1
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Zajki-Zechmeister K, Eibinger M, Kaira GS, Nidetzky B. Mechanochemical Coupling of Catalysis and Motion in a Cellulose-Degrading Multienzyme Nanomachine. ACS Catal 2024; 14:2656-2663. [PMID: 38384941 PMCID: PMC10877591 DOI: 10.1021/acscatal.3c05653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/13/2024] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
The cellulosome is a megadalton-size protein complex that functions as a biological nanomachine of cellulosic fiber degradation. We show that the cellulosome behaves as a Brownian ratchet that rectifies protein motions on the cellulose surface into a propulsion mechanism by coupling to the hydrolysis of cellulose chains. Movement on cellulose fibrils is unidirectional and results from "macromolecular crawl" composed of dynamic switches between elongated and compact spatial arrangements of enzyme subunits. Deletion of the main exocellulase Cel48S eliminates conformational bias for aligning the subunits to the long fibril axis, which we reveal as crucial for optimum coupling between directional movement and substrate degradation. Implications of the cellulosome acting as a mechanochemical motor suggest a distinct mechanism of enzymatic machinery in the deconstruction of cellulose assemblies.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
| | - Gaurav Singh Kaira
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, Graz 8010, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, Graz 8010, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, Graz 8010, Austria
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2
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Iglesias Rando MR, Gorojovsky N, Zylberman V, Goldbaum FA, Craig PO. Improvement of Cellulomonas fimi endoglucanase CenA by multienzymatic display on a decameric structural scaffold. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12581-6. [PMID: 37212884 DOI: 10.1007/s00253-023-12581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/27/2023] [Accepted: 05/06/2023] [Indexed: 05/23/2023]
Abstract
The development of multifunctional particles using polymeric scaffolds is an emerging technology for many nanobiotechnological applications. Here we present a system for the production of multifunctional complexes, based on the high affinity non-covalent interaction of cohesin and dockerin modules complementary fused to decameric Brucella abortus lumazine synthase (BLS) subunits, and selected target proteins, respectively. The cohesin-BLS scaffold was solubly expressed in high yield in Escherichia coli, and revealed a high thermostability. The production of multienzymatic particles using this system was evaluated using the catalytic domain of Cellulomonas fimi endoglucanase CenA recombinantly fused to a dockerin module. Coupling of the enzyme to the scaffold was highly efficient and occurred with the expected stoichiometry. The decavalent enzymatic complexes obtained showed higher cellulolytic activity and association to the substrate compared to equivalent amounts of the free enzyme. This phenomenon was dependent on the multiplicity and proximity of the enzymes coupled to the scaffold, and was attributed to an avidity effect in the polyvalent enzyme interaction with the substrate. Our results highlight the usefulness of the scaffold presented in this work for the development of multifunctional particles, and the improvement of lignocellulose degradation among other applications. KEY POINTS: • New system for multifunctional particle production using the BLS scaffold • Higher cellulolytic activity of polyvalent endoglucanase compared to the free enzyme • Amount of enzyme associated to cellulose is higher for the polyvalent endoglucanase.
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Affiliation(s)
- Matías R Iglesias Rando
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Natalia Gorojovsky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Vanesa Zylberman
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (CP 1405), Buenos Aires, Argentina
- Centro de Rediseño e Ingeniería de Proteínas (CRIP), UNSAM Campus Miguelete, 25 de Mayo y Francia (CP 1650), Gral. San Martín, Buenos Aires, Argentina
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
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3
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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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4
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Tatli M, Moraïs S, Tovar-Herrera OE, Bomble YJ, Bayer EA, Medalia O, Mizrahi I. Nanoscale resolution of microbial fiber degradation in action. eLife 2022; 11:76523. [PMID: 35638899 PMCID: PMC9191890 DOI: 10.7554/elife.76523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
The lives of microbes unfold at the micron scale, and their molecular machineries operate at the nanoscale. Their study at these resolutions is key toward achieving a better understanding of their ecology. We focus on cellulose degradation of the canonical Clostridium thermocellum system to comprehend how microbes build and use their cellulosomal machinery at these nanometer scales. Degradation of cellulose, the most abundant organic polymer on Earth, is instrumental to the global carbon cycle. We reveal that bacterial cells form ‘cellulosome capsules’ driven by catalytic product-dependent dynamics, which can increase the rate of hydrolysis. Biosynthesis of this energetically costly machinery and cell growth are decoupled at the single-cell level, hinting at a division-of-labor strategy through phenotypic heterogeneity. This novel observation highlights intrapopulation interactions as key to understanding rates of fiber degradation.
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Affiliation(s)
- Meltem Tatli
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sarah Moraïs
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omar E Tovar-Herrera
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Edward A Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zürich, Zurich, Switzerland
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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5
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Vanderstraeten J, da Fonseca MJM, De Groote P, Grimon D, Gerstmans H, Kahn A, Moraïs S, Bayer EA, Briers Y. Combinatorial assembly and optimisation of designer cellulosomes: a galactomannan case study. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:60. [PMID: 35637485 PMCID: PMC9153192 DOI: 10.1186/s13068-022-02158-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/14/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Designer cellulosomes are self-assembled chimeric enzyme complexes that can be used to improve lignocellulosic biomass degradation. They are composed of a synthetic multimodular backbone protein, termed the scaffoldin, and a range of different chimeric docking enzymes that degrade polysaccharides. Over the years, several functional designer cellulosomes have been constructed. Since many parameters influence the efficiency of these multi-enzyme complexes, there is a need to optimise designer cellulosome architecture by testing combinatorial arrangements of docking enzyme and scaffoldin variants. However, the modular cloning procedures are tedious and cumbersome. RESULTS VersaTile is a combinatorial DNA assembly method, allowing the rapid construction and thus comparison of a range of modular proteins. Here, we present the extension of the VersaTile platform to facilitate the construction of designer cellulosomes. We have constructed a tile repository, composed of dockerins, cohesins, linkers, tags and enzymatically active modules. The developed toolbox allows us to efficiently create and optimise designer cellulosomes at an unprecedented speed. As a proof of concept, a trivalent designer cellulosome able to degrade the specific hemicellulose substrate, galactomannan, was constructed and optimised. The main factors influencing cellulosome efficiency were found to be the selected dockerins and linkers and the docking enzyme ratio on the scaffoldin. The optimised designer cellulosome was able to hydrolyse the galactomannan polysaccharide and release mannose and galactose monomers. CONCLUSION We have eliminated one of the main technical hurdles in the designer cellulosome field and anticipate the VersaTile platform to be a starting point in the development of more elaborate multi-enzyme complexes.
