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Xu Y, Liu L, Jia M, Teng K, Mu N, Guo Y, Liu M, Wu J, Teng W, Huang L, Fan X, Yue Y. Transcriptomic and physiological analysis provide new insight into seed shattering mechanism in Pennisetum alopecuroides 'Liqiu'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:157. [PMID: 38861001 DOI: 10.1007/s00122-024-04655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024]
Abstract
KEY MESSAGE Through the histological, physiological, and transcriptome-level identification of the abscission zone of Pennisetum alopecuroides 'Liqiu', we explored the structure and the genes related to seed shattering, ultimately revealing the regulatory network of seed shattering in P. alopecuroides. Pennisetum alopecuroides is one of the most representative ornamental grass species of Pennisetum genus. It has unique inflorescence, elegant appearance, and strong stress tolerance. However, the shattering of seeds not only reduces the ornamental effect, but also hinders the seed production. In order to understand the potential mechanisms of seed shattering in P. alopecuroides, we conducted morphological, histological, physiological, and transcriptomic analyses on P. alopecuroides cv. 'Liqiu'. According to histological findings, the seed shattering of 'Liqiu' was determined by the abscission zone at the base of the pedicel. Correlation analysis showed that seed shattering was significantly correlated with cellulase, lignin, auxin, gibberellin, cytokinin and jasmonic acid. Through a combination of histological and physiological analyses, we observed the accumulation of cellulase and lignin during 'Liqiu' seed abscission. We used PacBio full-length transcriptome sequencing (SMRT) combined with next-generation sequencing (NGS) transcriptome technology to improve the transcriptome data of 'Liqiu'. Transcriptomics further identified many differential genes involved in cellulase, lignin and plant hormone-related pathways. This study will provide new insights into the research on the shattering mechanism of P. alopecuroides.
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Affiliation(s)
- Yue Xu
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
- College of Grassland Science and Technology, Sichuan Agriculture University, Chengdu, 610000, People's Republic of China
| | - Lingyun Liu
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Ming Jia
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Ke Teng
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Na Mu
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Yidi Guo
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Muye Liu
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Juying Wu
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Wenjun Teng
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agriculture University, Chengdu, 610000, People's Republic of China
| | - Xifeng Fan
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Yuesen Yue
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
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Pei Y, Xue Q, Shu P, Xu W, Du X, Wu M, Liu K, Pirrello J, Bouzayen M, Hong Y, Liu M. Bifunctional transcription factors SlERF.H5 and H7 activate cell wall and repress gibberellin biosynthesis genes in tomato via a conserved motif. Dev Cell 2024; 59:1345-1359.e6. [PMID: 38579721 DOI: 10.1016/j.devcel.2024.03.006] [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: 07/19/2023] [Revised: 12/31/2023] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
The plant cell wall is a dynamic structure that plays an essential role in development, but the mechanism regulating cell wall formation remains poorly understood. We demonstrate that two transcription factors, SlERF.H5 and SlERF.H7, control cell wall formation and tomato fruit firmness in an additive manner. Knockout of SlERF.H5, SlERF.H7, or both genes decreased cell wall thickness, firmness, and cellulose contents in fruits during early development, especially in double-knockout lines. Overexpressing either gene resulted in thicker cell walls and greater fruit firmness with elevated cellulose levels in fruits but severely dwarf plants with lower gibberellin contents. We further identified that SlERF.H5 and SlERF.H7 activate the cellulose biosynthesis gene SlCESA3 but repress the gibberellin biosynthesis gene GA20ox1. Moreover, we identified a conserved LPL motif in these ERFs responsible for their activities as transcriptional activators and repressors, providing insight into how bifunctional transcription factors modulate distinct developmental processes.
