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Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A 2022; 119:e2117467119. [PMID: 36215467 PMCID: PMC9586272 DOI: 10.1073/pnas.2117467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.
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Duarte M, Alves VD, Correia M, Caseiro C, Ferreira LM, Romão MJ, Carvalho AL, Najmudin S, Bayer EA, Fontes CM, Bule P. Structure-function studies can improve binding affinity of cohesin-dockerin interactions for multi-protein assemblies. Int J Biol Macromol 2022; 224:55-67. [DOI: 10.1016/j.ijbiomac.2022.10.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/28/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
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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] [Key Words] [Grants] [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.
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Affiliation(s)
- Jonathan Dorival
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, 29680, Roscoff, Bretagne, France
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Aurore Labourel
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Bartosz Rozycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Pierre-Andre Cazade
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Jérôme Dabin
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, 29680, Roscoff, Bretagne, France
| | - Eva Setter-Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | | | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Mirjam Czjzek
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, 29680, Roscoff, Bretagne, France.
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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: 3] [Impact Index Per Article: 1.5] [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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Surface-Related Kinetic Models for Anaerobic Digestion of Mi-crocrystalline Cellulose: The Role of Particle Size. MATERIALS 2021; 14:ma14030487. [PMID: 33498568 PMCID: PMC7864345 DOI: 10.3390/ma14030487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 11/17/2022]
Abstract
In this work, for modelling the anaerobic digestion of microcrystalline cellulose, two surface-related models based on cylindrical and spherical particles were developed and compared with the first-order kinetics model. A unique dataset consisting of particles with different sizes, the same crystallinity and polymerisation degree was used to validate the models. Both newly developed models outperformed the first-order kinetics model. Analysis of the kinetic constant data revealed that particle size is a key factor determining the anaerobic digestion kinetics of crystalline cellulose. Hence, crystalline cellulose particle size should be considered in the development and optimization of lignocellulose pre-treatment methods. Further research is necessary for the assessment of impact of the crystalline cellulose particle size and surface properties on the microbial cellulose hydrolysis rate.
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Galera-Prat A, Vera AM, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. Impact of scaffoldin mechanostability on cellulosomal activity. Biomater Sci 2020; 8:3601-3610. [PMID: 32232253 DOI: 10.1039/c9bm02052g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignocellulose is the most abundant renewable carbon source in the biosphere. However, the main bottleneck in its conversion to produce second generation biofuels is the saccharification step: the hydrolysis of lignocellulosic material into soluble fermentable sugars. Some anaerobic bacteria have developed an extracellular multi-enzyme complex called the cellulosome that efficiently degrades cellulosic substrates. Cellulosome complexes rely on enzyme-integrating scaffoldins that are large non-catalytic scaffolding proteins comprising several cohesin modules and additional functional modules that mediate the anchoring of the complex to the cell surface and the specific binding to its cellulosic substrate. It was proposed that mechanical forces may affect the cohesins positioned between the cell- and cellulose-anchoring points in the so-called connecting region. Consequently, the mechanical resistance of cohesins within the scaffoldin is of great importance, both to understand cellulosome function and as a parameter of industrial interest, to better mimic natural complexes through the use of the established designer cellulosome technology. Here we study how the mechanical stability of cohesins in a scaffoldin affects the enzymatic activity of a cellulosome. We found that when a cohesin of low mechanical stability is positioned in the connecting region of a scaffoldin, the activity of the resulting cellulosome is reduced as opposed to a cohesin of higher mechanical stability. This observation directly relates mechanical stability of the scaffoldin-borne cohesins to cellulosome activity and provides a rationale for the design of artificial cellulosomes for industrial applications, by incorporating mechanical stability as a new industrial parameter in the biotechnology toolbox.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, Department of Molecular, Cellular and Developmental Neurobiology. IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain.