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Affiliation(s)
- Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Maria João Maurício da Fonseca
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Philippe De Groote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Dennis Grimon
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Hans Gerstmans
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.,Laboratory for Biomolecular Discovery and Engineering, Department of Biology, VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001, Louvain, Belgium
| | - Amaranta Kahn
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.
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6
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Cerqueira FM, Photenhauer AL, Doden HL, Brown AN, Abdel-Hamid AM, Moraïs S, Bayer EA, Wawrzak Z, Cann I, Ridlon JM, Hopkins JB, Koropatkin NM. Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome. J Biol Chem 2022; 298:101896. [PMID: 35378131 PMCID: PMC9112005 DOI: 10.1016/j.jbc.2022.101896] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/08/2023] Open
Abstract
Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure-function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (Kd ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.
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Affiliation(s)
- Filipe M Cerqueira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Heidi L Doden
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Aric N Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ahmed M Abdel-Hamid
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Edward A Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Zdzislaw Wawrzak
- Northwestern University, Synchrotron Research Center, Life Science Collaborative Access Team, Lemont, Illinois, USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jesse B Hopkins
- Biophysics Collaborative Access Team, Illinois Institute of Technology, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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7
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Vera AM, Galera-Prat A, Wojciechowski M, Różycki B, Laurents DV, Carrión-Vázquez M, Cieplak M, Tinnefeld P. Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization. Structure 2021; 29:587-597.e8. [PMID: 33561387 DOI: 10.1016/j.str.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule fluorescence resonance energy transfer and molecular simulations on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.
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Affiliation(s)
- Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Albert Galera-Prat
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | | | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
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8
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Research progress and the biotechnological applications of multienzyme complex. Appl Microbiol Biotechnol 2021; 105:1759-1777. [PMID: 33564922 DOI: 10.1007/s00253-021-11121-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 11/26/2022]
Abstract
The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.
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9
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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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10
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Vanderstraeten J, Briers Y. Synthetic protein scaffolds for the colocalisation of co-acting enzymes. Biotechnol Adv 2020; 44:107627. [DOI: 10.1016/j.biotechadv.2020.107627] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
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11
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Dvořák P, Bayer EA, de Lorenzo V. Surface Display of Designer Protein Scaffolds on Genome-Reduced Strains of Pseudomonas putida. ACS Synth Biol 2020; 9:2749-2764. [PMID: 32877604 DOI: 10.1021/acssynbio.0c00276] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterium Pseudomonas putida KT2440 is gaining considerable interest as a microbial platform for biotechnological valorization of polymeric organic materials, such as lignocellulosic residues or plastics. However, P. putida on its own cannot make much use of such complex substrates, mainly because it lacks an efficient extracellular depolymerizing apparatus. We seek to address this limitation by adopting a recombinant cellulosome strategy for this host. In this work, we report an essential step in this endeavor-a display of designer enzyme-anchoring protein "scaffoldins", encompassing cohesin binding domains from divergent cellulolytic bacterial species on the P. putida surface. Two P. putida chassis strains, EM42 and EM371, with streamlined genomes and differences in the composition of the outer membrane were employed in this study. Scaffoldin variants were optimally delivered to their surface with one of four tested autotransporter systems (Ag43 from Escherichia coli), and the efficient display was confirmed by extracellular attachment of chimeric β-glucosidase and fluorescent proteins. Our results not only highlight the value of cell surface engineering for presentation of recombinant proteins on the envelope of Gram-negative bacteria but also pave the way toward designer cellulosome strategies tailored for P. putida.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, Darwin 3, 28049 Madrid, Spain
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12
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Ding SY, Bayer EA. Understanding Cellulosome Interaction with Cellulose by High-Resolution Imaging. ACS CENTRAL SCIENCE 2020; 6:1034-1036. [PMID: 32724836 PMCID: PMC7379103 DOI: 10.1021/acscentsci.0c00662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Shi-You Ding
- Department
of Plant Biology, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing 48824-1312, Michigan, United States
| | - Edward A. Bayer
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7610001, Israel
- Faculty
of Natural Sciences, Life Sciences, Ben-Gurion
University of the Negev, Beer-Sheva 8410501, Israel
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13
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Eibinger M, Ganner T, Plank H, Nidetzky B. A Biological Nanomachine at Work: Watching the Cellulosome Degrade Crystalline Cellulose. ACS CENTRAL SCIENCE 2020; 6:739-746. [PMID: 32490190 PMCID: PMC7256933 DOI: 10.1021/acscentsci.0c00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 05/14/2023]
Abstract
The cellulosome is a supramolecular multienzymatic protein complex that functions as a biological nanomachine of cellulosic biomass degradation. How the megadalton-size cellulosome adapts to a solid substrate is central to its mechanism of action and is also key for its efficient use in bioconversion applications. We report time-lapse visualization of crystalline cellulose degradation by individual cellulosomes from Clostridium thermocellum by atomic force microscopy. Upon binding to cellulose, the cellulosomes switch to elongated, even filamentous shapes and morph these dynamically at below 1 min time scale according to requirements of the substrate surface under attack. Compared with noncomplexed cellulases that peel off material while sliding along crystalline cellulose surfaces, the cellulosomes remain bound locally for minutes and remove the material lying underneath. The consequent roughening up of the surface leads to an efficient deconstruction of cellulose nanocrystals both from the ends and through fissions within. Distinct modes of cellulose nanocrystal deconstruction by nature's major cellulase systems are thus revealed.
