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Tolmachev DA, Malkamäki M, Linder MB, Sammalkorpi M. Spidroins under the Influence of Alcohol: Effect of Ethanol on Secondary Structure and Molecular Level Solvation of Silk-Like Proteins. Biomacromolecules 2023; 24:5638-5653. [PMID: 38019577 PMCID: PMC10716855 DOI: 10.1021/acs.biomac.3c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023]
Abstract
Future sustainable materials based on designer biomolecules require control of the solution assembly, but also interfacial interactions. Alcohol treatments of protein materials are an accessible means to this, making understanding of the process at the molecular level of seminal importance. We focus here on the influence of ethanol on spidroins, the main proteins of silk. By large-scale atomistically detailed molecular dynamics (MD) simulations and interconnected experiments, we characterize the protein aggregation, secondary structure changes, molecular level origins of them, and solvation environment changes for the proteins, as induced by ethanol as a solvation additive. The MD and circular dichoroism (CD) findings jointly show that ethanol promotes ordered structure in the protein molecules, leading to an increase of helix content and turns but also increased aggregation, as revealed by dynamic light scattering (DLS) and light microscopy. The structural changes correlate at the molecular level with increased intramolecular hydrogen bonding. The simulations reveal that polar amino acids, such as glutamine and serine, are most influenced by ethanol, whereas glycine residues are most prone to be involved in the ethanol-induced secondary structure changes. Furthermore, ethanol engages in interactions with the hydrophobic alanine-rich regions of the spidroin, significantly decreasing the hydrophobic interactions of the protein with itself and its surroundings. The protein solutes also change the microstructure of water/ethanol mixtures, essentially decreasing the level of larger local clustering. Overall, the work presents a systematic characterization of ethanol effects on a widely used, common protein type, spidroins, and generalizes the findings to other intrinsically disordered proteins by pinpointing the general features of the response. The results can aid in designing effective alcohol treatments for proteins, but also enable design and tuning of protein material properties by a relatively controllable solvation handle, the addition of ethanol.
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Affiliation(s)
- Dmitry A. Tolmachev
- Department
of Chemistry and Materials Science, Aalto
University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Maaria Malkamäki
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Markus B. Linder
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department
of Chemistry and Materials Science, Aalto
University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy
of Finland Center of Excellence in Life-Inspired Hybrid Materials
(LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
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2
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Morais MAB, Paiva JH, Murakami MT. Molecular plasticity of CBM3 ancillary domain leads to conformational changes in the cellulose binding interface. Biochem Biophys Res Commun 2023; 645:71-78. [PMID: 36680939 DOI: 10.1016/j.bbrc.2023.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/14/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023]
Abstract
Carbohydrate-binding modules (CBMs) constitute independently folded domains typically associated with carbohydrate-active enzymes (CAZymes). These modules are considered to have a rigid structure without notable conformational changes upon ligand binding, exhibiting a complementary topography in relation to the target carbohydrate. Herein, the high-resolution SAD-solved structure of a CBM from family 3 (BsCBM3) that binds to crystalline cellulose is reported in two crystalline forms. This module showed molecular plasticity with structural differences detected between the two crystalline forms and high RMSD values when compared to NMR ensemble of models. Pronounced structural variances were observed in the cellulose binding interface between NMR and XTAL structures, which were corroborated by molecular dynamics simulations. These findings support that family 3 CBMs targeting to cellulose are rather structurally dynamic modules than rigid entities, suggesting a potential role of conformational changes in polysaccharide recognition and modulation of enzyme activity.
