1
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Ye Y, Liu H, Wang Z, Qi Q, Du J, Tian S. A cellulosomal yeast reaction system of lignin-degrading enzymes for cellulosic ethanol fermentation. Biotechnol Lett 2024; 46:531-543. [PMID: 38607604 DOI: 10.1007/s10529-024-03485-0] [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: 12/08/2023] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
Biofuel production from lignocellulose feedstocks is sustainable and environmentally friendly. However, the lignocellulosic pretreatment could produce fermentation inhibitors causing multiple stresses and low yield. Therefore, the engineering construction of highly resistant microorganisms is greatly significant. In this study, a composite functional chimeric cellulosome equipped with laccase, versatile peroxidase, and lytic polysaccharide monooxygenase was riveted on the surface of Saccharomyces cerevisiae to construct a novel yeast strain YI/LVP for synergistic lignin degradation and cellulosic ethanol production. The assembly of cellulosome was assayed by immunofluorescence microscopy and flow cytometry. During the whole process of fermentation, the maximum ethanol concentration and cellulose conversion of engineering strain YI/LVP reached 8.68 g/L and 83.41%, respectively. The results proved the availability of artificial chimeric cellulosome containing lignin-degradation enzymes for cellulosic ethanol production. The purpose of the study was to improve the inhibitor tolerance and fermentation performance of S. cerevisiae through the construction and optimization of a synergistic lignin-degrading enzyme system based on cellulosome.
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Affiliation(s)
- Yutong Ye
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Han Liu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Zhipeng Wang
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Qi Qi
- Beijing Chaoyang Foreign Language School, Beijing, 100012, China
| | - Jiliang Du
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Shen Tian
- College of Life Science, Capital Normal University, Beijing, 100048, China.
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2
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Zhao M, Liu H, Liu M, Yue Z, Li C, Liu L, Li F. Metagenomics and metabolomics reveal that gut microbiome adapts to the diet transition in Hyla rabbits. Microbiol Res 2024; 283:127705. [PMID: 38554650 DOI: 10.1016/j.micres.2024.127705] [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: 11/06/2023] [Revised: 03/14/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
There is still a lack of longitudinal dynamic studies on the taxonomic features, functional reserves, and metabolites of the rabbit gut microbiome. An experiment was conducted to characterize the bacterial community of rabbits. By combining metagenomics and metabolomics, we have comprehensively analyzed the longitudinal dynamics of the rabbit gut microbiota and its effect on host adaptability. Our data reveal an overall increasing trend in microbial community and functional gene diversity and richness during the pre-harvest lifespan of rabbits. The introduction of solid feed is an important driving factor affecting rabbit gut microbiological compositions. Clostridium and Ruminococcus had significantly higher relative abundances in the solid feed stage. Further, the starch and fiber in solid feed promote the secretion of carbohydrate-degrading enzymes, which helps the host adapt to dietary changes. The rabbit gut microbiota can synthesize lysine, and the synthase is gradually enriched during the diet transformation. The gut microbiota of newborn rabbits has a higher abundance of lipid metabolism, which helps the host obtain more energy from breast milk lipids. The rabbit gut microbiota can also synthesize a variety of secondary bile acids after the introduction of solid feed. These findings provide a novel understanding of how the gut microbiota mediates adaptability to environment and diet in rabbits and provide multiple potential strategies for regulating intestinal health and promoting higher feed efficiency.
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Affiliation(s)
- Man Zhao
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Hongli Liu
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Mengqi Liu
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Zhengkai Yue
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Chenyang Li
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Lei Liu
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China.
| | - Fuchang Li
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China.
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3
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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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4
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Liang J, Zhang R, Chang J, Chen L, Nabi M, Zhang H, Zhang G, Zhang P. Rumen microbes, enzymes, metabolisms, and application in lignocellulosic waste conversion - A comprehensive review. Biotechnol Adv 2024; 71:108308. [PMID: 38211664 DOI: 10.1016/j.biotechadv.2024.108308] [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: 09/03/2023] [Revised: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
The rumen of ruminants is a natural anaerobic fermentation system that efficiently degrades lignocellulosic biomass and mainly depends on synergistic interactions between multiple microbes and their secreted enzymes. Ruminal microbes have been employed as biomass waste converters and are receiving increasing attention because of their degradation performance. To explore the application of ruminal microbes and their secreted enzymes in biomass waste, a comprehensive understanding of these processes is required. Based on the degradation capacity and mechanism of ruminal microbes and their secreted lignocellulose enzymes, this review concentrates on elucidating the main enzymatic strategies that ruminal microbes use for lignocellulose degradation, focusing mainly on polysaccharide metabolism-related gene loci and cellulosomes. Hydrolysis, acidification, methanogenesis, interspecific H2 transfer, and urea cycling in ruminal metabolism are also discussed. Finally, we review the research progress on the conversion of biomass waste into biofuels (bioethanol, biohydrogen, and biomethane) and value-added chemicals (organic acids) by ruminal microbes. This review aims to provide new ideas and methods for ruminal microbe and enzyme applications, biomass waste conversion, and global energy shortage alleviation.
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Affiliation(s)
- Jinsong Liang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Ru Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Jianning Chang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Le Chen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Mohammad Nabi
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Haibo Zhang
- College of Resources and Environment, Shanxi Agricultural University, Taigu 030801, China
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin 300130, China.
| | - Panyue Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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5
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Datta R. Enzymatic degradation of cellulose in soil: A review. Heliyon 2024; 10:e24022. [PMID: 38234915 PMCID: PMC10792583 DOI: 10.1016/j.heliyon.2024.e24022] [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: 10/11/2022] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.
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Affiliation(s)
- Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology. Mendel University In Brno, Czech Republic
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6
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Low KE, Tingley JP, Klassen L, King ML, Xing X, Watt C, Hoover SER, Gorzelak M, Abbott DW. Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates. Biotechnol Adv 2023; 69:108245. [PMID: 37652144 DOI: 10.1016/j.biotechadv.2023.108245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.
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Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Caitlin Watt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Monika Gorzelak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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Wang X, Jiang Y, Liu H, Yuan H, Huang D, Wang T. Research progress of multi-enzyme complexes based on the design of scaffold protein. BIORESOUR BIOPROCESS 2023; 10:72. [PMID: 38647916 PMCID: PMC10992622 DOI: 10.1186/s40643-023-00695-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/04/2023] [Indexed: 04/25/2024] Open
Abstract
Multi-enzyme complexes designed based on scaffold proteins are a current topic in molecular enzyme engineering. They have been gradually applied to increase the production of enzyme cascades, thereby achieving effective biosynthetic pathways. This paper reviews the recent progress in the design strategy and application of multi-enzyme complexes. First, the metabolic channels in the multi-enzyme complex have been introduced, and the construction strategies of the multi-enzyme complex emerging in recent years have been summarized. Then, the discovered enzyme cascades related to scaffold proteins are discussed, emphasizing on the influence of the linker on the fusion enzyme (fusion protein) and its possible mechanism. This review is expected to provide a more theoretical basis for the modification of multi-enzyme complexes and broaden their applications in synthetic biology.
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Affiliation(s)
- Xiangyi Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Di Huang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
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Wang X, Jiang Y, Liu H, Zhang X, Yuan H, Huang D, Wang T. In vitro assembly of the trehalose bi-enzyme complex with artificial scaffold protein. Front Bioeng Biotechnol 2023; 11:1251298. [PMID: 37711449 PMCID: PMC10497880 DOI: 10.3389/fbioe.2023.1251298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction: Trehalose is a significant rare sugar known for its stable properties and ability to protect biomolecules from environmental factors. Methods: In this study, we present a novel approach utilizing a scaffold protein-mediated assembly method for the formation of a trehalose bi-enzyme complex. This complex consists of maltooligosyltrehalose synthase (MTSase) and maltooligosyltrehalose trehalohydrolase (MTHase), which work in tandem to catalyze the substrate and enhance the overall catalytic efficiency. Utilizing the specific interaction between cohesin and dockerin, this study presents the implementation of an assembly, an analysis of its efficiency, and an exploration of strategies to enhance enzyme utilization through the construction of a bi-enzyme complex under optimal conditions in vitro. Results and Discussion: The bi-enzyme complex demonstrated a trehalose production level 1.5 times higher than that of the free enzyme mixture at 40 h, with a sustained upward trend. Compared to free enzyme mixtures, the adoption of a scaffold protein-mediated bi-enzyme complex may improve cascade reactions and catalytic effects, thus presenting promising prospects.