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Affiliation(s)
- Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Thomas Ganner
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz
Centre of Electron Microscopy, Steyrergasse 17, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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14
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García de la Torre J, Hernández Cifre J. Hydrodynamic Properties of Biomacromolecules and Macromolecular Complexes: Concepts and Methods. A Tutorial Mini-review. J Mol Biol 2020; 432:2930-2948. [DOI: 10.1016/j.jmb.2019.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 01/08/2023]
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15
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Vita N, Borne R, Perret S, de Philip P, Fierobe HP. Turning a potent family-9 free cellulase into an operational cellulosomal component and vice versa. FEBS J 2019; 286:3359-3373. [PMID: 31004451 DOI: 10.1111/febs.14858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/18/2019] [Accepted: 04/16/2019] [Indexed: 11/29/2022]
Abstract
Ruminiclostridium cellulolyticum and Lachnoclostridium phytofermentans are cellulolytic clostridia either producing extracellular multienzymatic complexes termed cellulosomes or secreting free cellulases respectively. In the free state, the cellulase Cel9A secreted by L. phytofermentans is much more active on crystalline cellulose than any cellulosomal family-9 enzyme produced by R. cellulolyticum. Nevertheless, the incorporation of Cel9A in vitro in hybrid cellulosomes was formerly shown to generate artificial complexes with altered activity, whereas its incorporation in vivo in native R. cellulolyticum cellulosomes resulted in a strain displaying a weakened cellulolytic phenotype. In this study, we investigated why Cel9A is so potent in the free state but functions poorly as a cellulosomal component, in contrast to the most similar enzyme synthesized by R. cellulolyticum, Cel9G, weakly active in the free state but whose activity on crystalline cellulose is drastically increased in cellulosomes. We show that the removal of the C-terminal moiety of Cel9A encompassing the two X2 modules and the family-3b carbohydrate binding module (CBM3b), reduces its activity on crystalline cellulose. Grafting a dockerin module further diminishes the activity, but this truncated cellulosomal form of Cel9A displays important synergies in hybrid cellulosomes with the pivotal family-48 cellulosomal enzyme of R. cellulolyticum. The exact inverse approach was applied to the cellulosomal Cel9G. Grafting the two X2 modules and the CBM3b of Cel9A to Cel9G strongly increases its activity on crystalline cellulose, to reach Cel9A activity levels. Altogether these data emphasize the specific features required to generate an efficient free or cellulosomal family-9 cellulase.
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16
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Roig-Solvas B, Brooks D, Makowski L. A direct approach to estimate the anisotropy of protein structures from small-angle X-ray scattering. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719000918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In the field of small-angle X-ray scattering (SAXS), the task of estimating the size of particles in solution is usually synonymous with the Guinier plot. The approximation behind this plot, developed by Guinier in 1939, provides a simple yet accurate characterization of the scattering behavior of particles at low scattering angle or momentum transfer q, together with a computationally efficient way of inferring their radii of gyration R
G. Moreover, this approximation is valid beyond spherical scatterers, making its use ubiquitous in the SAXS world. However, when it is important to estimate further particle characteristics, such as the anisotropy of the scatterer's shape, no similar or extended approximations are available. Existing tools to characterize the shape of scatterers rely either on prior knowledge of the scatterers' geometry or on iterative procedures to infer the particle shape ab initio. In this work, a low-angle approximation of the scattering intensity I(q) for ellipsoids of revolution is developed and it is shown how the size and anisotropy information can be extracted from the parameters of that approximation. The goal of the approximation is not to estimate a particle's full structure in detail, and thus this approach will be less accurate than well known iterative and ab initio reconstruction tools available in the literature. However, it can be considered as an extension of the Guinier approximation and used to generate initial estimates for the aforementioned iterative techniques, which usually rely on R
G and D
max for initialization. This formulation also demonstrates that nonlinearity in the Guinier plot can arise from anisotropy in the scattering particles. Beyond ideal ellipsoids of revolution, it is shown that this approximation can be used to estimate the size and shape of molecules in solution, in both computational and experimental scenarios. The limits of the approach are discussed and the impact of a particle's anisotropy in the Guinier estimate of R
G is assessed.
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17
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Fedorov BA, Smirnov AV, Yaroshenko VV, Porozov YB. SASCUBE: An Updated Method of Cubes for Calculation of the Intensity of X-Ray Scattering by Biopolymers in Solution. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Galera-Prat A, Pantoja-Uceda D, Laurents DV, Carrión-Vázquez M. Solution conformation of a cohesin module and its scaffoldin linker from a prototypical cellulosome. Arch Biochem Biophys 2018; 644:1-7. [PMID: 29486159 DOI: 10.1016/j.abb.2018.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Accepted: 02/23/2018] [Indexed: 11/26/2022]
Abstract
Bacterial cellulases are drawing increased attention as a means to obtain plentiful chemical feedstocks and fuels from renewable lignocellulosic biomass sources. Certain bacteria deploy a large extracellular multi-protein complex, called the cellulosome, to degrade cellulose. Scaffoldin, a key non-catalytic cellulosome component, is a large protein containing a cellulose-specific carbohydrate-binding module and several cohesin modules which bind and organize the hydrolytic enzymes. Despite the importance of the structure and protein/protein interactions of the cohesin module in the cellulosome, its structure in solution has remained unknown to date. Here, we report the backbone 1H, 13C and 15N NMR assignments of the Cohesin module 5 from the highly stable and active cellulosome from Clostridium thermocellum. These data reveal that this module adopts a tightly packed, well folded and rigid structure in solution. Furthermore, since in scaffoldin, the cohesin modules are connected by linkers we have also characterized the conformation of a representative linker segment using NMR spectroscopy. Analysis of its chemical shift values revealed that this linker is rather stiff and tends to adopt extended conformations. This suggests that the scaffoldin linkers act to minimize interactions between cohesin modules. These results pave the way towards solution studies on cohesin/dockerin's fascinating dual-binding mode.
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Affiliation(s)
| | - David Pantoja-Uceda
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 199, E-28006, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 199, E-28006, Madrid, Spain.
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19
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Wojciechowski M, Różycki B, Huy PDQ, Li MS, Bayer EA, Cieplak M. Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module. Sci Rep 2018; 8:5051. [PMID: 29568013 PMCID: PMC5864761 DOI: 10.1038/s41598-018-23380-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/05/2018] [Indexed: 01/09/2023] Open
Abstract
The assembly of the polysaccharide degradating cellulosome machinery is mediated by tight binding between cohesin and dockerin domains. We have used an empirical model known as FoldX as well as molecular mechanics methods to determine the free energy of binding between a cohesin and a dockerin from Clostridium thermocellum in two possible modes that differ by an approximately 180° rotation. Our studies suggest that the full-length wild-type complex exhibits dual binding at room temperature, i.e., the two modes of binding have comparable probabilities at equilibrium. The ability to bind in the two modes persists at elevated temperatures. However, single-point mutations or truncations of terminal segments in the dockerin result in shifting the equilibrium towards one of the binding modes. Our molecular dynamics simulations of mechanical stretching of the full-length wild-type cohesin-dockerin complex indicate that each mode of binding leads to two kinds of stretching pathways, which may be mistakenly taken as evidence of dual binding.
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Affiliation(s)
- Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
- Institute for Computational Sciences and Technology, SBI building, Quang Trung Software city, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland.
