. The biological significance of this dual binding mode is discussed with respect to the plasticity of the orientation of the catalytic subunits within this supramolecular assembly. The flexibility in the quaternary structure of the cellulosome may reflect the challenges presented by the degradation of a heterogenous recalcitrant insoluble substrate by an intricate macromolecular complex, in which the essential synergy between the catalytic subunits is a key feature of cellulosome function.
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Affiliation(s)
- Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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44
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Carvalho AL, Dias FMV, Nagy T, Prates JAM, Proctor MR, Smith N, Bayer EA, Davies GJ, Ferreira LMA, Romão MJ, Fontes CMGA, Gilbert HJ. Evidence for a dual binding mode of dockerin modules to cohesins. Proc Natl Acad Sci U S A 2007; 104:3089-94. [PMID: 17360613 PMCID: PMC1805526 DOI: 10.1073/pnas.0611173104] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Indexed: 11/18/2022] Open
Abstract
The assembly of proteins that display complementary activities into macromolecular complexes is critical to cellular function. One such enzyme complex, of environmental significance, is the plant cell wall degrading apparatus of anaerobic bacteria, termed the cellulosome. The complex assembles through the interaction of enzyme-derived "type I dockerin" modules with the multiple "cohesin" modules of the scaffolding protein. Clostridium thermocellum type I dockerin modules contain a duplicated 22-residue sequence that comprises helix-1 and helix-3, respectively. The crystal structure of a C. thermocellum type I cohesin-dockerin complex showed that cohesin recognition was predominantly through helix-3 of the dockerin. The sequence duplication is reflected in near-perfect 2-fold structural symmetry, suggesting that both repeats could interact with cohesins by a common mechanism in wild-type (WT) proteins. Here, a helix-3 disrupted mutant dockerin is used to visualize the reverse binding in which the dockerin mutant is indeed rotated 180 degrees relative to the WT dockerin such that helix-1 now dominates recognition of its protein partner. The dual binding mode is predicted to impart significant plasticity into the orientation of the catalytic subunits within this supramolecular assembly, which reflects the challenges presented by the degradation of a heterogeneous, recalcitrant, insoluble substrate by a tethered macromolecular complex.
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Affiliation(s)
- Ana Luísa Carvalho
- *Rede de Química e Tecnologia/Centro de Química Fina e Biotecnologia (REQUIMTE/CQFB), Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Fernando M. V. Dias
- Centro Interdisciplinar de Investigação em Sanidade Animal Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Tibor Nagy
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - José A. M. Prates
- Centro Interdisciplinar de Investigação em Sanidade Animal Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Mark R. Proctor
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicola Smith
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel; and
| | - Gideon J. Davies
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
| | - Luís M. A. Ferreira
- Centro Interdisciplinar de Investigação em Sanidade Animal Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Maria J. Romão
- *Rede de Química e Tecnologia/Centro de Química Fina e Biotecnologia (REQUIMTE/CQFB), Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M. G. A. Fontes
- Centro Interdisciplinar de Investigação em Sanidade Animal Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
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Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ. Approaching the CAPRI challenge with an efficient geometry-based docking. Proteins 2006; 60:217-23. [PMID: 15981251 DOI: 10.1002/prot.20561] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last 3 rounds (3-5) of CAPRI included a wide range of docking targets. Several targets were especially challenging, since they involved large-scale movements and symmetric rearrangement, while others were based on homology models. We have approached the targets with a variety of geometry-based docking algorithms that include rigid docking, symmetric docking, and flexible docking with symmetry constraints. For all but 1 docking target, we were able to submit at least 1 acceptable quality prediction. Here, we detail for each target the prediction methods used and the specific biological data employed, and supply a retrospective analysis of the results. We highlight the advantages of our techniques, which efficiently exploit the geometric shape complementarity properties of the interaction. These enable them to run only few minutes on a standard PC even for flexible docking, thus proving their scalability toward computational genomic scale experiments. We also outline the major required enhancements, such as the introduction of side-chain position refinement and the introduction of flexibility for both docking partners.
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Affiliation(s)
- Yuval Inbar
- School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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46
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Zhao G, Ali E, Sakka M, Kimura T, Sakka K. Binding of S-layer homology modules from Clostridium thermocellum SdbA to peptidoglycans. Appl Microbiol Biotechnol 2006; 70:464-9. [PMID: 16041572 DOI: 10.1007/s00253-005-0079-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2005] [Revised: 06/26/2005] [Accepted: 06/26/2005] [Indexed: 10/25/2022]
Abstract
S-layer homology (SLH) module polypeptides were derived from Clostridium josui xylanase Xyn10A, Clostridium stercorarium xylanase Xyn10B, and Clostridium thermocellum scafoldin dockerin binding protein SdbA as rXyn10A-SLH, rXyn10B-SLH, and rSdbA-SLH, respectively. Their binding specificities were investigated using various cell wall preparations. rXyn10A-SLH and rXyn10B-SLH bound to native peptidoglycan-containing sacculi consisting of peptidoglycan and secondary cell wall polymers (SCWP) prepared from these bacteria but not to hydrofluoric acid-extracted peptidoglycan-containing sacculi (HF-EPCS) lacking SCWP, suggesting that SCWP are responsible for binding with SLH modules. In contrast, rSdbA-SLH interacted with HF-EPCS, suggesting that this polypeptide had an affinity for peptidoglycans but not for SCWP. The affinity of rSdbA-SLH for peptidoglycans was confirmed by a binding assay using a peptidoglycan fraction prepared from Escherichia coli cells. The SLH modules of SdbA must be useful for cell surface engineering in bacteria that do not contain SCWP.