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da Silva VM, Cabral AD, Sperança MA, Squina FM, Muniz JRC, Martin L, Nicolet Y, Garcia W. High-resolution structure of a modular hyperthermostable endo-β-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140437. [PMID: 32325255 DOI: 10.1016/j.bbapap.2020.140437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/20/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022]
Abstract
The endo-β-1,4-mannanase from the hyperthermostable bacterium Thermotoga petrophila (TpMan) is an enzyme that catalyzes the hydrolysis of mannan and heteromannan polysaccharides. Of the three domains that comprise TpMan, the N-terminal GH5 catalytic domain and the C-terminal carbohydrate-binding domain are connected through a central ancillary domain of unknown structure and function. In this study, we report the partial crystal structure of the TpMan at 1.45 Å resolution, so far, the first modular hyperthermostable endo-β-1,4-mannanase structure determined. The structure exhibits two domains, a (β/α)8-barrel GH5 catalytic domain connected via a linker to the central domain with an immunoglobulin-like β-sandwich fold formed of seven β-strands. Functional analysis showed that whereas the immunoglobulin-like domain does not have the carbohydrate-binding function, it stacks on the GH5 catalytic domain acting as a thermostabilizing domain and allowing operation at hyperthermophilic conditions. The carbohydrate-binding domain is absent in the crystal structure most likely due to its high flexibility around the immunoglobulin-like domain which may act also as a pivot. These results represent new structural and functional information useful on biotechnological applications for biofuel and food industries.
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Affiliation(s)
- Viviam M da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil; Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Aline D Cabral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Marcia A Sperança
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - João Renato C Muniz
- São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil.
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Abstract
Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to colocalize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.
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Affiliation(s)
- Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, Taiwan
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.
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9
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Barth A, Hendrix J, Fried D, Barak Y, Bayer EA, Lamb DC. Dynamic interactions of type I cohesin modules fine-tune the structure of the cellulosome of Clostridium thermocellum. Proc Natl Acad Sci U S A 2018; 115:E11274-E11283. [PMID: 30429330 PMCID: PMC6275499 DOI: 10.1073/pnas.1809283115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Efficient degradation of plant cell walls by selected anaerobic bacteria is performed by large extracellular multienzyme complexes termed cellulosomes. The spatial arrangement within the cellulosome is organized by a protein called scaffoldin, which recruits the cellulolytic subunits through interactions between cohesin modules on the scaffoldin and dockerin modules on the enzymes. Although many structural studies of the individual components of cellulosomal scaffoldins have been performed, the role of interactions between individual cohesin modules and the flexible linker regions between them are still not entirely understood. Here, we report single-molecule measurements using FRET to study the conformational dynamics of a bimodular cohesin segment of the scaffoldin protein CipA of Clostridium thermocellum We observe compacted structures in solution that persist on the timescale of milliseconds. The compacted conformation is found to be in dynamic equilibrium with an extended state that shows distance fluctuations on the microsecond timescale. Shortening of the intercohesin linker does not destabilize the interactions but reduces the rate of contact formation. Upon addition of dockerin-containing enzymes, an extension of the flexible state is observed, but the cohesin-cohesin interactions persist. Using all-atom molecular-dynamics simulations of the system, we further identify possible intercohesin binding modes. Beyond the view of scaffoldin as "beads on a string," we propose that cohesin-cohesin interactions are an important factor for the precise spatial arrangement of the enzymatic subunits in the cellulosome that leads to the high catalytic synergy in these assemblies and should be considered when designing cellulosomes for industrial applications.
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Affiliation(s)
- Anders Barth
- Physical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Nanosystems Initative Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Nanosystems Initative Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Daniel Fried
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Barak
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany;
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Nanosystems Initative Munich, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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10
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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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Boniecki MT, Freibert SA, Mühlenhoff U, Lill R, Cygler M. Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Nat Commun 2017; 8:1287. [PMID: 29097656 PMCID: PMC5668364 DOI: 10.1038/s41467-017-01497-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/21/2017] [Indexed: 01/25/2023] Open
Abstract
Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.
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Affiliation(s)
- Michal T Boniecki
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5
| | - Sven A Freibert
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany.
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043, Marburg, Germany.
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5.
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada, H3G 0B1.
