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Jensen RO, Schulz F, Roux S, Klingeman DM, Mitchell WP, Udwary D, Moraïs S, Reynoso V, Winkler J, Nagaraju S, De Tissera S, Shapiro N, Ivanova N, Reddy TBK, Mizrahi I, Utturkar SM, Bayer EA, Woyke T, Mouncey NJ, Jewett MC, Simpson SD, Köpke M, Jones DT, Brown SD. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Sci Data 2024; 11:432. [PMID: 38693191 PMCID: PMC11063209 DOI: 10.1038/s41597-024-03210-6] [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: 10/15/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.
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Affiliation(s)
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | | | | | | | - Nicole Shapiro
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sagar M Utturkar
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Edward A Bayer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - David T Jones
- Department of Microbiology, University of Otago, Dunedin, New Zealand.
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2
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Chen C, Yang H, Dong S, You C, Moraïs S, Bayer EA, Liu Y, Xuan J, Cui Q, Mizrahi I, Feng Y. A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features. Protein Sci 2024; 33:e4937. [PMID: 38501488 PMCID: PMC10949318 DOI: 10.1002/pro.4937] [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: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Cellulosomes are intricate cellulose-degrading multi-enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohesin modules in structural scaffolding proteins (scaffoldins) and dockerin modules in enzymes. Although the number of tandem cohesins in the scaffoldins is believed to determine the complexity of the cellulosomes, tandem dockerins also exist, albeit very rare, in some cellulosomal components whose assembly and functional roles are currently unclear. In this study, we characterized the structure and mode of assembly of a tandem bimodular double-dockerin, which is connected to a putative S8 protease in the cellulosome-producing bacterium, Clostridium thermocellum. Crystal and NMR structures of the double-dockerin revealed two typical type I dockerin folds with significant interactions between them. Interaction analysis by isothermal titration calorimetry and NMR titration experiments revealed that the double-dockerin displays a preference for binding to the cell-wall anchoring scaffoldin ScaD through the first dockerin with a canonical dual-binding mode, while the second dockerin module was unable to bind to any of the tested cohesins. Surprisingly, the double-dockerin showed a much higher affinity to a cohesin from the CipC scaffoldin of Clostridium cellulolyticum than to the resident cohesins from C. thermocellum. These results contribute valuable insights into the structure and assembly of the double-dockerin module, and provide the basis for further functional studies on multiple-dockerin modules and cellulosomal proteases, thus highlighting the complexity and diversity of cellulosomal components.
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Affiliation(s)
- Chao Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongwu Yang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Present address:
College of PharmacyNankai University, Tongyan Road 38, Haihe Education Park, Jinnan DistrictTianjin 300350China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Cai You
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Edward A. Bayer
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Ya‐Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological EngineeringUniversity of Science and Technology BeijingBeijingChina
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
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3
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Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 2024; 383:eadj9223. [PMID: 38484069 PMCID: PMC7615765 DOI: 10.1126/science.adj9223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.
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Affiliation(s)
- Sarah Moraïs
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Sarah Winkler
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Falk S. P. Nagies
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Nils Kapust
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Eva Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - Avital Artan-Furman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - David N. Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Madhav P. Yadav
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Edward A. Bayer
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001 Israel
| | - William F. Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich-Heine-Universität Düsseldorf, D-40225, Düsseldorf, Germany
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Luo J, Liu T, Diao F, Hao B, Zhang Z, Hou Y, Guo W. Shift in rhizospheric and endophytic microbial communities of dominant plants around Sunit Alkaline Lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161503. [PMID: 36634786 DOI: 10.1016/j.scitotenv.2023.161503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Alkaline lakes are a special type of extreme saline-alkali ecosystem, and the dominant plants store a large number of microbial resources with salinity-tolerant or growth-promoting properties in the littoral zones. In this study, high-throughput sequencing technology and molecular ecological networks were used to analyze the bacteria and fungi from different rhizocompartments of three dominant plants along the salinity gradient in the littoral zones of Sunit Alkali Lake. The study found that fungal communities were more tolerant of environmental abiotic stress, and salinity was not the main environmental factor affecting the composition of microbial communities. Mantel test analysis revealed that SOC (soil organic carbon) was the primary environmental factor affecting the rhizosphere bacterial community as well as the rhizosphere endophyte bacteria and fungi, while CO32- (carbonate ions) had a greater impact on the rhizosphere fungal communities. In addition, keystones identified through the associated molecular network play an important role in helping plants resist saline-alkali environments. There were significant differences in the metabolic pathways of microorganisms from different rhizocompartments predicted by the PICRUSt2 database, which may help to understand how microorganisms resist environmental stress. This study is of great importance for understanding the salt environments around alkaline lakes and excavating potential microbial resources.
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Affiliation(s)
- Junqing Luo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Tai Liu
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Fengwei Diao
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Baihui Hao
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - ZheChao Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yazhou Hou
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China.