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Affiliation(s)
- Mariana Abrahão Bueno Morais
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Joice Helena Paiva
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mário Tyago Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
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3
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Brunet YR, Habib C, Brogan AP, Artzi L, Rudner DZ. Intrinsically disordered protein regions are required for cell wall homeostasis in Bacillus subtilis. Genes Dev 2022; 36:970-984. [PMID: 36265902 PMCID: PMC9732909 DOI: 10.1101/gad.349895.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 01/07/2023]
Abstract
Intrinsically disordered protein regions (IDRs) have been implicated in diverse nuclear and cytoplasmic functions in eukaryotes, but their roles in bacteria are less clear. Here, we report that extracytoplasmic IDRs in Bacillus subtilis are required for cell wall homeostasis. The B. subtilis σI transcription factor is activated in response to envelope stress through regulated intramembrane proteolysis (RIP) of its membrane-anchored anti-σ factor, RsgI. Unlike canonical RIP pathways, we show that ectodomain (site-1) cleavage of RsgI is constitutive, but the two cleavage products remain stably associated, preventing intramembrane (site-2) proteolysis. The regulated step in this pathway is their dissociation, which is triggered by impaired cell wall synthesis and requires RsgI's extracytoplasmic IDR. Intriguingly, the major peptidoglycan polymerase PBP1 also contains an extracytoplasmic IDR, and we show that this region is important for its function. Disparate IDRs can replace the native IDRs on both RsgI and PBP1, arguing that these unstructured regions function similarly. Our data support a model in which the RsgI-σI signaling system and PBP1 represent complementary pathways to repair gaps in the PG meshwork. The IDR on RsgI senses these gaps and activates σI, while the IDR on PBP1 directs the synthase to these sites to fortify them.
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Affiliation(s)
- Yannick R. Brunet
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cameron Habib
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna P. Brogan
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lior Artzi
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
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4
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Auernhammer J, Langhans M, Schäfer JL, Keil T, Meckel T, Biesalski M, Stark RW. Nanomechanical subsurface characterisation of cellulosic fibres. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-05017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Abstract
The mechanical properties of single fibres are highly important in the paper production process to produce and adjust properties for the favoured fields of application. The description of mechanical properties is usually characterised via linearized assumptions and is not resolved locally or spatially in three dimensions. In tensile tests or nanoindentation experiments on cellulosic fibres, only mechanical parameter for the whole fibre, such as elastic modulus or hardness, is usually obtained. To obtain a more detailed mechanical picture of the fibre, it is crucial to determine mechanical properties in depth. To this end, we discuss an atomic force microscopy-based approach to examine stepwise the local stiffness as a function of indentation depth via static force-distance curves. To our knowledge, we are the first authors to apply this method cellulosic fibres. The method was applied to linter fibres (extracted from a finished paper sheet) as well as to natural raw cotton fibres to better understand the influence of the pulp treatment process in paper production on the mechanical properties. Both types of fibres were characterised in dry and wet conditions with respect to alterations in their mechanical properties. The used stepwise analysis method of the force-distance curves allowed subsurface imaging of the fibres. It could be revealed how the walls in the fibre structure protects the fibre against mechanical loading. Via a combined 3D display of the mapped topography and the fitted elastic moduli in z-direction, a spatially resolved mechanical map of the fibre interior near the surface could be established. Additionally, we labelled the fibres with different carbohydrate binding modules tagged with fluorescent proteins to compare the AFM results with fluorescence confocal laser scanning microscopy imaging. Nanomechanical subsurface imaging in combination with fluorescent protein labelling is thus a tool to better understand the mechanical behaviour of cellulosic fibres, which have a complex, hierarchical structure.
Graphical abstract
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5
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Pelus A, Bordes G, Barbe S, Bouchiba Y, Burnard C, Cortés J, Enjalbert B, Esque J, Estaña A, Fauré R, Henras AK, Heux S, Le Men C, Millard P, Nouaille S, Pérochon J, Toanen M, Truan G, Verdier A, Wagner C, Romeo Y, Montanier CY. A tripartite carbohydrate-binding module to functionalize cellulose nanocrystals. Biomater Sci 2021; 9:7444-7455. [PMID: 34647546 DOI: 10.1039/d1bm01156a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The development of protein and microorganism engineering have led to rising expectations of biotechnology in the design of emerging biomaterials, putatively of high interest to reduce our dependence on fossil carbon resources. In this way, cellulose, a renewable carbon based polysaccharide and derived products, displays unique properties used in many industrial applications. Although the functionalization of cellulose is common, it is however limited in terms of number and type of functions. In this work, a Carbohydrate-Binding Module (CBM) was used as a central core to provide a versatile strategy to bring a large diversity of functions to cellulose surfaces. CBM3a from Clostridium thermocellum, which has a high affinity for crystalline cellulose, was flanked through linkers with a streptavidin domain and an azide group introduced through a non-canonical amino acid. Each of these two extra domains was effectively produced and functionalized with a variety of biological and chemical molecules. Structural properties of the resulting tripartite chimeric protein were investigated using molecular modelling approaches, and its potential for the multi-functionalization of cellulose was confirmed experimentally. As a proof of concept, we show that cellulose can be labelled with a fluorescent version of the tripartite protein grafted to magnetic beads and captured using a magnet.