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12
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Kruer-Zerhusen N, Alahuhta M, Lunin VV, Himmel ME, Bomble YJ, Wilson DB. Structure of a Thermobifida fusca lytic polysaccharide monooxygenase and mutagenesis of key residues. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:243. [PMID: 29213309 PMCID: PMC5708082 DOI: 10.1186/s13068-017-0925-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/06/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Auxiliary activity (AA) enzymes are produced by numerous bacterial and fungal species to assist in the degradation of biomass. These enzymes are abundant but have yet to be fully characterized. Here, we report the X-ray structure of Thermobifida fusca AA10A (TfAA10A), investigate mutational characterization of key surface residues near its active site, and explore the importance of the various domains of Thermobifida fusca AA10B (TfAA10B). The structure of TfAA10A is similar to other bacterial LPMOs (lytic polysaccharide monooxygenases), including signs of photo-reduction and a distorted active site, with mixed features showing both type I and II copper coordination. The point mutation experiments of TfAA10A show that Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for the binding of substrate, but that the X1 module does not affect binding or activity. RESULTS In TfAA10A, Trp82 and Asn83 are needed for binding, but only Trp82 affects activity. The TfAA10B domain truncation mutants reveal that CBM2 is crucial for substrate binding, but that the X1 module does not affect binding or activity. The structure of TfAA10A is similar to other bacterial lytic polysaccharide monooxygenases with mixed features showing both type I and II copper coordination. CONCLUSIONS The role of LPMOs and the variability of abundance in genomes are not fully explored. LPMOs likely perform initial attacks into crystalline cellulose to allow larger processive cellulases to bind and attack, but the precise nature of their synergistic behavior remains to be definitively characterized.
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Affiliation(s)
| | | | | | | | | | - David B. Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY USA
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13
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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14
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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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15
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Bernardi RC, Melo MCR, Schulten K. Enhanced sampling techniques in molecular dynamics simulations of biological systems. Biochim Biophys Acta Gen Subj 2014; 1850:872-877. [PMID: 25450171 DOI: 10.1016/j.bbagen.2014.10.019] [Citation(s) in RCA: 412] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 01/29/2023]
Abstract
BACKGROUND Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. SCOPE OF REVIEW In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. MAJOR CONCLUSIONS Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. GENERAL SIGNIFICANCE Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
| | - Marcelo C R Melo
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
| | - Klaus Schulten
- Beckman Institute, University of Illinois, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA; Department of Physics, University of Illinois, Urbana, IL 61801, USA.
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16
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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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17
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Bubner P, Plank H, Nidetzky B. Visualizing cellulase activity. Biotechnol Bioeng 2013; 110:1529-49. [DOI: 10.1002/bit.24884] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/08/2013] [Accepted: 02/22/2013] [Indexed: 11/08/2022]
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18
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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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19
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Waller BH, Olson DG, Currie DH, Guss AM, Lynd LR. Exchange of type II dockerin-containing subunits of the Clostridium thermocellum cellulosome as revealed by SNAP-tags. FEMS Microbiol Lett 2013; 338:46-53. [PMID: 23082914 DOI: 10.1111/1574-6968.12029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 11/30/2022] Open
Abstract
Clostridium thermocellum is a thermophilic anaerobic bacterium which efficiently hydrolyzes and metabolizes cellulose to ethanol through the action of its cellulosome, a multiprotein enzymatic complex. A fluorescent protein probe, consisting of a type II dockerin module fused to a SNAP-tag, was developed in order to gain insight into the quaternary configuration of the cellulosome and to investigate the effect of deleting cipA, the protein scaffold on which the cellulosome is built. Fluorescence microscopy suggested that the probe had localized to polycellulosomal protuberances on the cell surface. Surprisingly, fluorescence intensity did not substantially change in the cipA deletion mutants. Sequential labeling experiments suggested that this was a result of bound type II dockerins from CipA being replaced by unbound type II dockerins from the fluorophore-SNAP-XDocII probe. This mechanism of dockerin exchange could represent an efficient means for modifying cellulosome composition.