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Affiliation(s)
- Yangang Pei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Qihan Xue
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Peng Shu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Weijie Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xiaofei Du
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Mengbo Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang 524048, China
| | - Julien Pirrello
- Laboratoire de Recherche en Sciences Végétales-Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Mondher Bouzayen
- Laboratoire de Recherche en Sciences Végétales-Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Yiguo Hong
- School of Life Sciences, University of Warwick, Warwick CV4 7AL, UK; State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
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Sadaqat B, Dar MA, Sha C, Abomohra A, Shao W, Yong YC. Thermophilic β-mannanases from bacteria: production, resources, structural features and bioengineering strategies. World J Microbiol Biotechnol 2024; 40:130. [PMID: 38460032 DOI: 10.1007/s11274-024-03912-4] [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: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024]
Abstract
β-mannanases are pivotal enzymes that cleave the mannan backbone to release short chain mannooligosaccharides, which have tremendous biotechnological applications including food/feed, prebiotics and biofuel production. Due to the high temperature conditions in many industrial applications, thermophilic mannanases seem to have great potential to overcome the thermal impediments. Thus, structural analysis of thermostable β-mannanases is extremely important, as it could open up new avenues for genetic engineering, and protein engineering of these enzymes with enhanced properties and catalytic efficiencies. Under this scope, the present review provides a state-of-the-art discussion on the thermophilic β-mannanases from bacterial origin, their production, engineering and structural characterization. It covers broad insights into various molecular biology techniques such as gene mutagenesis, heterologous gene expression, and protein engineering, that are employed to improve the catalytic efficiency and thermostability of bacterial mannanases for potential industrial applications. Further, the bottlenecks associated with mannanase production and process optimization are also discussed. Finally, future research related to bioengineering of mannanases with novel protein expression systems for commercial applications are also elaborated.
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Affiliation(s)
- Beenish Sadaqat
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 22100, Lund, Sweden
| | - Mudasir A Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Chong Sha
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China
| | - Abdelfatah Abomohra
- Aquatic Ecophysiology and Phycology, Department of Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, 22609, Germany
| | - Weilan Shao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu province, People's Republic of China.
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Li X, Li M, Shi W, Li X, Xiang Z, Su L. Clostridium lamae sp. nov., a novel bacterium isolated from the fresh feces of alpaca. Antonie Van Leeuwenhoek 2024; 117:36. [PMID: 38367205 DOI: 10.1007/s10482-024-01931-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/21/2024] [Indexed: 02/19/2024]
Abstract
A novel Gram-positive, anaerobic, nonspore-forming, rod-shaped bacterium, designated strain NGMCC 1.200840 T, was isolated from the alpacas fresh feces. The taxonomic position of the novel strain was determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed strain NGMCC 1.200840 T was a member of the genus Clostridium and closely related to Clostridium tertium DSM 2485 T (98.16% sequence similarity). Between strains NGMCC 1.200840 T and C. tertium DSM 2485 T, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 79.91% and 23.50%, respectively. Genomic DNA G + C content is 28.44 mol%. The strain can utilise D-glucose, D-mannitol, D-lactose, D-saccharose, D-maltose, D-xylose, L-arabinose, D-cellobiose, D-mannose, D-melezitose, D-raffinose, D-sorbitol, L-rhamnose, D-trehalose, D-galactose and Arbutin to produce acid. The optimal growth pH was 7, the temperature was 37 °C, and the salt concentration was 0-0.5% (w/v). The major cellular fatty acids (> 10%) included iso-C15:0, anteiso-C15:0 and iso-C17:0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two unidentified aminolipids. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, NGMCC 1.200840 T represents a novel species within the genus Clostridium, for which the named Clostridium lamae sp. nov. is proposed. The type strain is NGMCC 1.200840 T (= CGMCC 1.18014 T = JCM 35704 T).
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Affiliation(s)
- Xue Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Ming Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Technology Support Platform, Beijing, 100193, China
| | - Weixiong Shi
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Xia Li
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Zhiguang Xiang
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China
- Changping National Laboratory (CPNL), Beijing, 102299, China
| | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Comparative Medicine Center, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100021, China.
- Changping National Laboratory (CPNL), Beijing, 102299, China.