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Affiliation(s)
- Angeline Pelus
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Gaëlle Bordes
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Sophie Barbe
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Younes Bouchiba
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Callum Burnard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Brice Enjalbert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Jeremy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | | | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Anthony K Henras
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Stéphanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Claude Le Men
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | | | - Julien Pérochon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Marion Toanen
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Amandine Verdier
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Camille Wagner
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - Yves Romeo
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
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Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules. MATERIALS 2021; 14:ma14123175. [PMID: 34207652 PMCID: PMC8227779 DOI: 10.3390/ma14123175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/14/2023]
Abstract
Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.
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7
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Hershko Rimon A, Livnah O, Rozman Grinberg I, Ortiz de Ora L, Yaniv O, Lamed R, Bayer EA, Frolow F, Voronov-Goldman M. Novel clostridial cell-surface hemicellulose-binding CBM3 proteins. Acta Crystallogr F Struct Biol Commun 2021; 77:95-104. [PMID: 33830074 PMCID: PMC8034430 DOI: 10.1107/s2053230x21002764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/15/2021] [Indexed: 11/10/2022] Open
Abstract
A novel member of the family 3 carbohydrate-binding modules (CBM3s) is encoded by a gene (Cthe_0271) in Clostridium thermocellum which is the most highly expressed gene in the bacterium during its growth on several types of biomass substrates. Surprisingly, CtCBM3-0271 binds to at least two different types of xylan, instead of the common binding of CBM3s to cellulosic substrates. CtCBM3-0271 was crystallized and its three-dimensional structure was solved and refined to a resolution of 1.8 Å. In order to learn more about the role of this type of CBM3, a comparative study with its orthologue from Clostridium clariflavum (encoded by the Clocl_1192 gene) was performed, and the three-dimensional structure of CcCBM3-1192 was determined to 1.6 Å resolution. Carbohydrate binding by CcCBM3-1192 was found to be similar to that by CtCBM3-0271; both exhibited binding to xylan rather than to cellulose. Comparative structural analysis of the two CBM3s provided a clear functional correlation of structure and binding, in which the two CBM3s lack the required number of binding residues in their cellulose-binding strips and thus lack cellulose-binding capabilities. This is an enigma, as CtCBM3-0271 was reported to be a highly expressed protein when the bacterium was grown on cellulose. An additional unexpected finding was that CcCBM3-1192 does not contain the calcium ion that was considered to play a structural stabilizing role in the CBM3 family. Despite the lack of calcium, the five residues that form the calcium-binding site are conserved. The absence of calcium results in conformational changes in two loops of the CcCBM3-1192 structure. In this context, superposition of the non-calcium-binding CcCBM3-1192 with CtCBM3-0271 and other calcium-binding CBM3s reveals a much broader two-loop region in the former compared with CtCBM3-0271.