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20
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Różycki B, Cieplak M. Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A. MOLECULAR BIOSYSTEMS 2017; 12:3589-3599. [PMID: 27714009 DOI: 10.1039/c6mb00606j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cellulosomes are complex multi-enzyme machineries which efficiently degrade plant cell-wall polysaccharides. The multiple domains of the cellulosome proteins are often tethered together by intrinsically disordered regions. The properties and functions of these disordered linkers are not well understood. In this work, we study endoglucanase Cel8A, which is a relevant enzymatic component of the cellulosomes of Clostridium thermocellum. We use both all-atom and coarse-grained simulations to investigate how the conformations of the catalytic domain of Cel8A are affected by the disordered linker at its C terminus. We find that when the endoglucanase is bound to its substrate, the effective stiffness of the linker can influence the distances between groups of amino-acid residues throughout the entire enzymatic domain. In particular, variations in the linker stiffness can lead to small changes in the geometry of the active-site cleft. We suggest that such geometrical changes may have an effect on the catalytic activity of the enzyme.
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Affiliation(s)
- Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
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21
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Artzi L, Bayer EA, Moraïs S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat Rev Microbiol 2017; 15:83-95. [PMID: 27941816 DOI: 10.1038/nrmicro.2016.164] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes are multienzyme complexes that are produced by anaerobic cellulolytic bacteria for the degradation of lignocellulosic biomass. They comprise a complex of scaffoldin, which is the structural subunit, and various enzymatic subunits. The intersubunit interactions in these multienzyme complexes are mediated by cohesin and dockerin modules. Cellulosome-producing bacteria have been isolated from a large variety of environments, which reflects their prevalence and the importance of this microbial enzymatic strategy. In a given species, cellulosomes exhibit intrinsic heterogeneity, and between species there is a broad diversity in the composition and configuration of cellulosomes. With the development of modern technologies, such as genomics and proteomics, the full protein content of cellulosomes and their expression levels can now be assessed and the regulatory mechanisms identified. Owing to their highly efficient organization and hydrolytic activity, cellulosomes hold immense potential for application in the degradation of biomass and are the focus of much effort to engineer an ideal microorganism for the conversion of lignocellulose to valuable products, such as biofuels.
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Affiliation(s)
- Lior Artzi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
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22
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Naughton KL, Phan L, Leung EM, Kautz R, Lin Q, Van Dyke Y, Marmiroli B, Sartori B, Arvai A, Li S, Pique ME, Naeim M, Kerr JP, Aquino MJ, Roberts VA, Getzoff ED, Zhu C, Bernstorff S, Gorodetsky AA. Self-Assembly of the Cephalopod Protein Reflectin. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:8405-8412. [PMID: 27454809 DOI: 10.1002/adma.201601666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 05/08/2016] [Indexed: 06/06/2023]
Abstract
Films from the cephalopod protein reflectin demonstrate multifaceted functionality as infrared camouflage coatings, proton transport media, and substrates for growth of neural stem cells. A detailed study of the in vitro formation, structural characteristics, and stimulus response of such films is presented. The reported observations hold implications for the design and development of advanced cephalopod-inspired functional materials.
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Affiliation(s)
- Kyle L Naughton
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, 92697, USA
| | - Long Phan
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Erica M Leung
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Rylan Kautz
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Qiyin Lin
- Laboratory for Electron and X-Ray Instrumentation, University of California, Irvine, Irvine, CA, 92697, USA
| | - Yegor Van Dyke
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Andy Arvai
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael E Pique
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Mahan Naeim
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Justin P Kerr
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mercedeez J Aquino
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - Victoria A Roberts
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chenhui Zhu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sigrid Bernstorff
- Elettra - Sincrotrone Trieste, Strada Statale 14, km 163.5, 34149, Trieste, Italy
| | - Alon A Gorodetsky
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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23
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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24
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Chundawat SPS, Paavola CD, Raman B, Nouailler M, Chan SL, Mielenz JR, Receveur-Brechot V, Trent JD, Dale BE. Saccharification of thermochemically pretreated cellulosic biomass using native and engineered cellulosomal enzyme systems. REACT CHEM ENG 2016. [DOI: 10.1039/c6re00172f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Tethering hydrolytic enzymes (e.g., cellulases) to protein scaffolds enhances biomass saccharification to sugars.
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Affiliation(s)
- Shishir P. S. Chundawat
- Department of Chemical & Biochemical Engineering
- The State University of New Jersey
- Piscataway
- USA
- DOE Great Lakes Bioenergy Research Center (GLBRC)
| | | | - Babu Raman
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - Matthieu Nouailler
- LISM-UMR 7255 Institut De Microbiologie De La Mediterranee
- CNRS and Aix-Marseille University
- 13402 Marseille Cedex 20
- France
| | | | - Jonathan R. Mielenz
- Biosciences Division and BioEnergy Science Center
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | | | - Jonathan D. Trent
- Bioengineering Branch
- NASA Ames
- Moffett Field
- USA
- Biomolecular Engineering Department
| | - Bruce E. Dale
- DOE Great Lakes Bioenergy Research Center (GLBRC)
- Michigan State University
- East Lansing
- USA
- Chemical Engineering and Materials Science
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25
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Deng L, Mori Y, Sermsathanaswadi J, Apiwatanapiwat W, Kosugi A. Cellulose hydrolysis ability of a Clostridium thermocellum cellulosome containing small-size scaffolding protein CipA. J Biotechnol 2015; 212:144-52. [PMID: 26302838 DOI: 10.1016/j.jbiotec.2015.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/29/2015] [Accepted: 08/18/2015] [Indexed: 12/14/2022]
Abstract
Mutant Clostridium thermocellum YM72 that produces small-size scaffolding protein CipA (ssCipA) was isolated from wild-type YM4. Sequencing of ssCipA revealed that two domains, cohesin 6 and cohesin 7, were not present. Cellulosome prepared from YM72 exhibited a significant reduction of hydrolysis ability on crystalline celluloses such as Sigmacell type-20 and cellulose from Halocynthia. To investigate this influence in vitro, artificial cellulosomes were assembled as recombinant CipA (rCipA) and ssCipA (rssCipA) using native free-cellulosomal subunits. The cellulosome assembled using rssCipA showed a 1.8-fold decrease in the hydrolysis of crystalline cellulose compared with that of rCipA. However, no significant differences in the hydrolysis of carboxymethylcellulose and acid-swollen cellulose were observed. One protein band was missing from the complex that was assembled using rssCipA (confirmed by native-PAGE). The missing protein was identified as CelJ, which is a major cellulosomal subunit. This suggests that insufficient cooperation of CelJ into the cellulosome results in the significant reduction of hydrolysis toward crystalline cellulose. These results indicate that cohesin 6 and 7 may be responsible for the cooperation of CelJ through cohesin and dockerin interactions, and adequate cooperation of CelJ into the cellulosome is important for significant hydrolysis of crystalline cellulose.
