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Duarte M, Viegas A, Alves VD, Prates JAM, Ferreira LMA, Najmudin S, Cabrita EJ, Carvalho AL, Fontes CMGA, Bule P. A dual cohesin-dockerin complex binding mode in Bacteroides cellulosolvens contributes to the size and complexity of its cellulosome. J Biol Chem 2021; 296:100552. [PMID: 33744293 PMCID: PMC8063739 DOI: 10.1016/j.jbc.2021.100552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/03/2022] Open
Abstract
The Cellulosome is an intricate macromolecular protein complex that centralizes the cellulolytic efforts of many anaerobic microorganisms through the promotion of enzyme synergy and protein stability. The assembly of numerous carbohydrate processing enzymes into a macromolecular multiprotein structure results from the interaction of enzyme-borne dockerin modules with repeated cohesin modules present in noncatalytic scaffold proteins, termed scaffoldins. Cohesin-dockerin (Coh-Doc) modules are typically classified into different types, depending on structural conformation and cellulosome role. Thus, type I Coh-Doc complexes are usually responsible for enzyme integration into the cellulosome, while type II Coh-Doc complexes tether the cellulosome to the bacterial wall. In contrast to other known cellulosomes, cohesin types from Bacteroides cellulosolvens, a cellulosome-producing bacterium capable of utilizing cellulose and cellobiose as carbon sources, are reversed for all scaffoldins, i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. It has been previously shown that type I B. cellulosolvens interactions possess a dual-binding mode that adds flexibility to scaffoldin assembly. Herein, we report the structural mechanism of enzyme recruitment into B. cellulosolvens cellulosome and the identification of the molecular determinants of its type II cohesin-dockerin interactions. The results indicate that, unlike other type II complexes, these possess a dual-binding mode of interaction, akin to type I complexes. Therefore, the plasticity of dual-binding mode interactions seems to play a pivotal role in the assembly of B. cellulosolvens cellulosome, which is consistent with its unmatched complexity and size.
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Affiliation(s)
- Marlene Duarte
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Aldino Viegas
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Victor D Alves
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, Lisboa, Portugal
| | - José A M Prates
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Luís M A Ferreira
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Shabir Najmudin
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Luísa Carvalho
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Carlos M G A Fontes
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, Lisboa, Portugal; Research and Development, NZYTech Genes & Enzymes, Lisboa, Portugal
| | - Pedro Bule
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, Lisboa, Portugal.
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Zhivin O, Dassa B, Moraïs S, Utturkar SM, Brown SD, Henrissat B, Lamed R, Bayer EA. Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:211. [PMID: 28912832 PMCID: PMC5590126 DOI: 10.1186/s13068-017-0898-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/29/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND (Pseudo) Bacteroides cellulosolvens is an anaerobic, mesophilic, cellulolytic, cellulosome-producing clostridial bacterium capable of utilizing cellulose and cellobiose as carbon sources. Recently, we sequenced the B. cellulosolvens genome, and subsequent comprehensive bioinformatic analysis, herein reported, revealed an unprecedented number of cellulosome-related components, including 78 cohesin modules scattered among 31 scaffoldins and more than 200 dockerin-bearing ORFs. In terms of numbers, the B. cellulosolvens cellulosome system represents the most intricate, compositionally diverse cellulosome system yet known in nature. RESULTS The organization of the B. cellulosolvens cellulosome is unique compared to previously described cellulosome systems. In contrast to all other known cellulosomes, the cohesin types are reversed for all scaffoldins i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. Many of the type II dockerin-bearing ORFs include X60 modules, which are known to stabilize type II cohesin-dockerin interactions. In the present work, we focused on revealing the architectural arrangement of cellulosome structure in this bacterium by examining numerous interactions between the various cohesin and dockerin modules. In total, we cloned and expressed 43 representative cohesins and 27 dockerins. The results revealed various possible architectures of cell-anchored and cell-free cellulosomes, which serve to assemble distinctive cellulosome types via three distinct cohesin-dockerin specificities: type I, type II, and a novel-type designated R (distinct from type III interactions, predominant in ruminococcal cellulosomes). CONCLUSIONS The results of this study provide novel insight into the architecture and function of the most intricate and extensive cellulosomal system known today, thereby extending significantly our overall knowledge base of cellulosome systems and their components. The robust cellulosome system of B. cellulosolvens, with its unique binding specificities and reversal of cohesin-dockerin types, has served to amend our view of the cellulosome paradigm. Revealing new cellulosomal interactions and arrangements is critical for designing high-efficiency artificial cellulosomes for conversion of plant-derived cellulosic biomass towards improved production of biofuels.