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Affiliation(s)
- Almog Hershko Rimon
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Oded Livnah
- The Wolfson Center for Applied and Structural Biology, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Inna Rozman Grinberg
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology Research, Tel Aviv University, Ramat Aviv 69978, Israel
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lizett Ortiz de Ora
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Oren Yaniv
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Raphael Lamed
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 760001, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8499000, Israel
| | - Felix Frolow
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Milana Voronov-Goldman
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
- The Daniella Rich Institute for Structural Biology Research, Tel Aviv University, Ramat Aviv 69978, Israel
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8
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Pinheiro MP, Reis RA, Dupree P, Ward RJ. Plant cell wall architecture guided design of CBM3-GH11 chimeras with enhanced xylanase activity using a tandem repeat left-handed β-3-prism scaffold. Comput Struct Biotechnol J 2021; 19:1108-1118. [PMID: 33680354 PMCID: PMC7890094 DOI: 10.1016/j.csbj.2021.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 01/19/2023] Open
Abstract
Effective use of plant biomass as an abundant and renewable feedstock for biofuel production and biorefinery requires efficient enzymatic mobilization of cell wall polymers. Knowledge of plant cell wall composition and architecture has been exploited to develop novel multifunctional enzymes with improved activity against lignocellulose, where a left-handed β-3-prism synthetic scaffold (BeSS) was designed for insertion of multiple protein domains at the prism vertices. This allowed construction of a series of chimeras fusing variable numbers of a GH11 β-endo-1,4-xylanase and the CipA-CBM3 with defined distances and constrained relative orientations between catalytic domains. The cellulose binding and endoxylanase activities of all chimeras were maintained. Activity against lignocellulose substrates revealed a rapid 1.6- to 3-fold increase in total reducing saccharide release and increased levels of all major oligosaccharides as measured by polysaccharide analysis using carbohydrate gel electrophoresis (PACE). A construct with CBM3 and GH11 domains inserted in the same prism vertex showed highest activity, demonstrating interdomain geometry rather than number of catalytic sites is important for optimized chimera design. These results confirm that the BeSS concept is robust and can be successfully applied to the construction of multifunctional chimeras, which expands the possibilities for knowledge-based protein design.
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Affiliation(s)
- Matheus P. Pinheiro
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP CEP 14040-901, Brazil
| | - Renata A.G. Reis
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, SP CEP 14040-901, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Richard J. Ward
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP CEP 14040-901, Brazil
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9
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Batys P, Fedorov D, Mohammadi P, Lemetti L, Linder MB, Sammalkorpi M. Self-Assembly of Silk-like Protein into Nanoscale Bicontinuous Networks under Phase-Separation Conditions. Biomacromolecules 2021; 22:690-700. [PMID: 33406825 DOI: 10.1021/acs.biomac.0c01506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Liquid-liquid phase separation of biomacromolecules is crucial in various inter- and extracellular biological functions. This includes formation of condensates to control, e.g., biochemical reactions and structural assembly. The same phenomenon is also found to be critically important in protein-based high-performance biological materials. Here, we use a well-characterized model triblock protein system to demonstrate the molecular level formation mechanism and structure of its condensate. Large-scale molecular modeling supported by analytical ultracentrifuge characterization combined with our earlier high magnification precision cryo-SEM microscopy imaging leads to deducing that the condensate has a bicontinuous network structure. The bicontinuous network rises from the proteins having a combination of sites with stronger mutual attraction and multiple weakly attractive regions connected by flexible, multiconfigurational linker regions. These attractive sites and regions behave as stickers of varying adhesion strength. For the examined model triblock protein construct, the β-sheet-rich end units are the stronger stickers, while additional weaker stickers, contributing to the condensation affinity, rise from spring-like connections in the flexible middle region of the protein. The combination of stronger and weaker sticker-like connections and the flexible regions between the stickers result in a versatile, liquid-like, self-healing structure. This structure also explains the high flexibility, easy deformability, and diffusion of the proteins, decreasing only 10-100 times in the bicontinuous network formed in the condensate phase in comparison to dilute protein solution. The here demonstrated structure and condensation mechanism of a model triblock protein construct via a combination of the stronger binding regions and the weaker, flexible sacrificial-bond-like network as well as its generalizability via polymer sticker models provide means to not only understand intracellular organization, regulation, and cellular function but also to identify direct control factors for and to enable engineering improved protein and polymer constructs to enhance control of advanced fiber materials, smart liquid biointerfaces, or self-healing matrices for pharmaceutics or bioengineering materials.