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Affiliation(s)
- Lan Deng
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 303-8686, Japan
| | - Yutaka Mori
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 303-8686, Japan
| | - Junjarus Sermsathanaswadi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 303-8686, Japan
| | - Waraporn Apiwatanapiwat
- University of Tsukuba Graduate School of Life and Environmental Sciences, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 303-8686, Japan; University of Tsukuba Graduate School of Life and Environmental Sciences, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.
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26
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Redmile-Gordon M, Evershed R, Hirsch P, White R, Goulding K. Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability. SOIL BIOLOGY & BIOCHEMISTRY 2015; 88:257-267. [PMID: 26339106 PMCID: PMC4534311 DOI: 10.1016/j.soilbio.2015.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 05/24/2023]
Abstract
An emerging paradigm in soil science suggests microbes can perform 'N mining' from recalcitrant soil organic matter (SOM) in conditions of low N availability. However, this requires the production of extracellular structures rich in N (including enzymes and structural components) and thus defies stoichiometric expectation. We set out to extract newly synthesised peptides from the extracellular matrix in soil and compare the amino acid (AA) profiles, N incorporation and AA dynamics in response to labile inputs of contrasting C/N ratio. Glycerol was added both with and without an inorganic source of N (10% 15N labelled NH4NO3) to a soil already containing a large pool of refractory SOM and incubated for 10 days. The resulting total soil peptide (TSP) and extracellular pools were compared using colorimetric methods, gas chromatography, and isotope ratio mass spectrometry. N isotope compositions showed that the extracellular polymeric substance (EPS) contained a greater proportion of products formed de novo than did TSP, with hydrophobic EPS-AAs (leucine, isoleucine, phenylalanine, hydroxyproline and tyrosine) deriving substantially more N from the inorganic source provided. Quantitative comparison between extracts showed that the EPS contained greater relative proportions of alanine, glycine, proline, phenylalanine and tyrosine. The greatest increases in EPS-peptide and EPS-polysaccharide concentrations occurred at the highest C/N ratios. All EPS-AAs responded similarly to treatment whereas the responses of TSP were more complex. The results suggest that extracellular investment of N (as EPS peptides) is a microbial survival mechanism in conditions of low N/high C which, from an evolutionary perspective, must ultimately lead to the tendency for increased N returns to the microbial biomass. A conceptual model is proposed that describes the dynamics of the extracellular matrix in response to the C/N ratio of labile inputs.
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Affiliation(s)
- M.A. Redmile-Gordon
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, BS8 1TS, UK
| | - R.P. Evershed
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, BS8 1TS, UK
| | - P.R. Hirsch
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - R.P. White
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
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27
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Malaby AW, Chakravarthy S, Irving TC, Kathuria SV, Bilsel O, Lambright DG. Methods for analysis of size-exclusion chromatography-small-angle X-ray scattering and reconstruction of protein scattering. J Appl Crystallogr 2015; 48:1102-1113. [PMID: 26306089 DOI: 10.1107/s1600576715010420] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 05/31/2015] [Indexed: 11/10/2022] Open
Abstract
Size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) has emerged as an important method for investigation of heterogeneous and self-associating systems, but presents specific challenges for data processing including buffer subtraction and analysis of overlapping peaks. This paper presents novel methods based on singular value decomposition (SVD) and Guinier-optimized linear combination (LC) to facilitate analysis of SEC-SAXS data sets and high-quality reconstruction of protein scattering directly from peak regions. It is shown that Guinier-optimized buffer subtraction can reduce common subtraction artifacts and that Guinier-optimized linear combination of significant SVD basis components improves signal-to-noise and allows reconstruction of protein scattering, even in the absence of matching buffer regions. In test cases with conventional SAXS data sets for cytochrome c and SEC-SAXS data sets for the small GTPase Arf6 and the Arf GTPase exchange factors Grp1 and cytohesin-1, SVD-LC consistently provided higher quality reconstruction of protein scattering than either direct or Guinier-optimized buffer subtraction. These methods have been implemented in the context of a Python-extensible Mac OS X application known as Data Evaluation and Likelihood Analysis (DELA), which provides convenient tools for data-set selection, beam intensity normalization, SVD, and other relevant processing and analytical procedures, as well as automated Python scripts for common SAXS analyses and Guinier-optimized reconstruction of protein scattering.
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Affiliation(s)
- Andrew W Malaby
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Thomas C Irving
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Sagar V Kathuria
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - David G Lambright
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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28
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Różycki B, Cieplak M, Czjzek M. Large conformational fluctuations of the multi-domain xylanase Z of Clostridium thermocellum. J Struct Biol 2015; 191:68-75. [DOI: 10.1016/j.jsb.2015.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/15/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
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29
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Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, Shively J, Cannon GC, Kerfeld CA. Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component. Life (Basel) 2015; 5:1141-71. [PMID: 25826651 PMCID: PMC4499774 DOI: 10.3390/life5021141] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in three model organisms and show that CsoS2 is vital for α-carboxysome biogenesis. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle (M)-, and C-terminal region. Repetitive motifs can be identified in the N- and M-regions. Multiple lines of evidence suggest CsoS2 is highly flexible, possibly an intrinsically disordered protein. Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome. Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.
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Affiliation(s)
- Fei Cai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Zhicheng Dou
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Susan L Bernstein
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Ryan Leverenz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Eric B Williams
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Sabine Heinhorst
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Jessup Shively
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Gordon C Cannon
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
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30
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Różycki B, Boura E. Large, dynamic, multi-protein complexes: a challenge for structural biology. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:463103. [PMID: 25335513 DOI: 10.1088/0953-8984/26/46/463103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Structural biology elucidates atomic structures of macromolecules such as proteins, DNA, RNA, and their complexes to understand the basic mechanisms of their functions. Among proteins that pose the most difficult problems to current efforts are those which have several large domains connected by long, flexible polypeptide segments. Although abundant and critically important in biological cells, such proteins have proven intractable by conventional techniques. This gap has recently led to the advancement of hybrid methods that use state-of-the-art computational tools to combine complementary data from various high- and low-resolution experiments. In this review, we briefly discuss the individual experimental techniques to illustrate their strengths and limitations, and then focus on the use of hybrid methods in structural biology. We describe how representative structures of dynamic multi-protein complexes are obtained utilizing the EROS hybrid method that we have co-developed.