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Affiliation(s)
- Xiangyi Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Xinyi Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Di Huang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, Shandong, China
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9
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Li G, Yuan Y, Jin B, Zhang Z, Murtaza B, Zhao H, Li X, Wang L, Xu Y. Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides. Front Microbiol 2023; 14:1205767. [PMID: 37608941 PMCID: PMC10440823 DOI: 10.3389/fmicb.2023.1205767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.
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Affiliation(s)
- Gen Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhiqiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Hong Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
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10
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Mattoo R, Mallikarjuna S. Soil microbiome influences human health in the context of climate change. Future Microbiol 2023; 18:845-859. [PMID: 37668469 DOI: 10.2217/fmb-2023-0098] [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] [Indexed: 09/06/2023] Open
Abstract
Soil microbiomes continue to evolve and shape the human microbiota according to external anthropogenic and climate change effects. Ancient microbes are being exposed as a result of glacier melting, soil erosion and poor agricultural practices. Soil microbes subtly regulate greenhouse gas emissions and undergo profound alterations due to poor soil maintenance. This review highlights how the soil microbiome influences human digestion processes, mineral and vitamin production, mental health and mood stimulation. Although much about microbial functions remains unknown, increasing evidence suggests that beneficial soil microbes are vital for enhancing human tolerance to diseases and pathogens. Further research is essential to delineate the specific role of the soil microbiome in promoting human health, especially in light of the increasing anthropogenic pressures and changing climatic conditions.
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Affiliation(s)
- Rohini Mattoo
- Divecha Center for Climate Change, Indian Institute of Science, Bangalore, 560038, India
| | - Suman Mallikarjuna
- Divecha Center for Climate Change, Indian Institute of Science, Bangalore, 560038, India
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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [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: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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12
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Ye C, Geng S, Zhang Y, Qiu H, Zhou J, Zeng Q, Zhao Y, Wu D, Yu G, Gong H, Hu B, Hong Y. The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis). Anim Microbiome 2023; 5:20. [PMID: 37005679 PMCID: PMC10067185 DOI: 10.1186/s42523-023-00239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/08/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND The gut microbiota of fish confers various effects on the host, including health, nutrition, metabolism, feeding behaviour, and immune response. Environment significantly impacts the community structure of fish gut microbiota. However, there is a lack of comprehensive research on the gut microbiota of bighead carp in culture systems. To demonstrate the impact of culture systems on the gut microbiome and metabolome in bighead carp and investigate a potential relationship between fish muscle quality and gut microbiota, we conducted a study using 16S ribosomal ribonucleic acid sequencing, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry techniques on bighead carp in three culture systems. RESULTS Our study revealed significant differences in gut microbial communities and metabolic profiles among the three culture systems. We also observed conspicuous changes in muscle structure. The reservoir had higher gut microbiota diversity indices than the pond and lake. We detected significant differences in phyla and genera, such as Fusobacteria, Firmicutes, and Cyanobacteria at the phylum level, Clostridium sensu stricto 1, Macellibacteroides, Blvii28 wastewater sludge group at the genus level. Multivariate statistical models, including principal component analysis and orthogonal projections to latent structures-discriminant analysis, indicated significant differences in the metabolic profiles. Key metabolites were significantly enriched in metabolic pathways involved in "arginine biosynthesis" and "glycine, serine, and threonine metabolism". Variation partitioning analysis revealed that environmental factors, such as pH, ammonium nitrogen, and dissolved oxygen, were the primary drivers of differences in microbial communities. CONCLUSIONS Our findings demonstrate that the culture system significantly impacted the gut microbiota of bighead carp, resulting in differences in community structure, abundance, and potential metabolic functions, and altered the host's gut metabolism, especially in pathways related to amino acid metabolism. These differences were influenced substantially by environmental factors. Based on our study, we discussed the potential mechanisms by which gut microbes affect muscle quality. Overall, our study contributes to our understanding of the gut microbiota of bighead carp under different culture systems.
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Affiliation(s)
- Chen Ye
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Shiyu Geng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yingyu Zhang
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Huimin Qiu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Jie Zhou
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Qi Zeng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yafei Zhao
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Di Wu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Guilan Yu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Haibo Gong
- Jiangxi Provincial Aquatic Biology Protection and Rescue Center, Nanchang, 330000, China
| | - Beijuan Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
| | - Yijiang Hong
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
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13
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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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14
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Cheng J, Hu J, Geng F, Nie S. Bacteroides utilization for dietary polysaccharides and their beneficial effects on gut health. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Fan G, Song W, Guan Z, Zhang W, Lu X. Some novel features of strong promoters discovered in Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2022; 106:2529-2540. [PMID: 35318522 DOI: 10.1007/s00253-022-11869-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Cytophaga hutchinsonii is an important Gram-negative bacterium belonging to the Bacteroides phylum that can efficiently degrade cellulose. But the promoter that mediates the initiation of gene transcription has been unknown for a long time. In this study, we determined the transcription start site (TSS) of C. hutchinsonii by 5' rapid amplification of cDNA ends (5'RACE). The promoter structure was first identified as TAAT and TATTG which are located -5 and -31 bp upstream of TSS, respectively. The function of -5 and -31 regions and the spacer length of the promoter Pchu_1284 were explored by site directed ligase-independent mutagenesis (SLIM). The results showed that the promoter activities were sharply decreased when the TTG motif was mutated into guanine (G) or cytosine (C). Interestingly, we found that the strong promoter was accompanied with many TTTG motifs which could enhance the promoter activities within certain copies. These characteristics were different from other promoters of Bacteriodes species. Furthermore, we carried out genome scanning analysis for C. hutchinsonii and another Bacteroides species by Perl6.0. The results indicated that the promoter structure of C. hutchinsonii possessed more unique features than other species. Also, the screened inducible promoter Pchu_2268 was used to overexpress protein CHU_2196 with a molecular weight of 120 kDa in C. hutchinsonii. The present study enriched the promoter structure of Bacteroidetes species and also provided a novel method for the highly expressed large protein (cellulase) in vivo, which was helpful to elucidate the unique cellulose degradation mechanism of C. hutchinsonii.Key points• The conserved structure of strong promoter of C. hutchinsonii was elucidated.• Two novel regulation motifs of TTTG and AATTATG in the promoter were discovered.• A new method for induced expression of cellulase in vivo was established.• Helpful for explained the unique cellulose degradation mechanism of C. hutchinsonii.
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Affiliation(s)
- Guoqing Fan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Wenxia Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Zhiwei Guan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.,School of Life Science, Qilu Normal University, Jinan, 250200, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.
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Biswal AK, Hengge NN, Black IM, Atmodjo MA, Mohanty SS, Ryno D, Himmel ME, Azadi P, Bomble YJ, Mohnen D. Composition and yield of non-cellulosic and cellulosic sugars in soluble and particulate fractions during consolidated bioprocessing of poplar biomass by Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:23. [PMID: 35227303 PMCID: PMC8887089 DOI: 10.1186/s13068-022-02119-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Terrestrial plant biomass is the primary renewable carbon feedstock for enabling transition to a sustainable bioeconomy. Consolidated bioprocessing (CBP) by the cellulolytic thermophile Clostridium thermocellum offers a single step microbial platform for production of biofuels and biochemicals via simultaneous solubilization of carbohydrates from lignocellulosic biomass and conversion to products. Here, solubilization of cell wall cellulosic, hemicellulosic, and pectic polysaccharides in the liquor and solid residues generated during CBP of poplar biomass by C. thermocellum was analyzed. RESULTS The total amount of biomass solubilized in the C. thermocellum DSM1313 fermentation platform was 5.8, 10.3, and 13.7% of milled non-pretreated poplar after 24, 48, and 120 h, respectively. These results demonstrate solubilization of 24% cellulose and 17% non-cellulosic sugars after 120 h, consistent with prior reports. The net solubilization of non-cellulosic sugars by C. thermocellum (after correcting for the uninoculated control fermentations) was 13 to 36% of arabinose (Ara), xylose (Xyl), galactose (Gal), mannose (Man), and glucose (Glc); and 15% and 3% of fucose and glucuronic acid, respectively. No rhamnose was solubilized and 71% of the galacturonic acid (GalA) was solubilized. These results indicate that C. thermocellum may be selective for the types and/or rate of solubilization of the non-cellulosic wall polymers. Xyl, Man, and Glc were found to accumulate in the fermentation liquor at levels greater than in uninoculated control fermentations, whereas Ara and Gal did not accumulate, suggesting that C. thermocellum solubilizes both hemicelluloses and pectins but utilizes them differently. After five days of fermentation, the relative amount of Rha in the solid residues increased 21% indicating that the Rha-containing polymer rhamnogalacturonan I (RG-I) was not effectively solubilized by C. thermocellum CBP, a result confirmed by immunoassays. Comparison of the sugars in the liquor versus solid residue showed that C. thermocellum solubilized hemicellulosic xylan and mannan, but did not fully utilize them, solubilized and appeared to utilize pectic homogalacturonan, and did not solubilize RG-I. CONCLUSIONS The significant relative increase in RG-I in poplar solid residues following CBP indicates that C. thermocellum did not solubilize RG-I. These results support the hypothesis that this pectic glycan may be one barrier for efficient solubilization of poplar by C. thermocellum.