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Affiliation(s)
- Piotr Batys
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.,Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Dmitrii Fedorov
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., FI-02044 Espoo, Finland
| | - Laura Lemetti
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland.,Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, FI-00076 Aalto, Finland
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10
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Kumar K, Singh S, Sharma K, Goyal A. Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405. J Mol Graph Model 2020; 103:107808. [PMID: 33248343 DOI: 10.1016/j.jmgm.2020.107808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022]
Abstract
The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (α/α)6 barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed β-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% α-helices and 11.0% β-strands which was validated through circular dichroism analysis that showed the presence of 42.6% α-helices and 14.5% β-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50 ± 0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.
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Affiliation(s)
- Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shubha Singh
- Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, Delhi, 110078, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Laboratory of Small Molecules & Macro Molecular Crystallography, Department of Bioengineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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11
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Enjalbert T, De La Mare M, Roblin P, Badruna L, Vernet T, Dumon C, Montanier CY. Characterisation of the Effect of the Spatial Organisation of Hemicellulases on the Hydrolysis of Plant Biomass Polymer. Int J Mol Sci 2020; 21:ijms21124360. [PMID: 32575393 PMCID: PMC7353053 DOI: 10.3390/ijms21124360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023] Open
Abstract
Synergism between enzymes is of crucial importance in cell metabolism. This synergism occurs often through a spatial organisation favouring proximity and substrate channelling. In this context, we developed a strategy for evaluating the impact of the geometry between two enzymes involved in nature in the recycling of the carbon derived from plant cell wall polymers. By using an innovative covalent association process using two protein fragments, Jo and In, we produced two bi-modular chimeric complexes connecting a xylanase and a xylosidase, involved in the deconstruction of xylose-based plant cell wall polymer. We first show that the intrinsic activity of the individual enzymes was preserved. Small Angle X-rays Scattering (SAXS) analysis of the complexes highlighted two different spatial organisations in solution, affecting both the distance between the enzymes (53 Å and 28 Å) and the distance between the catalytic pockets (94 Å and 75 Å). Reducing sugar and HPAEC-PAD analysis revealed different behaviour regarding the hydrolysis of Beechwood xylan. After 24 h of hydrolysis, one complex was able to release a higher amount of reducing sugar compare to the free enzymes (i.e., 15,640 and 14,549 µM of equivalent xylose, respectively). However, more interestingly, the two complexes were able to release variable percentages of xylooligosaccharides compared to the free enzymes. The structure of the complexes revealed some putative steric hindrance, which impacted both enzymatic efficiency and the product profile. This report shows that controlling the spatial geometry between two enzymes would help to better investigate synergism effect within complex multi-enzymatic machinery and control the final product.
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Affiliation(s)
- Thomas Enjalbert
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
| | - Marion De La Mare
- Toulouse White Biotechnology, UMS INRA 1337, UMS CNRS 3582, Institut National des Sciences Appliquées de Toulouse, 31077 Toulouse, France;
| | - Pierre Roblin
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31077 Toulouse, France;
| | - Louise Badruna
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
| | - Thierry Vernet
- Institut de Biologie Structurale, Univ., Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France;
| | - Claire Dumon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
| | - Cédric Y. Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; (T.E.); (L.B.); (C.D.)
- Correspondence: ; Tel.: +33-(0)5-61-55-97-13
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12
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Kumar K, Singal S, Goyal A. Role of carbohydrate binding module (CBM3c) of GH9 β-1,4 endoglucanase (Cel9W) from Hungateiclostridium thermocellum ATCC 27405 in catalysis. Carbohydr Res 2019; 484:107782. [DOI: 10.1016/j.carres.2019.107782] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/06/2019] [Accepted: 08/20/2019] [Indexed: 11/30/2022]
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13
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Mosina NL, Schubert WD, Cowan DA. Characterization and homology modelling of a novel multi-modular and multi-functional Paenibacillus mucilaginosus glycoside hydrolase. Extremophiles 2019; 23:681-686. [PMID: 31372752 DOI: 10.1007/s00792-019-01121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/21/2019] [Indexed: 10/26/2022]
Abstract
Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α)8 and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.