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Affiliation(s)
- Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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31
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Edwards AL, Matsui T, Weiss TM, Khosla C. Architectures of whole-module and bimodular proteins from the 6-deoxyerythronolide B synthase. J Mol Biol 2014; 426:2229-45. [PMID: 24704088 PMCID: PMC4284093 DOI: 10.1016/j.jmb.2014.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
Abstract
The 6-deoxyerythronolide B synthase (DEBS) is a prototypical assembly line polyketide synthase produced by the actinomycete Saccharopolyspora erythraea that synthesizes the macrocyclic core of the antibiotic erythromycin 6-deoxyerythronolide B. The megasynthase is a 2-MDa trimeric complex composed of three unique homodimers assembled from the gene products DEBS1, DEBS2, and DEBS3, which are housed within the erythromycin biosynthetic gene cluster. Each homodimer contains two clusters of catalytically independent enzymatic domains, each referred to as a module, which catalyzes one round of polyketide chain extension and modification. Modules are named sequentially to indicate the order in which they are utilized during synthesis of 6-deoxyerythronolide B. We report small-angle X-ray scattering (SAXS) analyses of a whole module and a bimodule from DEBS, as well as a set of domains for which high-resolution structures are available. In all cases, the solution state was probed under previously established conditions ensuring that each protein is catalytically active. SAXS data are consistent with atomic-resolution structures of DEBS fragments. Therefore, we used the available high-resolution structures of DEBS domains to model the architectures of the larger protein assemblies using rigid-body refinement. Our data support a model in which the third module of DEBS forms a disc-shaped structure capable of caging the acyl carrier protein domain proximal to each active site. The molecular envelope of DEBS3 is a thin elongated ellipsoid, and the results of rigid-body modeling suggest that modules 5 and 6 stack collinearly along the 2-fold axis of symmetry.
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Affiliation(s)
- Andrea L Edwards
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 14 2575 Sand Hill Road, MS69, Menlo Park, CA 94025, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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32
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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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Stern J, Anbar M, Moraïs S, Lamed R, Bayer EA. Insights into enhanced thermostability of a cellulosomal enzyme. Carbohydr Res 2014; 389:78-84. [DOI: 10.1016/j.carres.2014.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/13/2014] [Accepted: 01/17/2014] [Indexed: 10/25/2022]
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Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J 2014; 105:962-74. [PMID: 23972848 DOI: 10.1016/j.bpj.2013.07.020] [Citation(s) in RCA: 406] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 07/03/2013] [Accepted: 07/11/2013] [Indexed: 12/29/2022] Open
Abstract
A major challenge in structural biology is to characterize structures of proteins and their assemblies in solution. At low resolution, such a characterization may be achieved by small angle x-ray scattering (SAXS). Because SAXS analyses often require comparing profiles calculated from many atomic models against those determined by experiment, rapid and accurate profile computation from molecular structures is needed. We developed fast open-source x-ray scattering (FoXS) for profile computation. To match the experimental profile within the experimental noise, FoXS explicitly computes all interatomic distances and implicitly models the first hydration layer of the molecule. For assessing the accuracy of the modeled hydration layer, we performed contrast variation experiments for glucose isomerase and lysozyme, and found that FoXS can accurately represent density changes of this layer. The hydration layer model was also compared with a SAXS profile calculated for the explicit water molecules in the high-resolution structures of glucose isomerase and lysozyme. We tested FoXS on eleven protein, one DNA, and two RNA structures, revealing superior accuracy and speed versus CRYSOL, AquaSAXS, the Zernike polynomials-based method, and Fast-SAXS-pro. In addition, we demonstrated a significant correlation of the SAXS score with the accuracy of a structural model. Moreover, FoXS utility for analyzing heterogeneous samples was demonstrated for intrinsically flexible XLF-XRCC4 filaments and Ligase III-DNA complex. FoXS is extensively used as a standalone web server as a component of integrative structure determination by programs IMP, Chimera, and BILBOMD, as well as in other applications that require rapidly and accurately calculated SAXS profiles.
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Affiliation(s)
- Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
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35
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Vazana Y, Barak Y, Unger T, Peleg Y, Shamshoum M, Ben-Yehezkel T, Mazor Y, Shapiro E, Lamed R, Bayer EA. A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:182. [PMID: 24341331 PMCID: PMC3878649 DOI: 10.1186/1754-6834-6-182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/27/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Select cellulolytic bacteria produce multi-enzymatic cellulosome complexes that bind to the plant cell wall and catalyze its efficient degradation. The multi-modular interconnecting cellulosomal subunits comprise dockerin-containing enzymes that bind cohesively to cohesin-containing scaffoldins. The organization of the modules into functional polypeptides is achieved by intermodular linkers of different lengths and composition, which provide flexibility to the complex and determine its overall architecture. RESULTS Using a synthetic biology approach, we systematically investigated the spatial organization of the scaffoldin subunit and its effect on cellulose hydrolysis by designing a combinatorial library of recombinant trivalent designer scaffoldins, which contain a carbohydrate-binding module (CBM) and 3 divergent cohesin modules. The positions of the individual modules were shuffled into 24 different arrangements of chimaeric scaffoldins. This basic set was further extended into three sub-sets for each arrangement with intermodular linkers ranging from zero (no linkers), 5 (short linkers) and native linkers of 27-35 amino acids (long linkers). Of the 72 possible scaffoldins, 56 were successfully cloned and 45 of them expressed, representing 14 full sets of chimaeric scaffoldins. The resultant 42-component scaffoldin library was used to assemble designer cellulosomes, comprising three model C. thermocellum cellulases. Activities were examined using Avicel as a pure microcrystalline cellulose substrate and pretreated cellulose-enriched wheat straw as a model substrate derived from a native source. All scaffoldin combinations yielded active trivalent designer cellulosome assemblies on both substrates that exceeded the levels of the free enzyme systems. A preferred modular arrangement for the trivalent designer scaffoldin was not observed for the three enzymes used in this study, indicating that they could be integrated at any position in the designer cellulosome without significant effect on cellulose-degrading activity. Designer cellulosomes assembled with the long-linker scaffoldins achieved higher levels of activity, compared to those assembled with short-and no-linker scaffoldins. CONCLUSIONS The results demonstrate the robustness of the cellulosome system. Long intermodular scaffoldin linkers are preferable, thus leading to enhanced degradation of cellulosic substrates, presumably due to the increased flexibility and spatial positioning of the attached enzymes in the complex. These findings provide a general basis for improved designer cellulosome systems as a platform for bioethanol production.