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Affiliation(s)
- Olga Zhivin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sagar M. Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919 USA
- BioEnergy Science Center, Oak Ridge, TN USA
| | - Steven D. Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919 USA
- BioEnergy Science Center, Oak Ridge, TN USA
- Biosciences Division, Energy and Environment Directorate, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University and CNRS, Marseille, France
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01022-15. [PMID: 26404597 PMCID: PMC4582573 DOI: 10.1128/genomea.01022-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, wherein the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions, whereas enzymes are integrated via type-II interactions.
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Murray WD. Effects of cellobiose and glucose on cellulose hydrolysis by both growing and resting cells of Bacteroides cellulosolvens. Biotechnol Bioeng 2012; 29:1151-4. [PMID: 18576570 DOI: 10.1002/bit.260290916] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The cellulase system of Bacteroides cellulosolvens was subjected to both catabolite repression and feedback inhibition by cellobiose. Cellulose-solubilizing activity was 50% inhibited at a cellobiose concentration of 2.6 g/L and completely inhibited by 12 g/L. Glucose at 12 g/L (the highest concentration tested) had no effect on cellulase activity. Supplementation of B. cellulosolvens cellulase with beta-glucosidase resulted in increased conversion of cellobiose to glucose; however, a constant cellobiose pool size of approximately 7 g/L was maintained.
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Affiliation(s)
- W D Murray
- Division of Biological Sciences, National Research Council of Canada, Ottawa, Canada K1A OR6
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Potential of biofilm-based biofuel production. Appl Microbiol Biotechnol 2009; 83:1-18. [PMID: 19300995 DOI: 10.1007/s00253-009-1940-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 03/02/2009] [Accepted: 03/02/2009] [Indexed: 01/09/2023]
Abstract
Biofilm technology has been extensively applied to wastewater treatment, but its potential application in biofuel production has not been explored. Current technologies of converting lignocellulose materials to biofuel are hampered by costly processing steps in pretreatment, saccharification, and product recovery. Biofilms may have a potential to improve efficiency of these processes. Advantages of biofilms include concentration of cell-associated hydrolytic enzymes at the biofilm-substrate interface to increase reaction rates, a layered microbial structure in which multiple species may sequentially convert complex substrates and coferment hexose and pentose as hydrolysates diffuse outward, and the possibility of fungal-bacterial symbioses that allow simultaneous delignification and saccharification. More importantly, the confined microenvironment within a biofilm selectively rewards cells with better phenotypes conferred from intercellular gene or signal exchange, a process which is absent in suspended cultures. The immobilized property of biofilm, especially when affixed to a membrane, simplifies the separation of biofuel from its producer and promotes retention of biomass for continued reaction in the fermenter. Highly consolidated bioprocessing, including delignification, saccharification, fermentation, and separation in a single reactor, may be possible through the application of biofilm technology. To date, solid-state fermentation is the only biofuel process to which the advantages of biofilms have been applied, even though it has received limited attention and improvements. The transfer of biofilm technology from environmental engineering has the potential to spur great innovations in the optimization of biofuel production.
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Ding SY, Bayer EA, Steiner D, Shoham Y, Lamed R. A scaffoldin of the Bacteroides cellulosolvens cellulosome that contains 11 type II cohesins. J Bacteriol 2000; 182:4915-25. [PMID: 10940036 PMCID: PMC111372 DOI: 10.1128/jb.182.17.4915-4925.2000] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A cellulosomal scaffoldin gene, termed cipBc, was identified and sequenced from the mesophilic cellulolytic anaerobe Bacteroides cellulosolvens. The gene encodes a 2,292-residue polypeptide (excluding the signal sequence) with a calculated molecular weight of 242,437. CipBc contains an N-terminal signal peptide, 11 type II cohesin domains, an internal family III cellulose-binding domain (CBD), and a C-terminal dockerin domain. Its CBD belongs to family IIIb, like that of CipV from Acetivibrio cellulolyticus but unlike the family IIIa CBDs of other clostridial scaffoldins. In contrast to all other scaffoldins thus far described, CipBc lacks a hydrophilic domain or domain X of unknown function. The singularity of CipBc, however, lies in its numerous type II cohesin domains, all of which are very similar in sequence. One of the latter cohesin domains was expressed, and the expressed protein interacted selectively with cellulosomal enzymes, one of which was identified as a family 48 glycosyl hydrolase on the basis of partial sequence alignment. By definition, the dockerins, carried by the cellulosomal enzymes of this species, would be considered to be type II. This is the first example of authentic type II cohesins that are confirmed components of a cellulosomal scaffoldin subunit rather than a cell surface anchoring component. The results attest to the emerging diversity of cellulosomes and their component sequences in nature.