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Affiliation(s)
- Ntsoaki Leticia Mosina
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Wolf-Dieter Schubert
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Don A Cowan
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa.
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14
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Yano S, Hori Y, Kijima T, Konno H, Suyotha W, Takagi K, Wakayama M. Construction of Cellulose Binding Domain Fusion FMN-Dependent NADH-Azoreductase and Glucose 1-Dehydrogenase for the Development of Flow Injection Analysis with Fusion Enzymes Immobilized on Cellulose. J Appl Glycosci (1999) 2019; 66:65-72. [PMID: 34354522 PMCID: PMC8056932 DOI: 10.5458/jag.jag.jag-2018_0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/10/2019] [Indexed: 11/10/2022] Open
Abstract
The cellulose binding domain (CBD) of cellulosome-integrating protein A from Clostridium thermocellum NBRC 103400 was genetically fused to FMN-dependent NADH-azoreductase (AZR) and glucose 1-dehydrogenase (GDH) from Bacillus subtilis. The fusion enzymes, AZR-CBD and CBD-GDH, were expressed in Escherichia coli Rosetta-gami B (DE3). The enzymes were purified from cell-free extracts, and the specific activity of AZR-CBD was 15.1 U/mg and that of CBD-GDH was 22.6 U/mg. AZR-CBD and CBD-GDH bound strongly to 0.5 % swollen cellulose at approximately 95 and 98 % of the initial protein amounts, respectively. After immobilization onto the swollen cellulose, AZR-CBD and CBD-GDH retained their catalytic activity. Both enzymes bound weakly to 0.5 % microcrystalline cellulose, but the addition of a high concentration of microcrystalline cellulose (10 %) improved the binding rate of both enzymes. A reactor for flow injection analysis was filled with microcrystalline cellulose-immobilized AZR-CBD and CBD-GDH. This flow injection analysis system was successfully applied for the determination of glucose, and a linear calibration curve was observed in the range of approximately 0.16–2.5 mM glucose, with a correlation coefficient, r, of 0.998.
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Affiliation(s)
- Shigekazu Yano
- 1 Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University
| | - Yukari Hori
- 1 Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University
| | - Tatsuro Kijima
- 1 Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University
| | - Hiroyuki Konno
- 1 Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University
| | - Wasana Suyotha
- 2 Department of Industrial Biotechnology, Faculty of Agro-industry
| | - Kazuyoshi Takagi
- 3 Department of Applied Chemistry, Faculty of Life Sciences, Ritsumeikan University
| | - Mamoru Wakayama
- 4 Department of Biotechnology, Faculty of Life Sciences, Ritsumeikan University
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15
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Ben-Nissan G, Vimer S, Warszawski S, Katz A, Yona M, Unger T, Peleg Y, Morgenstern D, Cohen-Dvashi H, Diskin R, Fleishman SJ, Sharon M. Rapid characterization of secreted recombinant proteins by native mass spectrometry. Commun Biol 2018; 1:213. [PMID: 30534605 PMCID: PMC6277423 DOI: 10.1038/s42003-018-0231-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Characterization of overexpressed proteins is essential for assessing their quality, and providing input for iterative redesign and optimization. This process is typically carried out following purification procedures that require pronounced cost of time and labor. Therefore, quality assessment of recombinant proteins with no prior purification offers a major advantage. Here, we report a native mass spectrometry method that enables characterization of overproduced proteins directly from culture media. Properties such as solubility, molecular weight, folding, assembly state, overall structure, post-translational modifications and binding to relevant biomolecules are immediately revealed. We show the applicability of the method for in-depth characterization of secreted recombinant proteins from eukaryotic systems such as yeast, insect, and human cells. This method, which can be readily extended to high-throughput analysis, considerably shortens the time gap between protein production and characterization, and is particularly suitable for characterizing engineered and mutated proteins, and optimizing yield and quality of overexpressed proteins.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Aliza Katz