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Affiliation(s)
- Yael Vazana
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Barak
- Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Unger
- Structural Proteomics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Peleg
- Structural Proteomics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Melina Shamshoum
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tuval Ben-Yehezkel
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yair Mazor
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ehud Shapiro
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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36
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Borne R, Bayer EA, Pagès S, Perret S, Fierobe HP. Unraveling enzyme discrimination during cellulosome assembly independent of cohesin-dockerin affinity. FEBS J 2013; 280:5764-79. [PMID: 24033928 DOI: 10.1111/febs.12497] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/08/2013] [Accepted: 08/21/2013] [Indexed: 01/24/2023]
Abstract
Bacterial cellulosomes are generally believed to assemble at random, like those produced by Clostridium cellulolyticum. They are composed of one scaffolding protein bearing eight homologous type I cohesins that bind to any of the type I dockerins borne by the 62 cellulosomal subunits, thus generating highly heterogeneous complexes. In the present study, the heterogeneity and random assembly of the cellulosomes were evaluated with a simpler model: a miniscaffoldin containing three C. cellulolyticum cohesins and three cellulases of the same bacterium bearing the cognate dockerin (Cel5A, Cel48F, and Cel9G). Surprisingly, rather than the expected randomized integration of enzymes, the assembly of the minicellulosome generated only three distinct types of complex out of the 10 possible combinations, thus indicating preferential integration of enzymes upon binding to the scaffoldin. A hybrid scaffoldin that displays one cohesin from C. cellulolyticum and one from C. thermocellum, thus allowing sequential integration of enzymes, was exploited to further characterize this phenomenon. The initial binding of a given enzyme to the C. thermocellum cohesin was found to influence the type of enzyme that subsequently bound to the C. cellulolyticum cohesin. The preferential integration appears to be related to the length of the inter-cohesin linker. The data indicate that the binding of a cellulosomal enzyme to a cohesin has a direct influence on the dockerin-bearing proteins that will subsequently interact with adjacent cohesins. Thus, despite the general lack of specificity of the cohesin-dockerin interaction within a given species and type, bacterial cellulosomes are not necessarily assembled at random.
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Affiliation(s)
- Romain Borne
- Aix-Marseille Université-CNRS, LCB UMR7283, IMM, Marseille, France
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37
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Smith SP, Bayer EA. Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex. Curr Opin Struct Biol 2013; 23:686-94. [PMID: 24080387 DOI: 10.1016/j.sbi.2013.09.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 11/23/2022]
Abstract
Cellulosomes are multi-enzyme complexes produced by anaerobic bacteria for the efficient deconstruction of plant cell wall polysaccharides. The assembly of enzymatic subunits onto a central non-catalytic scaffoldin subunit is mediated by a highly specific interaction between the enzyme-bearing dockerin modules and the resident cohesin modules of the scaffoldin, which affords their catalytic activities to work synergistically. The scaffoldin also imparts substrate-binding and bacterial-anchoring properties, the latter of which involves a second cohesin-dockerin interaction. Recent structure-function studies reveal an ever-growing array of unique and increasingly complex cohesin-dockerin complexes and cellulosomal enzymes with novel activities. A 'build' approach involving multimodular cellulosomal segments has provided a structural model of an organized yet conformationally dynamic supramolecular assembly with the potential to form higher order structures.
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Affiliation(s)
- Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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38
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Kamat RK, Ma W, Yang Y, Zhang Y, Wang C, Kumar CV, Lin Y. Adsorption and hydrolytic activity of the polycatalytic cellulase nanocomplex on cellulose. ACS APPLIED MATERIALS & INTERFACES 2013; 5:8486-8494. [PMID: 23968137 DOI: 10.1021/am401916k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The formation of polycatalytic enzyme complexes may enhance the effectiveness of enzymes due to improved substrate interaction and synergistic actions of multiple enzymes in proximity. Much effort has been made to develop highly efficient polycatalytic cellulase complexes by immobilizing cellulases on low-cost polymer or nanoparticle scaffolds, aiming at their potential applications in biomass conversion to fuels. However, some key cellulases carry out the hydrolytic reaction on crystalline cellulose in a directional, processive manner. A large, artificial polycatalytic complex is unlikely to undergo a highly coordinated motion to slide on the cellulose surface as a whole unit. The mechanism underlying the activity enhancements observed in some artificial cellulase complexes and the limit of this approach remain elusive. Herein, we report the synthesis of polycatalytic cellulase complexes bound to colloidal polymer nanoparticles with a magnetic core and describe their unique adsorption, hydrolytic activities, and motions on cellulose. The polycatalytic clusters of cellulases on colloidal polymers show an increased rate of hydrolytic reactions on cellulose, but this was observed mainly at relatively low cellulase-to-cellulose ratios. Enhanced efficiency is mainly attributed to increased local concentrations of cellulases on the scaffolds and their polyvalent interactions with cellulose. However, once bound, the polycatalytic complexes can only carry out reactions locally and are not capable of relocating to new sites rapidly due to their lack of long-range surface mobility and their extremely tight binding. The development of highly optimized polycatalytic complexes may arise by developing novel nanoscaffolds that induce concerted motion of the complex as a whole.