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Lamote B, da Fonseca MJM, Vanderstraeten J, Meert K, Elias M, Briers Y. Current challenges in designer cellulosome engineering. Appl Microbiol Biotechnol 2023; 107:2755-2770. [PMID: 36941434 DOI: 10.1007/s00253-023-12474-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023]
Abstract
Designer cellulosomes (DCs) are engineered multi-enzyme complexes, comprising carbohydrate-active enzymes attached to a common backbone, the scaffoldin, via high-affinity cohesin-dockerin interactions. The use of DCs in the degradation of renewable biomass polymers is a promising approach for biorefineries. Indeed, DCs have shown significant hydrolytic activities due to the enhanced enzyme-substrate proximity and inter-enzyme synergies, but technical hurdles in DC engineering have hindered further progress towards industrial application. The challenge in DC engineering lies in the large diversity of possible building blocks and architectures, resulting in a multivariate and immense design space. Simultaneously, the precise DC composition affects many relevant parameters such as activity, stability, and manufacturability. Since protein engineers face a lack of high-throughput approaches to explore this vast design space, DC engineering may result in an unsatisfying outcome. This review provides a roadmap to guide researchers through the process of DC engineering. Each step, starting from concept to evaluation, is described and provided with its challenges, along with possible solutions, both for DCs that are assembled in vitro or are displayed on the yeast cell surface. KEY POINTS: • Construction of designer cellulosomes is a multi-step process. • Designer cellulosome research deals with multivariate construction challenges. • Boosting designer cellulosome efficiency requires exploring a vast design space.
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Affiliation(s)
- Babette Lamote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | | | - Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Kenan Meert
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Marte Elias
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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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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Vela Gurovic MS, Díaz ML, Gallo CA, Dietrich J. Phylogenomics, CAZyome and core secondary metabolome of Streptomyces albus species. Mol Genet Genomics 2021; 296:1299-1311. [PMID: 34564766 DOI: 10.1007/s00438-021-01823-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/13/2021] [Indexed: 12/27/2022]
Abstract
A phylogenomic study conducted with different bioinformatic tools such as TYGS, REALPHY and AAI comparisons revealed a high rate of misidentified Streptomyces albus genomes in GenBank. Only 9 of the 18 annotated genomes available in the public database were correctly identified as S. albus species. The pangenome of the nine in silico confirmed S. albus genomes was almost closed. Lignocellulosic agroresidues were a common niche among strains of the S. albus clade while carbohydrate active enzymes (CAZymes) were highly conserved. Relevant enzymes for cellulose degradation such as beta glucosidases belonging to the GH1 family, a GH6 cellulase and a monooxygenase AA10-CBM2 were encoded by all S. albus genomes. Among them, one GH1 glycosidase would be regulated by CebR. However, this regulatory mechanism was not confirmed for other genes related to cellulose degradation. Based on AntiSMASH predictions, the core secondary metabolome of S. albus encompassed a total of 23 biosynthetic gene clusters (BGCs), where 4 were related to common metabolites within Streptomyces genus. Species specific BGCs included those related to pseudouridimycin and xantholipin. Additionally, four BGCs encoded putative derivatives of ibomycin, the lasso peptide SSV-2086, the lanthipeptide SapB and the terpene isorenieratene. Known metabolites could not be assigned to ten BGCs and three clusters did not match with any previously described BGC. The core genome of S. albus retrieved from nine closely related genomes revealed a high potential for the discovery of novel bioactive metabolites and underexplored regulatory genomic elements related to lignocellulose deconstruction.
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Affiliation(s)
- María Soledad Vela Gurovic
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina. .,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina.
| | - Marina Lucía Díaz
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina.,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
| | - Cristian Andres Gallo
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina
| | - Julián Dietrich
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
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8
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Abstract
Glycoside hydrolase family 9 (GH9) endoglucanases are important enzymes for cellulose degradation. However, their activity on cellulose is diverse. Here, we cloned and expressed one GH9 enzyme (CalkGH9T) from Clostridium alkalicellulosi in Escherichia coli. CalkGH9T has a modular structure, containing one GH9 catalytic module, two family 3 carbohydrate binding modules, and one type I dockerin domain. CalkGH9T exhibited maximal activity at pH 7.0–8.0 and 55 °C and was resistant to urea and NaCl. It efficiently hydrolyzed carboxymethyl cellulose (CMC) but poorly degraded regenerated amorphous cellulose (RAC). Despite strongly binding to Avicel, CalkGH9T lacked the ability to hydrolyze this substrate. The hydrolysis of CMC by CalkGH9T produced a series of cello-oligomers, with cellotetraose being preferentially released. Similar proportions of soluble and insoluble reducing ends generated by hydrolysis of RAC indicated non-processive activity. Our study extends our knowledge of the molecular mechanism of cellulose hydrolysis by GH9 family endoglucanases with industrial relevance.