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Affiliation(s)
- Benjamin H Waller
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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20
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Salama-Alber O, Gat Y, Lamed R, Shimon LJW, Bayer EA, Frolow F. Crystallization and preliminary X-ray characterization of a type III cohesin-dockerin complex from the cellulosome system of Ruminococcus flavefaciens. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1116-9. [PMID: 22949209 PMCID: PMC3433212 DOI: 10.1107/s1744309112033088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/20/2012] [Indexed: 01/19/2023]
Abstract
In Ruminococcus flavefaciens, a predominant fibre-degrading bacterium found in ruminants, cellulosomal proteins are anchored to the bacterial cell wall through a relatively small ScaE scaffoldin which includes a single type III cohesin. The cotton-binding protein CttA consists of two cellulose-binding modules and a C-terminal modular pair (XDoc) comprising an X-module and a contiguous dockerin, which exhibits high affinity towards the ScaE cohesin. Seleno-L-methionine-labelled derivatives of the ScaE cohesin module and the XDoc from CttA have been expressed, copurified and cocrystallized. The crystals belonged to the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 78.7, c = 203.4 Å, and the unit cell contains a single cohesin-XDoc complex in the asymmetric unit. The diffraction data were phased to 2.0 Å resolution using the anomalous signal of the Se atoms.
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Affiliation(s)
- Orly Salama-Alber
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yair Gat
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology, Tel Aviv University, Tel Aviv 69978, Israel
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21
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Morisaka H, Matsui K, Tatsukami Y, Kuroda K, Miyake H, Tamaru Y, Ueda M. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources. AMB Express 2012; 2:37. [PMID: 22839966 PMCID: PMC3444338 DOI: 10.1186/2191-0855-2-37] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/20/2012] [Indexed: 12/04/2022] Open
Abstract
We performed a focused proteome analysis of cellulosomal proteins predicted by a genome analysis of Clostridium cellulovorans [Tamaru, Y., et al.. 2010. J. Bacteriol. 192:901–902]. Our system employed a long monolithic column (300 cm), which provides better performance and higher resolution than conventional systems. Twenty-three cellulosomal proteins were, without purification, identified by direct analysis of the culture medium. Proteome analysis of the C. cellulovorans cellulosome after culture in various carbon sources demonstrated the production of carbon source-adapted cellulosome components.
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22
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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: 28] [Impact Index Per Article: 2.3] [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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23
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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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24
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Brunecky R, Alahuhta M, Bomble YJ, Xu Q, Baker JO, Ding SY, Himmel ME, Lunin VV. Structure and function of theClostridium thermocellumcellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:292-9. [DOI: 10.1107/s0907444912001680] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 01/13/2012] [Indexed: 11/10/2022]
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25
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26
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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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27
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Engineering microbes to produce biofuels. Curr Opin Biotechnol 2010; 22:388-93. [PMID: 21071201 DOI: 10.1016/j.copbio.2010.10.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/13/2010] [Accepted: 10/18/2010] [Indexed: 11/24/2022]
Abstract
The current biofuels landscape is chaotic. It is controlled by the rules imposed by economic forces and driven by the necessity of finding new sources of energy, particularly motor fuels. The need is bringing forth great creativity in uncovering new candidate fuel molecules that can be made via metabolic engineering. These next generation fuels include long-chain alcohols, terpenoid hydrocarbons, and diesel-length alkanes. Renewable fuels contain carbon derived from carbon dioxide. The carbon dioxide is derived directly by a photosynthetic fuel-producing organism(s) or via intermediary biomass polymers that were previously derived from carbon dioxide. To use the latter economically, biomass depolymerization processes must improve and this is a very active area of research. There are competitive approaches with some groups using enzyme based methods and others using chemical catalysts. With the former, feedstock and end-product toxicity loom as major problems. Advances chiefly rest on the ability to manipulate biological systems. Computational and modular construction approaches are key. For example, novel metabolic networks have been constructed to make long-chain alcohols and hydrocarbons that have superior fuel properties over ethanol. A particularly exciting approach is to implement a direct utilization of solar energy to make a usable fuel. A number of approaches use the components of current biological systems, but re-engineer them for more direct, efficient production of fuels.
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28
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Protein engineering for bioenergy and biomass-based chemicals. Curr Opin Struct Biol 2010; 20:527-32. [DOI: 10.1016/j.sbi.2010.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 06/02/2010] [Indexed: 11/18/2022]
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