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Meital Yona
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yoav Peleg
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - David Morgenstern
- The De Botton protein Profiling Institute of the Nancy and Stephen Grand Israel national Center for Personalized Medicine, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Hadas Cohen-Dvashi
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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16
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Miller EA, Baniya S, Osorio D, Al Maalouf YJ, Sikes HD. Paper-based diagnostics in the antigen-depletion regime: High-density immobilization of rcSso7d-cellulose-binding domain fusion proteins for efficient target capture. Biosens Bioelectron 2018; 102:456-463. [PMID: 29182928 PMCID: PMC5983361 DOI: 10.1016/j.bios.2017.11.050] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/17/2017] [Accepted: 11/16/2017] [Indexed: 11/28/2022]
Abstract
In this work, we report the development of a general strategy for enhancing the efficiency of target capture in immunoassays, using a bifunctional fusion protein construct which incorporates a substrate-anchoring moiety for the high-abundance immobilization of an antigen-binding domain. This approach was informed by the development of a pseudo first-order rate constant model, and tested in a paper-based assay format using a fusion construct consisting of an rcSso7d binding module and a cellulose-binding domain. These rcSso7d-CBD fusion proteins were solubly expressed and purified from bacteria in high molar yields, and enable oriented, high-density adsorption of the rcSso7d binding species to unmodified cellulose within a 30-second incubation period. These findings were validated using two distinct, antigen-specific rcSso7d variants, which were isolated from a yeast surface display library via flow cytometry. Up to 1.6 micromoles of rcSso7d-CBD was found to adsorb per gram of cellulose, yielding a volume-averaged binder concentration of up to 760μM within the resulting active material. At this molar abundance, the target antigen is captured from solution with nearly 100% efficiency, maximizing the attainable sensitivity for any given diagnostic system.
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Affiliation(s)
- Eric A Miller
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Subha Baniya
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Daniel Osorio
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yara Jabbour Al Maalouf
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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17
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Orłowski A, Artzi L, Cazade PA, Gunnoo M, Bayer EA, Thompson D. On the distinct binding modes of expansin and carbohydrate-binding module proteins on crystalline and nanofibrous cellulose: implications for cellulose degradation by designer cellulosomes. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp07764e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transformation of cellulose into monosaccharides can be achieved by hydrolysis of the cellulose chains, carried out by a special group of enzymes known as cellulases.
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Affiliation(s)
- Adam Orłowski
- Department of Physics
- Bernal Institute
- University of Limerick
- Ireland
| | - Lior Artzi
- Department of Biomolecular Sciences
- The Weizmann Institute of Science
- Rehovot
- Israel
| | | | | | - Edward A. Bayer
- Department of Biomolecular Sciences
- The Weizmann Institute of Science
- Rehovot
- Israel
| | - Damien Thompson
- Department of Physics
- Bernal Institute
- University of Limerick
- Ireland
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18
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Rosa AMM, Prazeres DMF, Paulo PMR. Fluorescence correlation spectroscopy study of the complexation of DNA hybrids, IgG antibody, and a chimeric protein of IgG-binding ZZ domains fused with a carbohydrate binding module. Phys Chem Chem Phys 2017; 19:16606-16614. [DOI: 10.1039/c7cp00662d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) was used to characterize the molecular interactions between the four components of a DNA recognition system.