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Affiliation(s)
- Ajaya K. Biswal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Neal N. Hengge
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Ian M. Black
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Melani A. Atmodjo
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Sushree S. Mohanty
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - David Ryno
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Debra Mohnen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
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First Descriptive Analysis of the Faecal Microbiota of Wild and Anthropized Barbary Macaques (Macaca sylvanus) in the Region of Bejaia, Northeast Algeria. BIOLOGY 2022; 11:biology11020187. [PMID: 35205054 PMCID: PMC8869477 DOI: 10.3390/biology11020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 11/18/2022]
Abstract
Simple Summary The gut microbiota is very important for animal physiology and health. It has been demonstrated that the gut microbiota composition of several primate species is influenced by a variety of anthropogenic factors. However, these aspects are not documented for the gut microbiota of the endangered wild Barbary macaque. This study is the first to characterize the faecal microbiota of the species and investigate the impact on it of tourist food provisioning by comparing two groups of Barbary macaques: a tourist-provisioned group and a wild-feeding group. Our results revealed the presence of 209 bacterial genera from 17 phyla in the faecal microbiota of Barbary macaques. Firmicutes was the most abundant bacterial phylum, followed by Bacteroidetes and Verrucomicrobia. The tourism activity was associated with a significant alteration of this profile, probably due to tourist provisioning issues. Increasing risks of obesity and illness call for special management measures to reduce the provisioning rate in tourist areas. Abstract Previous research has revealed the gut microbiota profile of several primate species, as well as the impact of a variety of anthropogenic factors, such as tourist food supply, on these bacterial communities. However, there is no information on the gut microbiota of the endangered wild Barbary macaque (Macaca sylvanus). The present study is the first to characterize the faecal microbiota of this species, as well as to investigate the impact of tourist food provisioning on it. A total of 12 faecal samples were collected in two groups of M. sylvanus in the region of Bejaia in Algeria. The first group—a tourist-provisioned one—was located in the tourist area of the Gouraya National Park and the second group—a wild-feeding one—was located in the proximity of the village of Mezouara in the forest of Akfadou. After DNA extraction, the faecal microbiota composition was analysed using 16S rDNA sequencing. Statistical tests were performed to compare alpha diversity and beta diversity between the two groups. Non-metric multidimensional scaling analysis (NMDS) was applied to visualize biodiversity between groups. Behaviour monitoring was also conducted to assess the time allocated to the consumption of anthropogenic food by the tourist-provisioned group. Our results revealed the presence of 209 bacterial genera from 17 phyla in the faecal microbiota of Barbary macaques. Firmicutes was the most abundant bacterial phylum, followed by Bacteroidetes and Verrucomicrobia. On the other hand, the comparison between the faecal microbiota of the two study groups showed that tourism activity was associated with a significant change on the faecal microbiota of M.sylvanus, probably due to diet alteration (with 60% of feeding time allocated to the consumption of anthropogenic food). The potentially low-fibre diet at the tourist site adversely influenced the proliferation of bacterial genera found in abundance in the wild group such as Ruminococcaceae. Such an alteration of the faecal microbiota can have negative impacts on the health status of these animals by increasing the risk of obesity and illness and calls for special management measures to reduce the provisioning rate in tourist areas.
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A Single Nucleotide Change in the polC DNA Polymerase III in Clostridium thermocellum Is Sufficient To Create a Hypermutator Phenotype. Appl Environ Microbiol 2022; 88:e0153121. [PMID: 35015978 DOI: 10.1128/aem.01531-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium thermocellum is a thermophilic, anaerobic bacterium that natively ferments cellulose to ethanol and is a candidate for cellulosic biofuel production. Recently, we identified a hypermutator strain of C. thermocellum with a C669Y mutation in the polC gene, which encodes a DNA polymerase III enzyme. Here, we reintroduced this mutation using recently developed CRISPR tools to demonstrate that this mutation is sufficient to recreate the hypermutator phenotype. The resulting strain shows an approximately 30-fold increase in the mutation rate. This mutation is hypothesized to function by interfering with metal ion coordination in the PHP (polymerase and histidinol phosphatase) domain, which is responsible for proofreading. The ability to selectively increase the mutation rate in C. thermocellum is a useful tool for future directed evolution experiments. IMPORTANCE Cellulosic biofuels are a promising approach to decarbonize the heavy-duty-transportation sector. A longstanding barrier to cost-effective cellulosic biofuel production is the recalcitrance of cellulose to solubilization. Native cellulose-consuming organisms, such as Clostridium thermocellum, are promising candidates for cellulosic biofuel production; however, they often need to be genetically modified to improve product formation. One approach is adaptive laboratory evolution. Our findings demonstrate a way to increase the mutation rate in this industrially relevant organism, which can reduce the time needed for adaptive evolution experiments.
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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: 2] [Impact Index Per Article: 0.7] [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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Li J, Chen C, Liu YJ, Cui Q, Bayer EA, Feng Y. NMR chemical shift assignments of a module of unknown function in the cellulosomal secondary scaffoldin ScaF from Clostridium thermocellum. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:329-334. [PMID: 33876380 DOI: 10.1007/s12104-021-10025-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
The cellulosome is a highly efficient cellulolytic complex containing cellulolytic enzymes and non-catalytic subunits, i.e. scaffoldins, which are assembled by the interactions between the dockerin modules of the enzymes and the cohesin modules of the primary scaffoldins. The cellulosome attaches to the cell surface via the S-layer homology (SLH) modules of the anchoring scaffoldins. Clostridium thermocellum DSM1313 is a thermophilic cellulosome-producing bacterium with great potential in lignocellulose bioconversion and biofuel production. The bacterium contains four anchoring scaffoldins ScaB, ScaC, ScaD and ScaF, among which ScaF is the only one that contains an additional module of unknown function (ScaF-X) between the cohesin and SLH modules. The gene of ScaF is located outside the scaffoldin gene cluster of scaA, scaB, scaC and scaD. Previous studies showed unique regulation properties and function of ScaF compared to other anchoring scaffoldins, which might be related to the additional ScaF-X module. Here we report the NMR chemical shift assignments of ScaF-X from C. thermocellum DSM1313. The well-dispersed NMR spectrum and the secondary structure prediction based on the chemical shifts of ScaF-X indicated that ScaF-X is a well-folded protein module. The chemical shift assignments provide the basis for future studies on the structure of this module and its function in cellulosomes.
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
- Shandong Energy Institute, Qingdao, 266101, Shandong, China.
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Clostridium thermocellum as a Promising Source of Genetic Material for Designer Cellulosomes: An Overview. Catalysts 2021. [DOI: 10.3390/catal11080996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant biomass-based biofuels have gradually substituted for conventional energy sources thanks to their obvious advantages, such as renewability, huge quantity, wide availability, economic feasibility, and sustainability. However, to make use of the large amount of carbon sources stored in the plant cell wall, robust cellulolytic microorganisms are highly demanded to efficiently disintegrate the recalcitrant intertwined cellulose fibers to release fermentable sugars for microbial conversion. The Gram-positive, thermophilic, cellulolytic bacterium Clostridium thermocellum possesses a cellulolytic multienzyme complex termed the cellulosome, which has been widely considered to be nature’s finest cellulolytic machinery, fascinating scientists as an auspicious source of saccharolytic enzymes for biomass-based biofuel production. Owing to the supra-modular characteristics of the C. thermocellum cellulosome architecture, the cellulosomal components, including cohesin, dockerin, scaffoldin protein, and the plentiful cellulolytic and hemicellulolytic enzymes have been widely used for constructing artificial cellulosomes for basic studies and industrial applications. In addition, as the well-known microbial workhorses are naïve to biomass deconstruction, several research groups have sought to transform them from non-cellulolytic microbes into consolidated bioprocessing-enabling microbes. This review aims to update and discuss the current progress in these mentioned issues, point out their limitations, and suggest some future directions.