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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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Wang L, Zhu M, Li Y, Zhao Z. Assessing the effects of aquaculture on tidal flat ecological status using multi-metrics interaction-based index of biotic integrity (Mt-IBI). ENVIRONMENTAL RESEARCH 2023; 228:115789. [PMID: 37011797 DOI: 10.1016/j.envres.2023.115789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/16/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023]
Abstract
Given tidal flat special environmental conditions and the degree of pollution caused by human activities, there is an urgent need to quantitatively assess their ecological status. Bioindication has become an indispensable part of environmental quality monitoring on account of its sensitivity to environmental disturbance. Thus, this study used bio-indicators to establish a multi-metrics-based index of biotic integrity (Mt-IBI) to evaluate the ecological status of the tidal flats with/without aquaculture through metagenomic sequencing. Four core indexes that were significantly correlated to other indexes with redundancy (p < 0.05), including Escherichia, beta-lactam antibiotic resistance genes, cellulase and xyloglucanases and the keystone species with 21° in the network, were selected after the screening processes. By implementing Mt-IBI in the tidal flats, the ecological health of the sampling sites was categorized into three levels, with Mt-IBI values of 2.01-2.63 (severe level), 2.81-2.93 (moderate level) and 3.23-4.18 (mild level), respectively. Through SEM analysis, water chemical oxygen demand and antibiotics were determined to be the primary controlling factors of the ecological status of tidal flat regions influenced by aquaculture, followed by salinity and total nitrogen. It is worth noting that the alteration of microbial communities impacted ecological status through the mediation of antibiotics. It is hoped that the results of our study will provide a theoretical basis for coastal environment restoration and that the use of Mt-IBI to assess ecosystem status in different aquatic environments will be further popularized in the future.
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Affiliation(s)
- Linqiong Wang
- College of Oceanography, Hohai University, Xikang Road #1, Nanjing, China
| | - Mengjie Zhu
- College of Environment, Hohai University, Xikang Road #1, Nanjing, China
| | - Yi Li
- College of Environment, Hohai University, Xikang Road #1, Nanjing, China.
| | - Zhe Zhao
- College of Oceanography, Hohai University, Xikang Road #1, Nanjing, China
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Mandal A, Thakur A, Goyal A. Role of carbohydrate binding modules, CBM3A and CBM3B in stability and catalysis by a β-1,4 endoglucanase, AtGH9C-CBM3A-CBM3B from Acetivibrio thermocellus ATCC 27405. Int J Biol Macromol 2023:125164. [PMID: 37270124 DOI: 10.1016/j.ijbiomac.2023.125164] [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: 02/19/2023] [Revised: 05/05/2023] [Accepted: 05/29/2023] [Indexed: 06/05/2023]
Abstract
A recombinant β-1,4 endoglucanase, AtGH9C-CBM3A-CBM3B from Acetivibrio thermocellus ATCC27405 was explored for biochemical properties and the role of its associated CBMs in catalysis. The gene expressing full-length multi-modular β-1,4-endoglucanase (AtGH9C-CBM3A-CBM3B) and its truncated derivatives (AtGH9C-CBM3A, AtGH9C, CBM3A and CBM3B) were independently cloned and expressed in Escherichia coli BL21(DE3) cells and purified. AtGH9C-CBM3A-CBM3B showed maximal activity at 55 °C and pH 7.5. AtGH9C-CBM3A-CBM3B exhibited highest activity against carboxy methyl cellulose (58.8 U/mg) followed by lichenan (44.5 U/mg), β-glucan (36.2 U/mg) and hydroxy ethyl cellulose (17.9 U/mg). Catalytic module, AtGH9C showed insignificant activity against the substrates, signifying the essential requirement of CBMs in catalysis. AtGH9C-CBM3A-CBM3B displayed stability in pH range, 6.0-9.0 and thermostability up to 60 °C for 90 min with unfolding transition midpoint (Tm) of 65 °C. The generation of cellotetraose and other higher oligosaccharides by AtGH9C-CBM3A-CBM3B confirmed it as an endo-β-1,4-glucanase. AtGH9C activity was partially recovered by the addition of equimolar concentration of CBM3A, CBM3B or CBM3A + CBM3B by 47 %, 13 % or 50 %, respectively. Moreover, the associated CBMs imparted thermostability to the catalytic module, AtGH9C. These results showed that the physical association of AtGH9C with its associated CBMs and the cross-talk between CBMs are necessary for AtGH9C-CBM3A-CBM3B in effective cellulose catalysis.