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47
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May A, Pusztahelyi T, Hoffmann N, Fischer RJ, Bahl H. Mutagenesis of conserved charged amino acids in SLH domains of Thermoanaerobacterium thermosulfurigenes EM1 affects attachment to cell wall sacculi. Arch Microbiol 2006; 185:263-9. [PMID: 16470371 DOI: 10.1007/s00203-006-0092-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Revised: 01/17/2006] [Accepted: 01/20/2006] [Indexed: 02/03/2023]
Abstract
SLH domains (for surface layer homology) are involved in the attachment of proteins to bacterial cell walls. The data presented here assign the conserved TRAE motif within SLH domains a key role for the binding. The charged amino acids arginine (R) or/and glutamic acid (E) were replaced via site-directed mutagenesis by different amino acids. Effects were visualized in an in vitro binding assay using native cell wall sacculi of Thermoanaerobacterium thermosulfurigenes EM1 and different variants of an SLH protein which consisted of the triplicate SLH domain of xylanase XynA of this bacterium and which was purified after expression in Escherichia coli. The results indicated (1) that the TRAE motif is critical for the binding function of SLH domains, (2) that a functional TRAE motif is necessary in all three domains, (3) that a least one (preferentially positively) charged amino acid in the TRAE motif is required for the functionality of the SLH domain, and (4) that the position of the negatively and positively charged amino acids is important. The finding that the cell wall of T. thermosulfurigenes EM1 contains pyruvate (4 microg mg(-1)) is in agreement with the hypothesis that pyruvylated secondary cell wall polymers function as ligand for SLH domains.
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Affiliation(s)
- Antje May
- Institute of Biological Sciences, Division of Microbiology, University of Rostock, Albert-Einstein-Str. 3, 18051, Rostock, Germany
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48
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Adams JJ, Pal G, Jia Z, Smith SP. Mechanism of bacterial cell-surface attachment revealed by the structure of cellulosomal type II cohesin-dockerin complex. Proc Natl Acad Sci U S A 2005; 103:305-10. [PMID: 16384918 PMCID: PMC1326161 DOI: 10.1073/pnas.0507109103] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial cell-surface attachment of macromolecular complexes maintains the microorganism in close proximity to extracellular substrates and allows for optimal uptake of hydrolytic byproducts. The cellulosome is a large multienzyme complex used by many anaerobic bacteria for the efficient degradation of plant cell-wall polysaccharides. The mechanism of cellulosome retention to the bacterial cell surface involves a calcium-mediated protein-protein interaction between the dockerin (Doc) module from the cellulosomal scaffold and a cohesin (Coh) module of cell-surface proteins located within the proteoglycan layer. Here, we report the structure of an ultra-high-affinity (K(a) = 1.44 x 10(10) M(-1)) complex between type II Doc, together with its neighboring X module from the cellulosome scaffold of Clostridium thermocellum, and a type II Coh module associated with the bacterial cell surface. Identification of X module-Doc and X module-Coh contacts reveal roles for the X module in Doc stability and enhanced Coh recognition. This extremely tight interaction involves one face of the Coh and both helices of the Doc and comprises significant hydrophobic character and a complementary extensive hydrogen-bond network. This structure represents a unique mechanism for cell-surface attachment in anaerobic bacteria and provides a rationale for discriminating between type I and type II Coh modules.
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Affiliation(s)
- Jarrett J Adams
- Department of Biochemistry and Protein Function Discovery Group, Queen's University, Kingston, ON, Canada K7L 3N6
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49
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Hammel M, Fierobe HP, Czjzek M, Kurkal V, Smith JC, Bayer EA, Finet S, Receveur-Bréchot V. Structural Basis of Cellulosome Efficiency Explored by Small Angle X-ray Scattering. J Biol Chem 2005; 280:38562-8. [PMID: 16157599 DOI: 10.1074/jbc.m503168200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulose, the main structural component of plant cell walls, is the most abundant carbohydrate polymer in nature. To break down plant cell walls, anaerobic microorganisms have evolved a large extracellular enzyme complex termed cellulosome. This megadalton catalytic machinery organizes an enzymatic assembly, tenaciously bound to a scaffolding protein via specialized intermodular "cohesin-dockerin" interactions that serve to enhance synergistic activity among the different catalytic subunits. Here, we report the solution structure properties of cellulosome-like assemblies analyzed by small angle x-ray scattering and molecular dynamics. The atomic models, generated by our strategy for the free chimeric scaffoldin and for binary and ternary complexes, reveal the existence of various conformations due to intrinsic structural flexibility with no, or only coincidental, inter-cohesin interactions. These results provide primary evidence concerning the mechanisms by which these protein assemblies attain their remarkable synergy. The data suggest that the motional freedom of the scaffoldin allows precise positioning of the complexed enzymes according to the topography of the substrate, whereas short-scale motions permitted by residual flexibility of the enzyme linkers allow "fine-tuning" of individual catalytic domains.
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Affiliation(s)
- Michal Hammel
- Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, CNRS and Universities Aix-Marseille I and II, 163 Avenue de Luminy, Case 932, F-13288 Marseille Cedex 9, France
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50
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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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