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Berckman EA, Chen W. Self-assembling protein nanocages for modular enzyme assembly by orthogonal bioconjugation. Biotechnol Prog 2021; 37:e3190. [PMID: 34173352 DOI: 10.1002/btpr.3190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/24/2021] [Indexed: 11/06/2022]
Abstract
The wide variety of enzymatic pathways that can benefit from enzyme scaffolding is astronomical. While enzyme co-localization based on protein, DNA, and RNA scaffolds has been reported, we still lack scaffolds that offer well-defined and uniform three-dimensional structures for enzyme organization. Here we reported a new approach for protein co-localization using naturally occurring protein nanocages as a scaffold. Two different nanocages, the 25 nm E2 and the 34 nm heptatitis B virus, were used to demonstrate the successfully co-localization of the endoglucanase CelA and cellulose binding domain using the robust SpyTag/SpyCatcher bioconjugation chemistry. Because of the simplicity of the assembly, this strategy is useful not only for in vivo enzyme cascading but also the potential for in vivo applications as well.
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Affiliation(s)
- Emily A Berckman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA.,Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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Yan F, Wei R, Cui Q, Bornscheuer UT, Liu Y. Thermophilic whole-cell degradation of polyethylene terephthalate using engineered Clostridium thermocellum. Microb Biotechnol 2021; 14:374-385. [PMID: 32343496 PMCID: PMC7936307 DOI: 10.1111/1751-7915.13580] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/03/2022] Open
Abstract
Polyethylene terephthalate (PET) is a mass-produced synthetic polyester contributing remarkably to the accumulation of solid plastics waste and plastics pollution in the natural environments. Recently, bioremediation of plastics waste using engineered enzymes has emerged as an eco-friendly alternative approach for the future plastic circular economy. Here we genetically engineered a thermophilic anaerobic bacterium, Clostridium thermocellum, to enable the secretory expression of a thermophilic cutinase (LCC), which was originally isolated from a plant compost metagenome and can degrade PET at up to 70°C. This engineered whole-cell biocatalyst allowed a simultaneous high-level expression of LCC and conspicuous degradation of commercial PET films at 60°C. After 14 days incubation of a batch culture, more than 60% of the initial mass of a PET film (approximately 50 mg) was converted into soluble monomer feedstocks, indicating a markedly higher degradation performance than previously reported whole-cell-based PET biodegradation systems using mesophilic bacteria or microalgae. Our findings provide clear evidence that, compared to mesophilic species, thermophilic microbes are a more promising synthetic microbial chassis for developing future biodegradation processes of PET waste.
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Affiliation(s)
- Fei Yan
- CAS Key Laboratory of BiofuelsShandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- Dalian National Laboratory for Clean EnergyQingdao266101China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
| | - Ren Wei
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryGreifswald UniversityFelix-Hausdorff-Str. 4D-17487GreifswaldGermany
| | - Qiu Cui
- CAS Key Laboratory of BiofuelsShandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- Dalian National Laboratory for Clean EnergyQingdao266101China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryGreifswald UniversityFelix-Hausdorff-Str. 4D-17487GreifswaldGermany
| | - Ya‐Jun Liu
- CAS Key Laboratory of BiofuelsShandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- Dalian National Laboratory for Clean EnergyQingdao266101China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
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Research progress and the biotechnological applications of multienzyme complex. Appl Microbiol Biotechnol 2021; 105:1759-1777. [PMID: 33564922 DOI: 10.1007/s00253-021-11121-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 11/26/2022]
Abstract
The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.
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Souto BDM, de Araújo ACB, Hamann PRV, Bastos ADR, Cunha IDS, Peixoto J, Kruger RH, Noronha EF, Quirino BF. Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase. PLoS One 2021; 16:e0245118. [PMID: 33449963 PMCID: PMC7810302 DOI: 10.1371/journal.pone.0245118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022] Open
Abstract
Functional screening of metagenomic libraries is an effective approach for identification of novel enzymes. A Caatinga biome goat rumen metagenomic library was screened using esculin as a substrate, and a gene from an unknown bacterium encoding a novel GH3 enzyme, BGL11, was identified. None of the BGL11 closely related genes have been previously characterized. Recombinant BGL11 was obtained and kinetically characterized. Substrate specificity of the purified protein was assessed using seven synthetic aryl substrates. Activity towards nitrophenyl-β-D-glucopyranoside (pNPG), 4-nitrophenyl-β-D-xylopyranoside (pNPX) and 4-nitrophenyl-β-D-cellobioside (pNPC) suggested that BGL11 is a multifunctional enzyme with β-glucosidase, β-xylosidase, and cellobiohydrolase activities. However, further testing with five natural substrates revealed that, although BGL11 has multiple substrate specificity, it is most active towards xylobiose. Thus, in its native goat rumen environment, BGL11 most likely functions as an extracellular β-xylosidase acting on hemicellulose. Biochemical characterization of BGL11 showed an optimal pH of 5.6, and an optimal temperature of 50°C. Enzyme stability, an important parameter for industrial application, was also investigated. At 40°C purified BGL11 remained active for more than 15 hours without reduction in activity, and at 50°C, after 7 hours of incubation, BGL11 remained 60% active. The enzyme kinetic parameters of Km and Vmax using xylobiose were determined to be 3.88 mM and 38.53 μmol.min-1.mg-1, respectively, and the Kcat was 57.79 s-1. In contrast to BLG11, most β-xylosidases kinetically studied belong to the GH43 family and have been characterized only using synthetic substrates. In industry, β-xylosidases can be used for plant biomass deconstruction, and the released sugars can be fermented into valuable bio-products, ranging from the biofuel ethanol to the sugar substitute xylitol.
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Affiliation(s)
| | | | | | | | - Isabel de Souza Cunha
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Julianna Peixoto
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
| | - Ricardo Henrique Kruger
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
| | - Eliane Ferreira Noronha
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
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Ben‐David Y, Moraïs S, Bayer EA, Mizrahi I. Rapid adaptation for fibre degradation by changes in plasmid stoichiometry within Lactobacillus plantarum at the synthetic community level. Microb Biotechnol 2020; 13:1748-1764. [PMID: 32639625 PMCID: PMC7533337 DOI: 10.1111/1751-7915.13584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 12/19/2022] Open
Abstract
The multi-enzyme cellulosome complex can mediate the valorization of lignocellulosic biomass into soluble sugars that can serve in the production of biofuels and valuable products. A potent bacterial chassis for the production of active cellulosomes displayed on the cell surface is the bacterium Lactobacillus plantarum, a lactic acid bacterium used in many applications. Here, we developed a methodological pipeline to produce improved designer cellulosomes, using a cell-consortium approach, whereby the different components self-assemble on the surface of L. plantarum. The pipeline served as a vehicle to select and optimize the secretion efficiency of potent designer cellulosome enzyme components, to screen for the most efficient enzymatic combinations and to assess attempts to grow the engineered bacterial cells on wheat straw as a sole carbon source. Using this strategy, we were able to improve the secretion efficiency of the selected enzymes and to secrete a fully functional high-molecular-weight scaffoldin component. The adaptive laboratory process served to increase significantly the enzymatic activity of the most efficient cell consortium. Internal plasmid re-arrangement towards a higher enzymatic performance attested for the suitability of the approach, which suggests that this strategy represents an efficient way for microbes to adapt to changing conditions.
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Affiliation(s)
- Yonit Ben‐David
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovot7610001Israel
| | - Sarah Moraïs
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovot7610001Israel
- Department of Life SciencesNational Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8499000Israel
| | - Edward A. Bayer
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovot7610001Israel
| | - Itzhak Mizrahi
- Department of Life SciencesNational Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐Sheva8499000Israel
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Qin Y, Li Q, Luo F, Fu Y, He H. One-step purification of two novel thermotolerant β-1,4-glucosidases from a newly isolated strain of Fusarium chlamydosporum HML278 and their characterization. AMB Express 2020; 10:182. [PMID: 33030626 PMCID: PMC7544787 DOI: 10.1186/s13568-020-01116-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/24/2020] [Indexed: 01/07/2023] Open
Abstract
A newly identified cellulase-producing Fusarium chlamydosporum HML278 was cultivated under solid-state fermentation of sugarcane bagasse, and two new β-glucosides enzymes (BG FH1, BG FH2) were recovered from fermentation solution by modified non-denaturing active gel electrophoresis and gel filtration chromatography. SDS-PAGE analysis showed that the molecular weight of BG FH1 and BG FH2 was 93 kDa and 52 kDa, respectively, and the enzyme activity was 5.6 U/mg and 11.5 U/mg, respectively. The optimal reaction temperature of the enzymes was 60 ℃, and the enzymes were stable with a temperature lower than 70 ℃. The optimal pH of the purified enzymes was 6.0, and the enzymes were stable between pH 4–10. Km and Vmax values were 2.76 mg/mL and 20.6 U/mg for pNPG, respectively. Thin-layer chromatography and high-performance liquid chromatography analysis showed that BG FH1and BG FH2 had hydrolysis activity toward cellobiose and could hydrolyze cellobiose into glucose. In addition, both enzymes exhibited transglycoside activity, which could use glucose to synthesize cellobiose and cellotriose, and preferentially synthesize alcohol. In conclusion, our study demonstrated that F. chlamydosporum HML278 produces heat-resistant β-glucosidases with both hydrolytic activity and transglycosidic activity, and these β-glucosidases have potential application in bioethanol and papermaking industries.