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Affiliation(s)
- Ardhendu Mandal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Abhijeet Thakur
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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Gharechahi J, Vahidi MF, Sharifi G, Ariaeenejad S, Ding XZ, Han JL, Salekdeh GH. Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses. ENVIRONMENTAL RESEARCH 2023; 229:115925. [PMID: 37086884 DOI: 10.1016/j.envres.2023.115925] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/26/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Animal Science Research Department, Qom Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Qom, Iran
| | - Golandam Sharifi
- Department of Basic Sciences, Encyclopedia Research Center, Institute for Humanities and Cultural Studies, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), 00100, Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
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9
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Novak JK, Gardner JG. Galactomannan utilization by Cellvibrio japonicus relies on a single essential α-galactosidase encoded by the aga27A gene. Mol Microbiol 2023; 119:312-325. [PMID: 36604822 DOI: 10.1111/mmi.15024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
Plant mannans are a component of lignocellulose that can have diverse compositions in terms of its backbone and side-chain substitutions. Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides that can include mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has 10 predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential mannan-degrading components in this bacterium. The transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode carbohydrate active enzymes (CAZymes) when mannan was actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme-encoding genes in the context of mannan utilization. Growth analysis of the mutant strains found that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α-galactosidase, and mannosidase, respectively, were important for the deconstruction of galactomannan, with Aga27A being essential. Our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the complete degradation of this hemicellulose.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
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Nano-biocatalytic Systems for Cellulose de-polymerization: A Drive from Design to Applications. Top Catal 2023. [DOI: 10.1007/s11244-023-01785-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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11
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Osorio-Doblado AM, Feldmann KP, Lourenco JM, Stewart RL, Smith WB, Tedeschi LO, Fluharty FL, Callaway TR. Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology. J Anim Sci 2023; 101:skad178. [PMID: 37257501 PMCID: PMC10313095 DOI: 10.1093/jas/skad178] [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: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.
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Affiliation(s)
- A M Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - K P Feldmann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - R L Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - W B Smith
- Department Animal Science, Auburn University, Auburn, AL, USA
| | - L O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - F L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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12
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Moye J, Schenk T, Hess S. Experimental evidence for enzymatic cell wall dissolution in a microbial protoplast feeder (Orciraptor agilis, Viridiraptoridae). BMC Biol 2022; 20:267. [PMID: 36464670 PMCID: PMC9721047 DOI: 10.1186/s12915-022-01478-x] [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: 08/24/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Several protists have evolved the ability to perforate the cell walls of algae and fungi to specifically feed on their cell contents. These phagotrophic "protoplast feeders" represent an interesting mechanistic intermediate between predators and parasites and pose a number of cell biological questions. Although their fascinating feeding behaviour has been observed for the last 150 years, it is still unknown how protoplast feeders produce the well-defined and species-specific perforations in biochemically diverse cell walls. Differential expression analyses of the algivorous flagellate Orciraptor agilis (Viridiraptoridae, Cercozoa, Rhizaria) suggested the involvement of a highly expressed putative glycoside hydrolase of family GH5_5. To assess the importance of this carbohydrate-active enzyme in the feeding act of Orciraptor, we recombinantly produced its catalytic domain and studied the enzymatic activity, cellular localisation and function. RESULTS The GH5_5 catalytic domain from Orciraptor showed pronounced activity on soluble cellulose derivatives and mixed-linkage glucans, with reaction optima comparable to known GH5_5 representatives. Crystalline cellulose was not digested by the enzyme, which suggests a typical endocellulase activity. Immunocytochemistry with a polyclonal antibody raised against the GH5_5 domain revealed that the native endocellulase localises to the contact zone of Orciraptor and the algal cell wall (= perforation zone) and to intracellular granules, which were enriched during attack. Furthermore, the anti-GH5_5 antibody applied to live cells significantly reduced the feeding success of Orciraptor. The cells attacked the algae, which, however, resulted in numerous incomplete perforations. CONCLUSIONS Our experimental data from enzymatic assays, immunocytochemistry and inhibition experiments strongly suggest a key role of the GH5_5 endocellulase in cell wall dissolution by Orciraptor agilis. With that, we provide evidence that the well-defined perforations produced by protoplast feeders are caused by extracellular carbohydrate-active enzymes and made a first step towards establishing the molecular basis of a fascinating, yet poorly understood microbial feeding strategy.
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Affiliation(s)
- Jannika Moye
- grid.6190.e0000 0000 8580 3777Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Tobias Schenk
- grid.6190.e0000 0000 8580 3777Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Sebastian Hess
- grid.6190.e0000 0000 8580 3777Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
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Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A 2022; 119:e2117467119. [PMID: 36215467 PMCID: PMC9586272 DOI: 10.1073/pnas.2117467119] [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: 11/18/2022] Open
Abstract
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.