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Affiliation(s)
- S Y Ding
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Bichet-Hébé I, Pourcher AM, Sutra L, Comel C, Moguedet G. Detection of a whitening fluorescent agent as an indicator of white paper biodegradation: a new approach to study the kinetics of cellulose hydrolysis by mixed cultures. J Microbiol Methods 1999; 37:101-9. [PMID: 10445310 DOI: 10.1016/s0167-7012(99)00043-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A simple and reliable method to estimate paper degradation by cellulolytic bacteria is described. This method is based on the detection in the culture medium of a fluorescent whitening agent (FWA) added to white paper during the manufacturing process. Preliminary results using a Cellulomonas strain cultivated in a liquid medium containing FWA, indicated that this component is non-toxic at a final concentration of 0.01 per thousand (v/v) and that the fluorescence decreased during the first 24 h of incubation, i.e. during exponential growth phase, suggesting an adsorption of FWA on bacterial cells. Consequently, all experiments have been performed with a liquid medium containing FWA (0.01 per thousand v/v) and white paper (8.0 g/l) as cellulose source. Mixed bacterial populations (MBPs) were prepared from refuse samples. These MBPs, which mainly consisted of bacterial rod cells, were used as inocula and fluorescence was measured after 30 h of incubation, i.e. after the stationary phase was reached. A high linear correlation (R(2) = 0.979) was found between the percentages of degraded paper (%P) deduced from residual paper weight and the fluorescence values (F) of the culture medium and the following equation between %P and F was determined: %P = 8.71x10(-5) x F. An additional experiment using a second MBP showed a strong correlation (R(2) = 0.990) between the measured %P and the %P estimated from F values, confirming the reproducibility of the method. Moreover, the time course of paper degradation by five replicate flasks from a unique MBP was set up. Paper degradation was detected 3 to 5 days after the beginning of the stationary phase. The average degradation rate between the 7th and the 11th day of incubation was 11.4% per day. Rates of paper degradation ranged from 31 to 60% after 10 days and from 77 to 88% after 3 weeks of incubation, depending on the inoculum.
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Affiliation(s)
- I Bichet-Hébé
- Laboratoire des Sciences de l'Environnement et de l'Aménagement, Faculté des Sciences, Angers, France
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Krishnan S, Lalitha K. Interactive metabolic regulations during biomethanation ofLeucaena leucocephala. Appl Biochem Biotechnol 1990. [DOI: 10.1007/bf02798394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lamed R, Bayer EA. The Cellulosome of Clostridium thermocellum. ADVANCES IN APPLIED MICROBIOLOGY 1988. [DOI: 10.1016/s0065-2164(08)70203-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Mayer F. Cellulolysis: ultrastructural aspects of bacterial systems. ELECTRON MICROSCOPY REVIEWS 1988; 1:69-85. [PMID: 3155019 DOI: 10.1016/s0892-0354(98)90006-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- F Mayer
- Institut für Mikrobiologie, Georg-August-Universität Göttingen, F.R.G
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Lamed R, Naimark J, Morgenstern E, Bayer EA. Specialized cell surface structures in cellulolytic bacteria. J Bacteriol 1987; 169:3792-800. [PMID: 3301817 PMCID: PMC212468 DOI: 10.1128/jb.169.8.3792-3800.1987] [Citation(s) in RCA: 190] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The cell surface topology of various gram-negative and -positive, anaerobic and aerobic, mesophilic and thermophilic, cellulolytic and noncellulolytic bacteria was investigated by scanning electron microscopic visualization using cationized ferritin. Characteristic protuberant structures were observed on cells of all cellulolytic strains. These structures appeared to be directly related to the previously described exocellular cellulase-containing polycellulosomes of Clostridium thermocellum YS (E. A. Bayer and R. Lamed, J. Bacteriol. 167:828-836, 1986). Immunochemical evidence and lectin-binding studies suggested a further correlation on the molecular level among cellulolytic bacteria. The results indicate that such cell surface cellulase-containing structures may be of general consequence to the bacterial interaction with and degradation of cellulose.
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