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Lin TL, Lu CC, Lai WF, Wu TS, Lu JJ, Chen YM, Tzeng CM, Liu HT, Wei H, Lai HC. Role of gut microbiota in identification of novel TCM-derived active metabolites. Protein Cell 2020; 12:394-410. [PMID: 32929698 PMCID: PMC8106560 DOI: 10.1007/s13238-020-00784-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/29/2020] [Indexed: 02/08/2023] Open
Abstract
Traditional Chinese Medicine (TCM) has been extensively used to ameliorate diseases in Asia for over thousands of years. However, owing to a lack of formal scientific validation, the absence of information regarding the mechanisms underlying TCMs restricts their application. After oral administration, TCM herbal ingredients frequently are not directly absorbed by the host, but rather enter the intestine to be transformed by gut microbiota. The gut microbiota is a microbial community living in animal intestines, and functions to maintain host homeostasis and health. Increasing evidences indicate that TCM herbs closely affect gut microbiota composition, which is associated with the conversion of herbal components into active metabolites. These may significantly affect the therapeutic activity of TCMs. Microbiota analyses, in conjunction with modern multiomics platforms, can together identify novel functional metabolites and form the basis of future TCM research.
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Affiliation(s)
- Tzu-Lung Lin
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Gueishan, Taoyuan, 33302, Taiwan, China
| | - Chia-Chen Lu
- Department of Respiratory Therapy, Fu Jen Catholic University, New Taipei City, 24205, Taiwan, China.,Department of Chest Medicine, Internal Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, 24205, Taiwan, China
| | - Wei-Fan Lai
- Department of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, China
| | - Ting-Shu Wu
- Department of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, China.,Department of Laboratory Medicine and Internal Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan, China.,Central Research Laboratory, Xiamen Chang Gung Hospital, Xiamen, 361026, China
| | - Jang-Jih Lu
- Department of Laboratory Medicine and Internal Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan, China.,Central Research Laboratory, Xiamen Chang Gung Hospital, Xiamen, 361026, China
| | - Young-Mao Chen
- Bachelor Degree Program in Marine Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung, 20224, Taiwan, China
| | - Chi-Meng Tzeng
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361005, China
| | - Hong-Tao Liu
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Hong Wei
- Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200435, China
| | - Hsin-Chih Lai
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Gueishan, Taoyuan, 33302, Taiwan, China. .,Department of Laboratory Medicine and Internal Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33305, Taiwan, China. .,Central Research Laboratory, Xiamen Chang Gung Hospital, Xiamen, 361026, China. .,Microbiota Research Center and Emerging Viral Infections Research Center, Chang Gung University, Taoyuan, 33302, Taiwan, China. .,Research Center for Chinese Herbal Medicine and Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Gueishan, Taoyuan, 33303, Taiwan, China.
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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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Galera-Prat A, Vera AM, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. Impact of scaffoldin mechanostability on cellulosomal activity. Biomater Sci 2020; 8:3601-3610. [PMID: 32232253 DOI: 10.1039/c9bm02052g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignocellulose is the most abundant renewable carbon source in the biosphere. However, the main bottleneck in its conversion to produce second generation biofuels is the saccharification step: the hydrolysis of lignocellulosic material into soluble fermentable sugars. Some anaerobic bacteria have developed an extracellular multi-enzyme complex called the cellulosome that efficiently degrades cellulosic substrates. Cellulosome complexes rely on enzyme-integrating scaffoldins that are large non-catalytic scaffolding proteins comprising several cohesin modules and additional functional modules that mediate the anchoring of the complex to the cell surface and the specific binding to its cellulosic substrate. It was proposed that mechanical forces may affect the cohesins positioned between the cell- and cellulose-anchoring points in the so-called connecting region. Consequently, the mechanical resistance of cohesins within the scaffoldin is of great importance, both to understand cellulosome function and as a parameter of industrial interest, to better mimic natural complexes through the use of the established designer cellulosome technology. Here we study how the mechanical stability of cohesins in a scaffoldin affects the enzymatic activity of a cellulosome. We found that when a cohesin of low mechanical stability is positioned in the connecting region of a scaffoldin, the activity of the resulting cellulosome is reduced as opposed to a cohesin of higher mechanical stability. This observation directly relates mechanical stability of the scaffoldin-borne cohesins to cellulosome activity and provides a rationale for the design of artificial cellulosomes for industrial applications, by incorporating mechanical stability as a new industrial parameter in the biotechnology toolbox.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, Department of Molecular, Cellular and Developmental Neurobiology. IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain.
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Jensen MH, Morris EJ, Tran H, Nash MA, Tan C. Stochastic ordering of complexoform protein assembly by genetic circuits. PLoS Comput Biol 2020; 16:e1007997. [PMID: 32598355 PMCID: PMC7351240 DOI: 10.1371/journal.pcbi.1007997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 07/10/2020] [Accepted: 05/28/2020] [Indexed: 11/18/2022] Open
Abstract
Top-down proteomics has enabled the elucidation of heterogeneous protein complexes with different cofactors, post-translational modifications, and protein membership. This heterogeneity is believed to play a previously unknown role in cellular processes. The different molecular forms of a protein complex have come to be called “complex isoform” or “complexoform”. Despite the elucidation of the complexoform, it remains unclear how and whether cellular circuits control the distribution of a complexoform. To help address this issue, we first simulate a generic three-protein complexoform to reveal the control of its distribution by the timing of gene transcription, mRNA translation, and protein transport. Overall, we ran 265 computational experiments: each averaged over 1,000 stochastic simulations. Based on the experiments, we show that genes arranged in a single operon, a cascade, or as two operons all give rise to the different protein composition of complexoform because of timing differences in protein-synthesis order. We also show that changes in the kinetics of expression, protein transport, or protein binding dramatically alter the distribution of the complexoform. Furthermore, both stochastic and transient kinetics control the assembly of the complexoform when the expression and assembly occur concurrently. We test our model against the biological cellulosome system. With biologically relevant rates, we find that the genetic circuitry controls the average final complexoform assembly and the variation in the assembly structure. Our results highlight the importance of both the genetic circuit architecture and kinetics in determining the distribution of a complexoform. Our work has a broad impact on our understanding of non-equilibrium processes in both living and synthetic biological systems. Multiple protein subunits can come together to form protein complexes that play critical functional roles in a cell. Recent advancement in measurement technologies has revealed tremendous variation in the members of protein complexes. The recent results motivate further research into the importance and the underlying mechanisms of the variation. Here, we study the arrangement of genes as a key factor that modulates the variation of protein complexes. We run computer simulations to investigate how various reaction parameters control the variation of a protein complex. Finally, we extend our framework to study the variation of an enzymatic complex that digests cellulose. Our work has a broad impact on the understanding of protein-complex assembly and set up the new research direction about the variation of protein complexes.