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Enteric Methane Emission, Rumen Fermentation and Microbial Profiles of Meat-Master Lambs Supplemented with Barley Fodder Sprouts. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8090434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study evaluated the effects of barley sprout on the ruminal fermentation characteristics, enteric methane emission and microbiome profiles of meat-master lambs. Twelve uncastrated lambs aged 3 months were used. They were randomly assigned to three dietary treatments: Eragrostis curvula hay as a control diet (T1), grass hay plus 25% barley sprouts (T2) and grass hay plus 50% barley sprouts (T3). Animals were fed the diet for 61 days, including 10 days of adaptation. Four animals per treatment were used to collect methane and rumen fluid. Methane emission was recorded for nine consecutive days, from day 52 to 60, using a hand-held laser detector. Rumen fluid was collected on day 61 using an esophageal stomach tube for volatile fatty acid and DNA sequencing. The sprout supplementation had significant (p < 0.05) effects on methane emission and ruminal fermentation. Significant effects on rumen fermentation were observed with regards to ammonia–nitrogen (NH3-N), acetic acid and a tendency (p < 0.0536) to increase propionic acid. Barley sprouts reduced methane gas emission, ammonia–nitrogen and the enhanced body weight of the animals. The bacteria Bacteroidota and Firmicutes were predominant among the identified phyla. In addition, there was a shift in the relative abundance of phylum among the treatments. The principal coordinate analysis showed a clear difference in microbiome among animals in T1 and those in T2 and T3. The sprout supplementation improves feed utilization efficiency by the animals. In conclusion, barley sprouts may be strategically used as a climate-smart feed resource for ruminants.
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Toward modular construction of cell-free multienzyme systems. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(21)64002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential. 3 Biotech 2022; 12:132. [PMID: 35611093 DOI: 10.1007/s13205-022-03190-7] [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: 11/24/2021] [Accepted: 04/26/2022] [Indexed: 11/01/2022] Open
Abstract
Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03190-7.
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Sinha N, Patra SK, Ghosh S. Secretome Analysis of Macrophomina phaseolina Identifies an Array of Putative Virulence Factors Responsible for Charcoal Rot Disease in Plants. Front Microbiol 2022; 13:847832. [PMID: 35479629 PMCID: PMC9037145 DOI: 10.3389/fmicb.2022.847832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
Macrophomina phaseolina is a global devastating necrotrophic fungal pathogen. It causes charcoal rot disease in more than 500 host plants including major food crops, pulse crops, fiber crops, and oil crops. Despite having the whole-genome sequence of M. phaseolina, understanding the M. phaseolina genome-based plant–pathogen interactions is limited in the absence of direct experimental proof of secretion. Thus, it is essential to understand the host–microbe interaction and the disease pathogenesis, which can ensure global agricultural crop production and security. An in silico–predicted secretome of M. phaseolina is unable to represent the actual secretome. We could identify 117 proteins present in the secretome of M. phaseolina using liquid chromatography–electrospray ionization–tandem mass spectrometry. Data are available via ProteomeXchange with identifier PXD032749. An array of putative virulence factors of M. phaseolina were identified in the present study using solid-state culture. Similar virulence factors have been reported in other plant pathogenic fungi also. Among the secretory fungal proteins with positive economic impacts, lignocellulolytic enzymes are of prime importance. Further, we validated our results by detecting the cell wall–degrading enzymes xylanase, endoglucanase, and amylase in the secretome of M. phaseolina. The present study may provide a better understanding about the necrotrophic fungi M. phaseolina, which modulate the host plant defense barriers using secretory proteins.