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9
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Multi-omic Directed Discovery of Cellulosomes, Polysaccharide Utilization Loci, and Lignocellulases from an Enriched Rumen Anaerobic Consortium. Appl Environ Microbiol 2020; 86:AEM.00199-20. [PMID: 32680862 PMCID: PMC7480376 DOI: 10.1128/aem.00199-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
The lignocellulolytic ERAC displays a unique set of plant polysaccharide-degrading enzymes (with multimodular characteristics), cellulosomal complexes, and PULs. The MAGs described here represent an expansion of the genetic content of rumen bacterial genomes dedicated to plant polysaccharide degradation, therefore providing a valuable resource for the development of biocatalytic toolbox strategies to be applied to lignocellulose-based biorefineries. Lignocellulose is one of the most abundant renewable carbon sources, representing an alternative to petroleum for the production of fuel and chemicals. Nonetheless, the lignocellulose saccharification process, to release sugars for downstream applications, is one of the most crucial factors economically challenging to its use. The synergism required among the various carbohydrate-active enzymes (CAZymes) for efficient lignocellulose breakdown is often not satisfactorily achieved with an enzyme mixture from a single strain. To overcome this challenge, enrichment strategies can be applied to develop microbial communities with an efficient CAZyme arsenal, incorporating complementary and synergistic properties, to improve lignocellulose deconstruction. We report a comprehensive and deep analysis of an enriched rumen anaerobic consortium (ERAC) established on sugarcane bagasse (SB). The lignocellulolytic abilities of the ERAC were confirmed by analyzing the depolymerization of bagasse by scanning electron microscopy, enzymatic assays, and mass spectrometry. Taxonomic analysis based on 16S rRNA sequencing elucidated the community enrichment process, which was marked by a higher abundance of Firmicutes and Synergistetes species. Shotgun metagenomic sequencing of the ERAC disclosed 41 metagenome-assembled genomes (MAGs) harboring cellulosomes and polysaccharide utilization loci (PULs), along with a high diversity of CAZymes. The amino acid sequences of the majority of the predicted CAZymes (60% of the total) shared less than 90% identity with the sequences found in public databases. Additionally, a clostridial MAG identified in this study produced proteins during consortium development with scaffoldin domains and CAZymes appended to dockerin modules, thus representing a novel cellulosome-producing microorganism. IMPORTANCE The lignocellulolytic ERAC displays a unique set of plant polysaccharide-degrading enzymes (with multimodular characteristics), cellulosomal complexes, and PULs. The MAGs described here represent an expansion of the genetic content of rumen bacterial genomes dedicated to plant polysaccharide degradation, therefore providing a valuable resource for the development of biocatalytic toolbox strategies to be applied to lignocellulose-based biorefineries.
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Zhao D, Zhang S, Xue Q, Chen J, Zhou J, Cheng F, Li M, Zhu Y, Yu H, Hu S, Zheng Y, Liu S, Xiang H. Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia. Front Microbiol 2020; 11:1740. [PMID: 32793172 PMCID: PMC7393216 DOI: 10.3389/fmicb.2020.01740] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Soda-saline lakes are a special type of alkaline lake in which the chloride concentration is greater than the carbonate/bicarbonate concentration. Due to the high pH and a usually higher osmotic pressure than that of a normal soda lake, the microbes may need more energy to thrive in such a double-extreme environment. In this study, we systematically investigated the microbiome of the brine and sediment samples of nine artificially separated ponds (salinities from 5.5% to saturation) within two soda-saline lakes in Inner Mongolia of China, assisted by deep metagenomic sequencing. The main inorganic ions shaped the microbial community in both the brines and sediments, and the chloride concentration exhibited the most significant effect. A total of 385 metagenome-assembled genomes (MAGs) were generated, in which 38 MAGs were revealed as the abundant species in at least one of the eighteen different samples. Interestingly, these abundant species also represented the most branches of the microbiome of the soda-saline lakes at the phylum level. These abundant taxa were close relatives of microorganisms from classic soda lakes and neutral saline environments, but forming a combination of both habitats. Notably, approximately half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling. These MAGs included four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with the potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration. The possible reason is that reductive sulfur compounds could provide additional energy for the related species, and reductions of oxidative sulfur compounds are more prone to occur under alkaline conditions which support the sulfur cycling. In addition, a unique 1,4-alpha-glucan phosphorylation pathway, but not a normal hydrolysis one, was found in the abundant Candidatus Nanohaloarchaeota MAG NHA-1, which would produce more energy in polysaccharide degradation. In summary, this work has revealed the abundant taxa and favorable pathways in the soda-saline lakes, indicating that efficient energy regeneration pathway may increase the capacity for environmental adaptation in such saline-alkaline environments. These findings may help to elucidate the relationship between microbial metabolism and adaptation to extreme environments.
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Affiliation(s)
- Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feiyue Cheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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