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Affiliation(s)
- Mikkel Herholdt Jensen
- Department of Physics and Astronomy, California State University, Sacramento, California, United States of America
- * E-mail: (MHJ); (CT)
| | - Eliza J. Morris
- Department of Physics and Astronomy, California State University, Sacramento, California, United States of America
| | - Hai Tran
- Department of Chemistry, California State University, Sacramento, California, United States of America
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, California, United States of America
- * E-mail: (MHJ); (CT)
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Dong C, Qiao J, Wang X, Sun W, Chen L, Li S, Wu K, Ma L, Liu Y. Engineering Pichia pastoris with surface-display minicellulosomes for carboxymethyl cellulose hydrolysis and ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:108. [PMID: 32549912 PMCID: PMC7296672 DOI: 10.1186/s13068-020-01749-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUNDS Engineering yeast as a consolidated bioprocessing (CBP) microorganism by surface assembly of cellulosomes has been aggressively utilized for cellulosic ethanol production. However, most of the previous studies focused on Saccharomyces cerevisiae, achieving efficient conversion of phosphoric acid-swollen cellulose (PASC) or microcrystalline cellulose (Avicel) but not carboxymethyl cellulose (CMC) to ethanol, with an average titer below 2 g/L. RESULTS Harnessing an ultra-high-affinity IM7/CL7 protein pair, here we describe a method to engineer Pichia pastoris with minicellulosomes by in vitro assembly of three recombinant cellulases including an endoglucanase (EG), an exoglucanase (CBH) and a β-glucosidase (BGL), as well as a carbohydrate-binding module (CBM) on the cell surface. For the first time, the engineered yeasts enable efficient and direct conversion of CMC to bioethanol, observing an impressive ethanol titer of 5.1 g/L. CONCLUSIONS The research promotes the application of P. pastoris as a CBP cell factory in cellulosic ethanol production and provides a promising platform for screening the cellulases from different species to construct surface-assembly celluosome.
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Affiliation(s)
- Ce Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Jie Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Xinping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Wenli Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Lixia Chen
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Shuntang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Ke Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- BravoVax Co., Ltd., Wuhan, 430000 Hubei China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
- Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
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Li J, Zhong H, Ramayo-Caldas Y, Terrapon N, Lombard V, Potocki-Veronese G, Estellé J, Popova M, Yang Z, Zhang H, Li F, Tang S, Yang F, Chen W, Chen B, Li J, Guo J, Martin C, Maguin E, Xu X, Yang H, Wang J, Madsen L, Kristiansen K, Henrissat B, Ehrlich SD, Morgavi DP. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. Gigascience 2020; 9:5849033. [PMID: 32473013 PMCID: PMC7260996 DOI: 10.1093/gigascience/giaa057] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/07/2019] [Accepted: 05/06/2020] [Indexed: 01/10/2023] Open
Abstract
Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.
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Affiliation(s)
- Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Huanzi Zhong
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Yuliaxis Ramayo-Caldas
- INRAE, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France
| | | | - Jordi Estellé
- INRAE, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Ziyi Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Hui Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fang Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shanmei Tang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fangming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
| | | | - Bing Chen
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jiyang Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jing Guo
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Cécile Martin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Emmanuelle Maguin
- INRAE, Micalis Institute, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Lise Madsen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark.,Institute of Marine Research (IMR), Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stanislav D Ehrlich
- BGI-Shenzhen, Shenzhen 518083, China.,MGP MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy en Josas, France.,Centre for Host Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - Diego P Morgavi
- BGI-Shenzhen, Shenzhen 518083, China.,Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
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Consolidated bio-saccharification: Leading lignocellulose bioconversion into the real world. Biotechnol Adv 2020; 40:107535. [DOI: 10.1016/j.biotechadv.2020.107535] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 11/22/2022]
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36
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Aikawa S, Thianheng P, Baramee S, Ungkulpasvich U, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A. Phenotypic characterization and comparative genome analysis of two strains of thermophilic, anaerobic, cellulolytic-xylanolytic bacterium Herbivorax saccincola. Enzyme Microb Technol 2020; 136:109517. [PMID: 32331721 DOI: 10.1016/j.enzmictec.2020.109517] [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: 10/11/2019] [Revised: 01/09/2020] [Accepted: 01/25/2020] [Indexed: 11/25/2022]
Abstract
The genome sequences of thermophilic, anaerobic, and cellulolytic-xylanolytic bacterium Herbivorax saccincola strains A7 and GGR1 have recently been determined. Although both strains belong to the same species, A7 is alkaliphilic, non-endospore-forming, and ammonium-assimilating, whereas GGR1 is neutrophilic, endospore-forming, and weak-ammonium-assimilating. To better understand the phenotypic diversity among H. saccincola strains, the genome sequences of A7 and GGR1 were compared. A7 contained three additional genes showing similarity to an alkaline stress-associated ABC-transporter but lacked four endospore formation-associated genes, AUG58543 and AUG58618 (encoding SpoVT), AUG57258 (encoding SpoVS), and AUG58614 (encoding YdhD), all of which were present in GGR1. In addition, A7 contained key ammonia assimilation genes PQQ67145 and PQQ66619, encoding ornithine cyclodeaminase and arginase, respectively, which were absent in GGR1. There was no difference in the number and types of cellulosomal-scaffolding proteins and glycosyl hydrolases between the two strains. However, cellulase and xylanase enzymes from A7 demonstrated greater activity and stability at an alkaline pH compared with those from GGR1, and amino acid substitutions were identified in 11 glycosyl hydrolases from A7. This characterization though comparative genomic analysis provides useful information for understanding the genetic basis of the phenotypic differences between H. saccincola strains isolated from distinct areas and environments.
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Affiliation(s)
- Shimpei Aikawa
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Phakhinee Thianheng
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Umbhorn Ungkulpasvich
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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37
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A novel multifunctional GH9 enzyme from Paenibacillus curdlanolyticus B-6 exhibiting endo/exo functions of cellulase, mannanase and xylanase activities. Appl Microbiol Biotechnol 2020; 104:2079-2096. [DOI: 10.1007/s00253-020-10388-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022]
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38
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Zayulina KS, Kochetkova TV, Piunova UE, Ziganshin RH, Podosokorskaya OA, Kublanov IV. Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis. Front Microbiol 2020; 10:2972. [PMID: 31998263 PMCID: PMC6965361 DOI: 10.3389/fmicb.2019.02972] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/10/2019] [Indexed: 01/16/2023] Open
Abstract
A novel hyperthermophilic, anaerobic filamentous archaeon, Thermofilum adornatum strain 1910bT, is capable of growing with cellulose as its sole carbon and energy source. This strain was isolated from a terrestrial hot spring in Kamchatka, Russia. The isolate 1910bT grew optimally at a temperature of 80°C and a pH of 5.5-6.0, producing cell-bound inducible cellulases. During genome analysis, genes, encoding various glycosidases (GHs) involved in oligo- and polysaccharide hydrolysis and genes for the fermentation of sugars were identified. No homologs of currently known cellulase families were found among the GHs encoded by the 1910bT genome, suggesting that novel proteins are involved. To figure this out, a proteomic analysis of cells grown on cellulose or pyruvate (as a control) was performed. Both in-depth genomic and proteomic analyses revealed four proteins (Cel25, Cel30, Cel40, and Cel45) that were the most likely to be involved in the cellulose hydrolysis in this archaeon. Two of these proteins (Cel30 and Cel45) were hypothetical according to genome analysis, while the other two (Cel25 and Cel40) have GH3 and GH1 domains, respectively. The respective genes were heterologously expressed in Escherichia coli BL21 (DE3), and enzymatic activities of recombinant proteins were measured with carboxymethyl cellulose (CMC), Avicel and cellobiose as substrates. It was revealed that the Cel30 and Cel25 proteins were likely exoglucanases with side beta-glucosidase and endoglucanase activities, that Cel40 was a multifunctional glucanase capable of hydrolyzing beta-1,4-glucosides of various lengths, and that Cel45 was an endoglucanase with side exoglucanase activity. Taking into account that the cellulolytic activity of T. adornatum 1910bT surface protein fractions was inducible, that recombinant Cel25 and Cel30 were much less active than Cel40 and Cel45, and that their gene expressions were (almost) non-induced by CMC, we suggest that Cel40 and Cel45 play a major role in the degradation of cellulose, while Cel25 and Cel30 act only as accessory enzymes.