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Affiliation(s)
- Nilanjan Sinha
- Department of Biochemistry, University of Calcutta, Kolkata, India
| | | | - Sanjay Ghosh
- Department of Biochemistry, University of Calcutta, Kolkata, India
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Wang Y, Li L, Xia Y, Zhang T. Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data. FRONTIERS IN BIOINFORMATICS 2022; 2:813771. [PMID: 36304268 PMCID: PMC9580877 DOI: 10.3389/fbinf.2022.813771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 11/23/2022] Open
Abstract
In the era of high-throughput sequencing, genetic information that is inherently whispering hints of the microbes’ functional niches is becoming easily accessible; however, properly identifying and characterizing these genetic hints to infer the microbes’ functional niches remains a challenge. Regarding genome-centric interpretation on the specific functional niche of cellulose hydrolysis for anaerobes, often encountered in practice is a lack of confidence in predicting the anaerobes’ real cellulolytic competency based solely on abundances of the varying carbohydrate-active enzyme modules annotated or on their taxonomy affiliation. Recognition of the synergy machineries that include but not limited to the cellulosome gene clusters is equally important as the annotation of individual carbohydrate-active modules or genes. In the interpretation of complete genomes of 2,768 microbe strains whose phenotypes have been well documented, with the incorporation of an automatic recognition of synergy among the carbohydrate active elements annotated, an explicit genotype–phenotype correlation was evidenced to be feasible for cellulolytic anaerobes, and a bioinformatic pipeline was developed accordingly. This genome-centric pipeline would categorize putative cellulolytic anaerobes into six genotype groups based on differential cellulose-hydrolyzing capacity and varying synergy mechanisms. Suggested in this genotype–phenotype correlation analysis was a finer categorization of the cellulosome gene clusters: although cellulosome complexes, by their nature, could enable the assembly of a number of carbohydrate-active units, they do not certainly guarantee the formation of the cellulose–enzyme–microbe complex or the cellulose-hydrolyzing activity of the corresponding anaerobe strains, for example, the well-known Clostridium acetobutylicum strains. Also, recognized in this genotype-phenotype correlation analysis was the genetic foundation of a previously unrecognized machinery that may mediate the microbe–cellulose adhesion, to be specific, enzymes encoded by genes harboring both the surface layer homology and cellulose-binding CBM modules. Applicability of this pipeline on scalable annotation of large genome datasets was further tested with the annotation of 7,902 reference genomes downloaded from NCBI, from which 14 genomes of putative paradigm cellulose-hydrolyzing anaerobes were identified. We believe the pipeline developed in this study would be a good add as a bioinformatic tool for genome-centric interpretation of uncultivated anaerobes, specifically on their functional niche of cellulose hydrolysis.
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Affiliation(s)
- Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
| | - Yu Xia
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- *Correspondence: Tong Zhang,
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19
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Scheffer G, Rachel NM, Ng KK, Sen A, Gieg LM. Preparation and identification of carboxymethyl cellulose-degrading enzyme candidates for oilfield applications. J Biotechnol 2022; 347:18-25. [DOI: 10.1016/j.jbiotec.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/21/2022] [Accepted: 02/01/2022] [Indexed: 11/28/2022]
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20
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Ichikawa S, Ito D, Asaoka S, Abe R, Katsuo N, Ito T, Ito D, Karita S. The expression of alternative sigma-I7 factor induces the transcription of cellulosomal genes in the cellulolytic bacterium Clostridium thermocellum. Enzyme Microb Technol 2022; 156:110002. [DOI: 10.1016/j.enzmictec.2022.110002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
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21
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Schulz D, Pšenková-Profousová I, Červená B, Procter M, Neba TF, Modrý D, Petrželková KJ, Qablan MA. Occurrence and diversity of anaerobic gut fungi in wild forest elephants and buffaloes inhabiting two separated forest ecosystems in Central West Africa. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Doreen Schulz
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ilona Pšenková-Profousová
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Barbora Červená
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Miranda Procter
- Department of Veterinary Medicine, United Arab Emirates University, College of Agriculture and Veterinary Medicine, Al Ain, Abu Dhabi, United Arab Emirates; e-mail: ,
| | - Terence Fuh Neba
- World Wildlife Fund, Primate Habituation Project, Dzanga-Sangha Protected Areas, Bangui, Central African Republic; e-mail:
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic; e-mail: ,
| | - Klára J. Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; e-mail: ,
| | - Moneeb A. Qablan
- Department of Veterinary Medicine, United Arab Emirates University, College of Agriculture and Veterinary Medicine, Al Ain, Abu Dhabi, United Arab Emirates; e-mail: ,
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Blyton MDJ, Soo RM, Hugenholtz P, Moore BD. Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environ Microbiol 2021; 24:475-493. [PMID: 34863030 DOI: 10.1111/1462-2920.15858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/02/2021] [Accepted: 11/20/2021] [Indexed: 11/27/2022]
Abstract
The acquisition and maturation of the gastrointestinal microbiome is a crucial aspect of mammalian development, particularly for specialist herbivores such as the koala (Phascolarctos cinereus). Joey koalas are thought to be inoculated with microorganisms by feeding on specialized maternal faeces (pap). We found that compared to faeces, pap has higher microbial density, higher microbial evenness and a higher proportion of rare taxa, which may facilitate the establishment of those taxa in joey koalas. We show that the microbiomes of captive joey koalas were on average more similar to those of their mothers than to other koalas, indicating strong maternal inheritance of the faecal microbiome, which can lead to intergenerational gut dysbiosis when the mother is ill. Directly after pap feeding, the joey koalas' microbiomes were enriched for milk-associated bacteria including Bacteroides fragilis, suggesting a conserved role for this species across mammalian taxa. The joeys' microbiomes then changed slowly over 5 months to resemble those of adults by 1 year of age. The relative abundance of fibrolytic bacteria and genes involved in the degradation of plant cell walls also increased in the infants over this time, likely in response to an increased proportion of Eucalyptus leaves in their diets.
