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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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A new landscape of rabbit gut microbiota shaped by the infection of precocious parasites of Eimeria intestinalis. Vet Parasitol 2021; 300:109579. [PMID: 34784535 DOI: 10.1016/j.vetpar.2021.109579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022]
Abstract
Rabbit intestinal coccidiosis is caused by one or several Eimeria species, which cause intestinal damage and secondary bacterial infection. However, the impact of Eimeria infection on gut microbiota is much unknown. To evaluate the influence, we detected the feces flora of SPF rabbits infected with the 1 × 104 oocysts of E. intestinalis wild type (WT) and a precocious line (EIP8), a highly pathogenic species, by 16S rRNA sequencing. The microbiota of newly weaned rabbits post vaccination with low doses of EIP8 oocysts was also detected. In SPF rabbits, while Ruminococcaceae, Lachnospiraceae, and Bacteroidaceae were dominant families in all groups, EIP8 infection induced less changes in beta-diversity. In EIP8-infected rabbits, the intestinal flora whose abundance changed post infection accounted for less than 5.23 % of the entire flora. In comparison, it accounted for 27.18 % in WT group on d14 PI, while it was more than 20 % in diclazuril control group on d7 or d10 PI. The amount of fecal IgA and the abundance of IgA-production-related bacteria were similar in either EIP8 or WT infected rabbits. In the newly weaned rabbits, vaccination with EIP8 provided sufficient protection against challenge with WT parasites, as the body weight gain of vaccinated rabbits was similar to that of untreated animals, as well as more than 80 % reduction of oocyst output was detected when compared with unimmunized and challenged animals. Moreover, the vaccination had no significant impact on rabbit microbiota. Together, our findings suggested that the precocious line of E. intestinalis, compared with WT, induced a new fecal microbiota biodiversity in rabbits.
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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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Slutzki M, Reshef D, Barak Y, Haimovitz R, Rotem-Bamberger S, Lamed R, Bayer EA, Schueler-Furman O. Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface. J Biol Chem 2015; 290:13654-66. [PMID: 25833947 PMCID: PMC4447945 DOI: 10.1074/jbc.m115.651208] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 11/06/2022] Open
Abstract
Interactions between cohesin and dockerin modules play a crucial role in the assembly of multienzyme cellulosome complexes. Although intraspecies cohesin and dockerin modules bind in general with high affinity but indiscriminately, cross-species binding is rare. Here, we combined ELISA-based experiments with Rosetta-based computational design to evaluate the contribution of distinct residues at the Clostridium thermocellum cohesin-dockerin interface to binding affinity, specificity, and promiscuity. We found that single mutations can show distinct and significant effects on binding affinity and specificity. In particular, mutations at cohesin position Asn(37) show dramatic variability in their effect on dockerin binding affinity and specificity: the N37A mutant binds promiscuously both to cognate (C. thermocellum) as well as to non-cognate Clostridium cellulolyticum dockerin. N37L in turn switches binding specificity: compared with the wild-type C. thermocellum cohesin, this mutant shows significantly increased preference for C. cellulolyticum dockerin combined with strongly reduced binding to its cognate C. thermocellum dockerin. The observation that a single mutation can overcome the naturally observed specificity barrier provides insights into the evolutionary dynamics of this system that allows rapid modulation of binding specificity within a high affinity background.
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Affiliation(s)
- Michal Slutzki
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dan Reshef
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, 9112102 Jerusalem, Israel, and
| | - Yoav Barak
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Rachel Haimovitz
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, 9112102 Jerusalem, Israel, and
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Ramat Aviv, Israel
| | - Edward A Bayer
- From the Department of Biological Chemistry, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, 9112102 Jerusalem, Israel, and
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