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Affiliation(s)
- Kseniya S. Zayulina
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V. Kochetkova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ulyana E. Piunova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga A. Podosokorskaya
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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39
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Khan S, Chousalkar KK. Short-term feeding of probiotics and synbiotics modulates caecal microbiota during Salmonella Typhimurium infection but does not reduce shedding and invasion in chickens. Appl Microbiol Biotechnol 2019; 104:319-334. [PMID: 31758235 DOI: 10.1007/s00253-019-10220-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022]
Abstract
Positive modulation of gut microbiota in laying chickens may offer a strategy for reduction of Salmonella Typhimurium shedding and production of safer poultry products. In the current study, the caecal luminal microbiota of laying chicks was studied using 16S rRNA amplicon sequencing on DNA obtained from the chicks that were offered supplementation with commercial probiotics, synbiotics and/or Salmonella Typhimurium challenge. The load of Salmonella Typhimurium in various organs was quantified. Irrespective of the probiotics and synbiotics supplementation and Salmonella Typhimurium challenge, caecal microbiota was dominated by 22 distinct bacterial genera and 14 families that clustered into Actinobacteria, Proteobacteria and Firmicutes at phylum level. Taken together, probiotics and synbiotics supplementation increased (false discovery rate; FDR < 0.05) the abundance of Ruminococcus, Trabulsiella, Bifidobacterium, Holdemania and Oscillospira, indicating their role in maintaining gut health through lowering luminal pH and digestion of complex polysaccharides. Salmonella Typhimurium challenge decreased the abundance of Trabulsiella, Oscillospira, Holdemania, Coprococcus, Bifidobacterium and Lactobacillus and increased Klebsiella and Escherichia, indicating its role in caecal dysbiosis. Although probiotics and synbiotics supplementation positively modulated the caecal microbiota, they were not effective in significantly (P > 0.05) reducing Salmonella Typhimurium load in caecal tissue and invasion into vital organs such as liver and spleen. The early colonisation of laying chick caeca by probiotics and synbiotics had the potential to positively influence luminal microbiota; however, the microbial abundance and diversity were not sufficient to significantly reduce the shedding of Salmonella Typhimurium in faeces or invasion into internal organs during this study.
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Affiliation(s)
- Samiullah Khan
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - Kapil K Chousalkar
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, 5371, Australia.
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40
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Raut MP, Couto N, Karunakaran E, Biggs CA, Wright PC. Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85. Sci Rep 2019; 9:16542. [PMID: 31719545 PMCID: PMC6851124 DOI: 10.1038/s41598-019-52675-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 10/22/2019] [Indexed: 02/04/2023] Open
Abstract
Fibrobacter succinogenes S85, isolated from the rumen of herbivores, is capable of robust lignocellulose degradation. However, the mechanism by which it achieves this is not fully elucidated. In this study, we have undertaken the most comprehensive quantitative proteomic analysis, to date, of the changes in the cell envelope protein profile of F. succinogenes S85 in response to growth on cellulose. Our results indicate that the cell envelope proteome undergoes extensive rearrangements to accommodate the cellulolytic degradation machinery, as well as associated proteins involved in adhesion to cellulose and transport and metabolism of cellulolytic products. Molecular features of the lignocellulolytic enzymes suggest that the Type IX secretion system is involved in the translocation of these enzymes to the cell envelope. Finally, we demonstrate, for the first time, that cyclic-di-GMP may play a role in mediating catabolite repression, thereby facilitating the expression of proteins involved in the adhesion to lignocellulose and subsequent lignocellulose degradation and utilisation. Understanding the fundamental aspects of lignocellulose degradation in F. succinogenes will aid the development of advanced lignocellulosic biofuels.
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Affiliation(s)
- Mahendra P Raut
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Narciso Couto
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.,Centre for Applied Pharmacokinetic Research, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | - Esther Karunakaran
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Catherine A Biggs
- School of Engineering, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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41
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Pason P, Sermsathanaswadi J, Waeonukul R, Tachaapaikoon C, Baramee S, Ratanakhanokchai K, Kosugi A. Molecular characterization of hypothetical scaffolding-like protein S1 in multienzyme complex produced by Paenibacillus curdlanolyticus B-6. AMB Express 2019; 9:171. [PMID: 31673804 PMCID: PMC6823336 DOI: 10.1186/s13568-019-0896-0] [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: 08/08/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022] Open
Abstract
Paenibacillus curdlanolyticus B-6 produces an extracellular multienzyme complex containing a hypothetical scaffolding-like protein and several xylanases and cellulases. The largest (280-kDa) component protein, called S1, has cellulose-binding ability and xylanase activity, thus was considered to function like the scaffolding proteins found in cellulosomes. S1 consists of 863 amino acid residues with predicted molecular mass 91,029 Da and includes two N-terminal surface layer homology (SLH) domains, but most of its sequence shows no homology with proteins of known function. Native S1 (nS1) was highly glycosylated. Purified nS1 and recombinant Xyn11A (rXyn11A) as a major xylanase subunit could assemble in a complex, but recombinant S1 (rS1) could not interact with rXyn11A, indicating that S1 glycosylation is necessary for assembly of the multienzyme complex. nS1 and rS1 showed weak, typical endo-xylanase activity, even though they have no homology with known glycosyl hydrolase family enzymes. S1 and its SLH domains bound tightly to the peptide-glycan layer of P. curdlanolyticus B-6, microcrystalline cellulose, and insoluble xylan, indicating that the SLHs of S1 bind to carbohydrate polymers and the cell surface. When nS1 and rXyn11A were co-incubated with birchwood xylan, the degradation ability was synergistically increased compared with that for each protein; however synergy was not observed for rS1 and rXynA. These results indicate that S1 may have a scaffolding protein-like function by interaction with enzyme subunits and polysaccharides through its glycosylated sites and SLH domains.
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42
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The Cellulosome Paradigm in An Extreme Alkaline Environment. Microorganisms 2019; 7:microorganisms7090347. [PMID: 31547347 PMCID: PMC6780208 DOI: 10.3390/microorganisms7090347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/01/2019] [Accepted: 09/10/2019] [Indexed: 11/19/2022] Open
Abstract
Rapid decomposition of plant biomass in soda lakes is associated with microbial activity of anaerobic cellulose-degrading communities. The alkaliphilic bacterium, Clostridium alkalicellulosi, is the single known isolate from a soda lake that demonstrates cellulolytic activity. This microorganism secretes cellulolytic enzymes that degrade cellulose under anaerobic and alkaliphilic conditions. A previous study indicated that the protein fraction of cellulose-grown cultures showed similarities in composition and size to known components of the archetypical cellulosome Clostridium thermocellum. Bioinformatic analysis of the C. alkalicellulosi draft genome sequence revealed 44 cohesins, organized into 22 different scaffoldins, and 142 dockerin-containing proteins. The modular organization of the scaffoldins shared similarities to those of C. thermocellum and Acetivibrio cellulolyticus, whereas some exhibited unconventional arrangements containing peptidases and oxidative enzymes. The binding interactions among cohesins and dockerins assessed by ELISA, revealed a complex network of cellulosome assemblies and suggested both cell-associated and cell-free systems. Based on these interactions, C. alkalicellulosi cellulosomal systems have the genetic potential to create elaborate complexes, which could integrate up to 105 enzymatic subunits. The alkalistable C. alkalicellulosi cellulosomal systems and their enzymes would be amenable to biotechnological processes, such as treatment of lignocellulosic biomass following prior alkaline pretreatment.
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43
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Lee LL, Crosby JR, Rubinstein GM, Laemthong T, Bing RG, Straub CT, Adams MW, Kelly RM. The biology and biotechnology of the genus Caldicellulosiruptor: recent developments in ‘Caldi World’. Extremophiles 2019; 24:1-15. [DOI: 10.1007/s00792-019-01116-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/09/2019] [Indexed: 12/01/2022]
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Wang Y, Leng L, Islam MK, Liu F, Lin CSK, Leu SY. Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization. Int J Mol Sci 2019; 20:ijms20133354. [PMID: 31288425 PMCID: PMC6651384 DOI: 10.3390/ijms20133354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks.