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Affiliation(s)
- Michaela D J Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, Qld, St Lucia, 4072, Australia
| | - Rochelle M Soo
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Qld, St Lucia, 4072, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Qld, St Lucia, 4072, Australia
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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Rubio-Portillo E, Martin-Cuadrado AB, Ramos-Esplá AÁ, Antón J. Metagenomics Unveils Posidonia oceanica "Banquettes" as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes). mSystems 2021; 6:e0086621. [PMID: 34519521 PMCID: PMC8547425 DOI: 10.1128/msystems.00866-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/25/2021] [Indexed: 11/20/2022] Open
Abstract
Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." In recent years, interest in the potential uses of these P. oceanica banquettes has increased, and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, we performed a metagenomic study to investigate the microbial community associated with P. oceanica banquettes. Our results showed that the microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria. Pseudoalteromonas was the dominant genus, followed by Alteromonas, Labrenzia, and Aquimarina. The metagenome reads were binned and assembled into 23 nearly complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota, and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges, and hydrothermal vents, indicated that banquettes have numbers of natural products and carbohydrate active enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found. These results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes. IMPORTANCE Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concern due to their impact on beach use. Furthermore, Posidonia dry material has been considered a source of traditional remedies in several areas of the Mediterranean, and a few studies have been carried out to explore pharmacological activities of Posidonia extracts. The work presented here provides the first characterization of the microbiome associated with Posidonia banquettes. We carried out a metagenomic analysis together with an in-depth comparison of the banquette metagenome with 60 published metagenomes from different environments. This comparative analysis has unveiled the potential that Posidonia banquettes have for the synthesis of natural products, both in abundance (only surpassed by marine biofilms) and novelty. These products include mainly nonribosomal peptides and carbohydrate active enzymes. Thus, the interest of our work lies in the interest of Posidonia "waste" material as a source of new bioactive compounds and CAZymes.
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Affiliation(s)
- Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | | | - Alfonso Ángel Ramos-Esplá
- Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
- CIMAR, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
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Bhardwaj N, Kumar B, Agrawal K, Verma P. Current perspective on production and applications of microbial cellulases: a review. BIORESOUR BIOPROCESS 2021; 8:95. [PMID: 38650192 PMCID: PMC10992179 DOI: 10.1186/s40643-021-00447-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/21/2021] [Indexed: 12/27/2022] Open
Abstract
The potential of cellulolytic enzymes has been widely studied and explored for bioconversion processes and plays a key role in various industrial applications. Cellulase, a key enzyme for cellulose-rich waste feedstock-based biorefinery, has increasing demand in various industries, e.g., paper and pulp, juice clarification, etc. Also, there has been constant progress in developing new strategies to enhance its production, such as the application of waste feedstock as the substrate for the production of individual or enzyme cocktails, process parameters control, and genetic manipulations for enzyme production with enhanced yield, efficiency, and specificity. Further, an insight into immobilization techniques has also been presented for improved reusability of cellulase, a critical factor that controls the cost of the enzyme at an industrial scale. In addition, the review also gives an insight into the status of the significant application of cellulase in the industrial sector, with its techno-economic analysis for future applications. The present review gives a complete overview of current perspectives on the production of microbial cellulases as a promising tool to develop a sustainable and greener concept for industrial applications.