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Affiliation(s)
- Ranjan K Kamat
- Polymer Program, Institute of Material Science, §Department of Chemistry, and ∥Department of Molecular and Cellular Biology, University of Connecticut , Storrs, Connecticut 06269, United States
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Amorós D, Ortega A, García de la Torre J. Prediction of Hydrodynamic and Other Solution Properties of Partially Disordered Proteins with a Simple, Coarse-Grained Model. J Chem Theory Comput 2013; 9:1678-85. [DOI: 10.1021/ct300948u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Amorós
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
| | - A. Ortega
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
| | - J. García de la Torre
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
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40
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Currie MA, Cameron K, Dias FMV, Spencer HL, Bayer EA, Fontes CMGA, Smith SP, Jia Z. Small angle X-ray scattering analysis of Clostridium thermocellum cellulosome N-terminal complexes reveals a highly dynamic structure. J Biol Chem 2013; 288:7978-7985. [PMID: 23341454 DOI: 10.1074/jbc.m112.408757] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clostridium thermocellum produces the prototypical cellulosome, a large multienzyme complex that efficiently hydrolyzes plant cell wall polysaccharides into fermentable sugars. This ability has garnered great interest in its potential application in biofuel production. The core non-catalytic scaffoldin subunit, CipA, bears nine type I cohesin modules that interact with the type I dockerin modules of secreted hydrolytic enzymes and promotes catalytic synergy. Because the large size and flexibility of the cellulosome preclude structural determination by traditional means, the structural basis of this synergy remains unclear. Small angle x-ray scattering has been successfully applied to the study of flexible proteins. Here, we used small angle x-ray scattering to determine the solution structure and to analyze the conformational flexibility of two overlapping N-terminal cellulosomal scaffoldin fragments comprising two type I cohesin modules and the cellulose-specific carbohydrate-binding module from CipA in complex with Cel8A cellulases. The pair distribution functions, ab initio envelopes, and rigid body models generated for these two complexes reveal extended structures. These two N-terminal cellulosomal fragments are highly dynamic and display no preference for extended or compact conformations. Overall, our work reveals structural and dynamic features of the N terminus of the CipA scaffoldin that may aid in cellulosome substrate recognition and binding.
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Affiliation(s)
- Mark A Currie
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Kate Cameron
- Centro Interdisciplinar de Investigacao em Sanidade Animal, Faculdade de Medincina Veterinaria, Universidade Tecnica de Lisboa, 1300-477 Lisbon, Portugal
| | - Fernando M V Dias
- Centro Interdisciplinar de Investigacao em Sanidade Animal, Faculdade de Medincina Veterinaria, Universidade Tecnica de Lisboa, 1300-477 Lisbon, Portugal
| | - Holly L Spencer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Carlos M G A Fontes
- Centro Interdisciplinar de Investigacao em Sanidade Animal, Faculdade de Medincina Veterinaria, Universidade Tecnica de Lisboa, 1300-477 Lisbon, Portugal
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada; Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada.
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada; Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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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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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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Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:789-99. [PMID: 22639100 PMCID: PMC3462898 DOI: 10.1007/s00249-012-0820-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 04/22/2012] [Accepted: 05/05/2012] [Indexed: 01/25/2023]
Abstract
The dynamics of macromolecular conformations are critical to the action of cellular networks. Solution X-ray scattering studies, in combination with macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR), strive to determine complete and accurate states of macromolecules, providing novel insights describing allosteric mechanisms, supramolecular complexes, and dynamic molecular machines. This review addresses theoretical and practical concepts, concerns, and considerations for using these techniques in conjunction with computational methods to productively combine solution-scattering data with high-resolution structures. I discuss the principal means of direct identification of macromolecular flexibility from SAXS data followed by critical concerns about the methods used to calculate theoretical SAXS profiles from high-resolution structures. The SAXS profile is a direct interrogation of the thermodynamic ensemble and techniques such as, for example, minimal ensemble search (MES), enhance interpretation of SAXS experiments by describing the SAXS profiles as population-weighted thermodynamic ensembles. I discuss recent developments in computational techniques used for conformational sampling, and how these techniques provide a basis for assessing the level of the flexibility within a sample. Although these approaches sacrifice atomic detail, the knowledge gained from ensemble analysis is often appropriate for developing hypotheses and guiding biochemical experiments. Examples of the use of SAXS and combined approaches with X-ray crystallography, NMR, and computational methods to characterize dynamic assemblies are presented.
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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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Interactions Between Family 3 Carbohydrate Binding Modules (CBMs) and Cellulosomal Linker Peptides. Methods Enzymol 2012; 510:247-59. [DOI: 10.1016/b978-0-12-415931-0.00013-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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47
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Structural Characterization of Intramolecular Hg2+ Transfer between Flexibly Linked Domains of Mercuric Ion Reductase. J Mol Biol 2011; 413:639-56. [DOI: 10.1016/j.jmb.2011.08.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 08/20/2011] [Accepted: 08/22/2011] [Indexed: 11/20/2022]
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48
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Feller G, Dehareng D, Lage JLD. How to remain nonfolded and pliable: the linkers in modular α-amylases as a case study. FEBS J 2011; 278:2333-40. [DOI: 10.1111/j.1742-4658.2011.08154.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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49
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Molecular Architecture and Structural Transitions of a Clostridium thermocellum Mini-Cellulosome. J Mol Biol 2011; 407:571-80. [DOI: 10.1016/j.jmb.2011.01.060] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/14/2011] [Accepted: 01/31/2011] [Indexed: 11/19/2022]
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Bomble YJ, Beckham GT, Matthews JF, Nimlos MR, Himmel ME, Crowley MF. Modeling the self-assembly of the cellulosome enzyme complex. J Biol Chem 2011; 286:5614-23. [PMID: 21098021 PMCID: PMC3037675 DOI: 10.1074/jbc.m110.186031] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/16/2010] [Indexed: 11/06/2022] Open
Abstract
Most bacteria use free enzymes to degrade plant cell walls in nature. However, some bacteria have adopted a different strategy wherein enzymes can either be free or tethered on a protein scaffold forming a complex called a cellulosome. The study of the structure and mechanism of these large macromolecular complexes is an active and ongoing research topic, with the goal of finding ways to improve biomass conversion using cellulosomes. Several mechanisms involved in cellulosome formation remain unknown, including how cellulosomal enzymes assemble on the scaffoldin and what governs the population of cellulosomes created during self-assembly. Here, we present a coarse-grained model to study the self-assembly of cellulosomes. The model captures most of the physical characteristics of three cellulosomal enzymes (Cel5B, CelS, and CbhA) and the scaffoldin (CipA) from Clostridium thermocellum. The protein structures are represented by beads connected by restraints to mimic the flexibility and shapes of these proteins. From a large simulation set, the assembly of cellulosomal enzyme complexes is shown to be dominated by their shape and modularity. The multimodular enzyme, CbhA, binds statistically more frequently to the scaffoldin than CelS or Cel5B. The enhanced binding is attributed to the flexible nature and multimodularity of this enzyme, providing a longer residence time around the scaffoldin. The characterization of the factors influencing the cellulosome assembly process may enable new strategies to create designers cellulosomes.
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Affiliation(s)
- Yannick J Bomble
- Biosciences Center, Colorado School of Mines, Golden, Colorado 80401, USA.
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