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Affiliation(s)
- Ying Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ling Leng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Md Khairul Islam
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Fanghua Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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Dou TY, Chen J, Qian XK, Li K, Ge GB. Biotransformation of Glycoginsenosides to Intermediate Products and Aglycones using a Hemicellulosome Produced by Cellulosimicrobium cellulan. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819020054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhivin-Nissan O, Dassa B, Morag E, Kupervaser M, Levin Y, Bayer EA. Unraveling essential cellulosomal components of the ( Pseudo) Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:115. [PMID: 31086567 PMCID: PMC6507058 DOI: 10.1186/s13068-019-1447-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/20/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND (Pseudo)Bacteroides cellulosolvens is a cellulolytic bacterium that produces the most extensive and intricate cellulosomal system known in nature. Recently, the elaborate architecture of the B. cellulosolvens cellulosomal system was revealed from analysis of its genome sequence, and the first evidence regarding the interactions between its structural and enzymatic components were detected in vitro. Yet, the understanding of the cellulolytic potential of the bacterium in carbohydrate deconstruction is inextricably linked to its high-molecular-weight protein complexes, which are secreted from the bacterium. RESULTS The current proteome-wide work reveals patterns of protein expression of the various cellulosomal components, and explores the signature of differential expression upon growth of the bacterium on two major carbon sources-cellobiose and microcrystalline cellulose. Mass spectrometry analysis of the bacterial secretome revealed the expression of 24 scaffoldin structural units and 166 dockerin-bearing components (mainly enzymes), in addition to free enzymatic subunits. The dockerin-bearing components comprise cell-free and cell-bound cellulosomes for more efficient carbohydrate degradation. Various glycoside hydrolase (GH) family members were represented among 102 carbohydrate-degrading enzymes, including the omnipresent, most abundant GH48 exoglucanase. Specific cellulosomal components were found in different molecular-weight fractions associated with cell growth on different carbon sources. Overall, microcrystalline cellulose-derived cellulosomes showed markedly higher expression levels of the structural and enzymatic components, and exhibited the highest degradation activity on five different cellulosic and/or hemicellulosic carbohydrates. The cellulosomal activity of B. cellulosolvens showed high degradation rates that are very promising in biotechnological terms and were compatible with the activity levels exhibited by Clostridium thermocellum purified cellulosomes. CONCLUSIONS The current research demonstrates the involvement of key cellulosomal factors that participate in the mechanism of carbohydrate degradation by B. cellulosolvens. The powerful ability of the bacterium to exhibit different degradation strategies on various carbon sources was revealed. The novel reservoir of cellulolytic components of the cellulosomal degradation machineries may serve as a pool for designing new cellulolytic cocktails for biotechnological purposes.
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Affiliation(s)
- Olga Zhivin-Nissan
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Meital Kupervaser
- Proteomics Unit, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Proteomics Unit, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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Santos-Marcos JA, Perez-Jimenez F, Camargo A. The role of diet and intestinal microbiota in the development of metabolic syndrome. J Nutr Biochem 2019; 70:1-27. [PMID: 31082615 DOI: 10.1016/j.jnutbio.2019.03.017] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/28/2019] [Accepted: 03/25/2019] [Indexed: 02/09/2023]
Abstract
Metabolic syndrome (MetS) is a cluster of metabolic factors that increase the risk of cardiovascular disease and type 2 diabetes mellitus (T2DM), which is in itself a major cardiovascular disease risk factor. The aim of this review is to summarize the data related to the influence of the gut microbiota on the development of obesity and the MetS, highlighting the role of diet in controlling the MetS by modifying the gut microbiota. The main alterations in the gut microbiota of individuals with MetS consist of an increased Firmicutes/Bacteriodetes ratio and a reduced capacity to degrade carbohydrates to short-chain fatty acids, which in turn is related with the metabolic dysfunction of the host organism rather than with obesity itself. In addition to a low-fat, high-carbohydrate diet, with its high fiber intake, a diet with 30% fat content but with a high content in fruit and vegetables, such as the Mediterranean diet, is beneficial and partially restores the dysbiosis found in individuals with MetS. Overall, the shaping of the gut microbiota through the administration of prebiotics or probiotics increases the short-chain fatty acid production and is therefore a valid alternative in MetS treatment.
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Affiliation(s)
- Jose A Santos-Marcos
- Lipids and Atherosclerosis Research Unit, GC9 Nutrigenomic-Metabolic Syndrome, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Francisco Perez-Jimenez
- Lipids and Atherosclerosis Research Unit, GC9 Nutrigenomic-Metabolic Syndrome, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Antonio Camargo
- Lipids and Atherosclerosis Research Unit, GC9 Nutrigenomic-Metabolic Syndrome, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain.
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Chen C, Yang H, Xuan J, Cui Q, Feng Y. Resonance assignments of a cellulosomal double-dockerin from Clostridium thermocellum. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:97-101. [PMID: 30377946 DOI: 10.1007/s12104-018-9859-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 06/08/2023]
Abstract
Cellulosomes are highly efficient multienzyme complexes for lignocellulose degradation secreted by some lignocellulolytic bacteria. Cellulosomes are assembled through protein modules named cohesin and dockerin, and multiple cohesin modules in the scaffold protein generally determine the complexity of the cellulosomes. Some cellulosomal proteins contain multiple dockerin modules, which may generate more complex cellulosomal architectures. Genome mining revealed that cellulosomal proteins containing double dockerin modules and a protease module exist in many cellulosome-producing bacteria, and these proteins together with cellulosomal protease inhibitors were proposed to have regulatory roles. However, the structures and functions of these multiple-dockerin proteins in cellulosome have not been reported before. In this paper, we present the NMR chemical shift assignments of the double-dockerin of a cellulosomal protease from Clostridium thermocellum DSM1313. The secondary structures predicted from the chemical shifts agree with the structural arrangement of the tandem dockerin modules. The chemical shift assignments here provide the basis for the structural and functional studies of multiple-dockerin proteins in future.
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Affiliation(s)
- Chao Chen
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Hongwu Yang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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Foley MH, Déjean G, Hemsworth GR, Davies GJ, Brumer H, Koropatkin NM. A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus. J Mol Biol 2019; 431:981-995. [PMID: 30668971 PMCID: PMC6478033 DOI: 10.1016/j.jmb.2019.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/04/2019] [Indexed: 01/07/2023]
Abstract
Dietary fiber is an important food source for members of the human gut microbiome. Members of the dominant Bacteroidetes phylum capture diverse polysaccharides via the action of multiple cell surface proteins encoded within polysaccharide utilization loci (PUL). The independent activities of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) for the harvest of various glycans have been studied in detail, but how these proteins work together to coordinate uptake is poorly understood. Here, we combine genetic and biochemical approaches to discern the interplay between the BoGH9 endoglucanase and the xyloglucan-binding proteins SGBP-A and SGBP-B from the Bacteroides ovatus xyloglucan utilization locus (XyGUL). The expression of BoGH9, a weakly active xyloglucanase in isolation, is required in a strain that expresses a non-binding version of SGBP-A (SGBP-A*). The crystal structure of the BoGH9 enzyme suggests the molecular basis for its robust activity on mixed-linkage β-glucan compared to xyloglucan. However, catalytically inactive site-directed mutants of BoGH9 fail to complement the deletion of the active BoGH9 in a SGBP-A* strain. We also find that SGBP-B is needed in an SGBP-A* background to support growth on xyloglucan, but that the non-binding SGBP-B* protein acts in a dominant negative manner to inhibit growth on xyloglucan. We postulate a model whereby the SGBP-A, SGBP-B, and BoGH9 work together at the cell surface, likely within a discrete complex, and that xyloglucan binding by SGBP-B and BoGH9 may facilitate the orientation of the xyloglucan for transfer across the outer membrane.
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Affiliation(s)
- Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Glyn R Hemsworth
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Dou TY, Chen J, Hao YF, Qi X. Effects of Different Carbon Sources on Enzyme Production and Ultrastructure of Cellulosimicrobium cellulans. Curr Microbiol 2019; 76:355-360. [PMID: 30684027 DOI: 10.1007/s00284-019-01633-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/17/2019] [Indexed: 01/18/2023]
Abstract
The secretomes of the strain Cellulosimicrobium cellulans F16 grown on different carbon sources were analyzed by zymography, and the subcellular surface structures were extensively studied by electron microscope. The exo-cellulase and xylanase systems were sparse when cells were grown on soluble oligosaccharides, but were significantly increased when grown on complex and water-insoluble polysaccharides, such as Avicel, corn cob, and birchwood xylan. The cellulosome-like protuberant structures were clearly observed on the cell surfaces of strain F16 grown on cellulose, with diameters of 15-20 nm. Fibrous structures that connected the adjacent cells can be seen under microscope. Moreover, protuberances that adsorbed the cell to cellulose were also observed. As the adhesion of Cellulosimicrobium cellulans cells onto cellulose surfaces occurs via thick bacterial curdlan-type exopolysaccharides (EPS), such surface layer is potentially important in the digestion of insoluble substrates such as cellulose or hemicellulose, and the previously reported xylanosomes are part of such complex glycocalyx layer on the surface of the bacterial cell.
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Affiliation(s)
- Tong-Yi Dou
- School of Life Science and Medicine, Dalian University of Technology, Dagong Road No. 2, LiaoDongWan New District, Panjin, 124221, China.
| | - Jing Chen
- School of Life Science and Medicine, Dalian University of Technology, Dagong Road No. 2, LiaoDongWan New District, Panjin, 124221, China
| | - Yi-Fu Hao
- School of Life Science and Medicine, Dalian University of Technology, Dagong Road No. 2, LiaoDongWan New District, Panjin, 124221, China
| | - Xiaohui Qi
- College of Life Science, Dalian Minzu University, Dalian, 116600, China
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