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Affiliation(s)
- A. M. M. Rosa
- iBB – Institute for Bioengineering and Biosciences
- Department of Bioengineering
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisbon
| | - D. M. F. Prazeres
- iBB – Institute for Bioengineering and Biosciences
- Department of Bioengineering
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisbon
| | - P. M. R. Paulo
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisbon
- Portugal
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19
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Decoding Biomass-Sensing Regulons of Clostridium thermocellum Alternative Sigma-I Factors in a Heterologous Bacillus subtilis Host System. PLoS One 2016; 11:e0146316. [PMID: 26731480 PMCID: PMC4711584 DOI: 10.1371/journal.pone.0146316] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/15/2015] [Indexed: 11/25/2022] Open
Abstract
The Gram-positive, anaerobic, cellulolytic, thermophile Clostridium (Ruminiclostridium) thermocellum secretes a multi-enzyme system called the cellulosome to solubilize plant cell wall polysaccharides. During the saccharolytic process, the enzymatic composition of the cellulosome is modulated according to the type of polysaccharide(s) present in the environment. C. thermocellum has a set of eight alternative RNA polymerase sigma (σ) factors that are activated in response to extracellular polysaccharides and share sequence similarity to the Bacillus subtilis σI factor. The aim of the present work was to demonstrate whether individual C. thermocellum σI-like factors regulate specific cellulosomal genes, focusing on C. thermocellum σI6 and σI3 factors. To search for putative σI6- and σI3-dependent promoters, bioinformatic analysis of the upstream regions of the cellulosomal genes was performed. Because of the limited genetic tools available for C. thermocellum, the functionality of the predicted σI6- and σI3-dependent promoters was studied in B. subtilis as a heterologous host. This system enabled observation of the activation of 10 predicted σI6-dependent promoters associated with the C. thermocellum genes: sigI6 (itself, Clo1313_2778), xyn11B (Clo1313_0522), xyn10D (Clo1313_0177), xyn10Z (Clo1313_2635), xyn10Y (Clo1313_1305), cel9V (Clo1313_0349), cseP (Clo1313_2188), sigI1 (Clo1313_2174), cipA (Clo1313_0627), and rsgI5 (Clo1313_0985). Additionally, we observed the activation of 4 predicted σI3-dependent promoters associated with the C. thermocellum genes: sigI3 (itself, Clo1313_1911), pl11 (Clo1313_1983), ce12 (Clo1313_0693) and cipA. Our results suggest possible regulons of σI6 and σI3 in C. thermocellum, as well as the σI6 and σI3 promoter consensus sequences. The proposed -35 and -10 promoter consensus elements of σI6 are CNNAAA and CGAA, respectively. Additionally, a less conserved CGA sequence next to the C in the -35 element and a highly conserved AT sequence three bases downstream of the -10 element were also identified as important nucleotides for promoter recognition. Regarding σI3, the proposed -35 and -10 promoter consensus elements are CCCYYAAA and CGWA, respectively. The present study provides new clues for understanding these recently discovered alternative σI factors.
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20
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Sand A, Holwerda EK, Ruppertsberger NM, Maloney M, Olson DG, Nataf Y, Borovok I, Sonenshein AL, Bayer EA, Lamed R, Lynd LR, Shoham Y. Three cellulosomal xylanase genes inClostridium thermocellumare regulated by both vegetative SigA (σA) and alternative SigI6 (σI6) factors. FEBS Lett 2015; 589:3133-40. [DOI: 10.1016/j.febslet.2015.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/10/2015] [Accepted: 08/14/2015] [Indexed: 11/29/2022]
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21
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Yaniv O, Fichman G, Borovok I, Shoham Y, Bayer EA, Lamed R, Shimon LJW, Frolow F. Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-σI factors. ACTA ACUST UNITED AC 2014; 70:522-34. [PMID: 24531486 DOI: 10.1107/s139900471302926x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/23/2013] [Indexed: 11/11/2022]
Abstract
The anaerobic, thermophilic, cellulosome-producing bacterium Clostridium thermocellum relies on a variety of carbohydrate-active enzymes in order to efficiently break down complex carbohydrates into utilizable simple sugars. The regulation mechanism of the cellulosomal genes was unknown until recently, when genomic analysis revealed a set of putative operons in C. thermocellum that encode σI factors (i.e. alternative σ factors that control specialized regulon activation) and their cognate anti-σI factor (RsgI). These putative anti-σI-factor proteins have modules that are believed to be carbohydrate sensors. Three of these modules were crystallized and their three-dimensional structures were solved. The structures show a high overall degree of sequence and structural similarity to the cellulosomal family 3 carbohydrate-binding modules (CBM3s). The structures of the three carbohydrate sensors (RsgI-CBM3s) and a reference CBM3 are compared in the context of the structural determinants for the specificity of cellulose and complex carbohydrate binding. Fine structural variations among the RsgI-CBM3s appear to result in alternative substrate preferences for each of the sensors.
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Affiliation(s)
- Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Galit Fichman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
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22
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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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