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Affiliation(s)
- Nisha Bhardwaj
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
- Department of Chemical Engineering, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai, Maharashtra, 400019, India
| | - Bikash Kumar
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Komal Agrawal
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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Kallscheuer N, Jogler C. The bacterial phylum Planctomycetes as novel source for bioactive small molecules. Biotechnol Adv 2021; 53:107818. [PMID: 34537319 DOI: 10.1016/j.biotechadv.2021.107818] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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Ellis LD, Rorrer NA, Sullivan KP, Otto M, McGeehan JE, Román-Leshkov Y, Wierckx N, Beckham GT. Chemical and biological catalysis for plastics recycling and upcycling. Nat Catal 2021. [DOI: 10.1038/s41929-021-00648-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Xie F, Jin W, Si H, Yuan Y, Tao Y, Liu J, Wang X, Yang C, Li Q, Yan X, Lin L, Jiang Q, Zhang L, Guo C, Greening C, Heller R, Guan LL, Pope PB, Tan Z, Zhu W, Wang M, Qiu Q, Li Z, Mao S. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. MICROBIOME 2021; 9:137. [PMID: 34118976 PMCID: PMC8199421 DOI: 10.1186/s40168-021-01078-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/15/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species. RESULTS Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future. CONCLUSIONS Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. Video abstract.
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Affiliation(s)
- Fei Xie
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wei Jin
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Ye Tao
- Shanghai BIOZERON Biotechnology Company Ltd, Shanghai, China
| | - Junhua Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxu Wang
- Department of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chengjian Yang
- Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Qiushuang Li
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xiaoting Yan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Limei Lin
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qian Jiang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lei Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Changzheng Guo
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chris Greening
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Australia
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Min Wang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.
- Department of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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Yan Z, Xu Q, Hsu WH, Esser SS, Ayala J, Hou R, Yao Y, Jiang D, Yuan S, Wang H. Consuming Different Structural Parts of Bamboo Induce Gut Microbiome Changes in Captive Giant Pandas. Curr Microbiol 2021; 78:2998-3009. [PMID: 34109451 PMCID: PMC8289812 DOI: 10.1007/s00284-021-02503-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/19/2021] [Indexed: 01/05/2023]
Abstract
Giant pandas consume different structural parts of bamboo (shoots, leaves and culms) during different seasons. Previous research showed different bamboo parts have varying nutritional content and that a long-term diet consisting of a single part of bamboo resulted in remarkable metabolic changes within captive giant pandas. However, the effects on the gut microbiome of giant pandas, as a result of a single bamboo part diet, have not been investigated. Here, we evaluated the changes in gut microbial communities based on single bamboo part diets and their potential implications by using 16S rRNA gene-based amplicon sequencing and metagenome shotgun sequencing. We found that the composition and function of the gut microbiome from captive giant pandas fed exclusively culms were significantly different from that of individuals fed shoots or leaves. During the culm feeding period, the gut microbiome showed strongest digestive capabilities for cellulose, hemicellulose and starch, and had the highest potential abilities for the biosynthesis of bile acids, fatty acids and amino acids. This suggests the microbiome aids in breaking down culm, which is more difficult for giant pandas to digest, as a means to compensate for the nutrient poor content of the culm. Genes related to fatty acid metabolism and tricarboxylic acid cycle enzymes were more abundant during the leaf stage diet than that in the shoot and culm stages. Thus, the microbiome may help giant pandas, which typically have low lipase levels, with fat digestion. These results illustrate that adaptive changes in the gut microbiome community and function may be an important mechanism to aid giant panda digestion when consuming different structural parts of bamboo.
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Affiliation(s)
- Zheng Yan
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, Nanchong, 637009, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Walter H Hsu
- Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | | | - James Ayala
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Dandan Jiang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Shibin Yuan
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, Nanchong, 637009, China.
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.
- Sichuan Academy of Giant Panda, Chengdu, 610081, China.
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Unconventional β-Glucosidases: A Promising Biocatalyst for Industrial Biotechnology. Appl Biochem Biotechnol 2021; 193:2993-3016. [PMID: 33871765 DOI: 10.1007/s12010-021-03568-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
β-Glucosidases primarily catalyze removal of terminal glucosyl residues from a variety of glucoconjugates and also perform transglycosylation and reverse hydrolysis. These catalytic properties can be readily exploited for degradation of lignocellulosic biomass as well as for pharmaceutical, food and flavor industries. β-Glucosidases have been either isolated in the native form from the producer organism or recombinantly expressed and gaged for their biochemical properties and substrate specificities. Although almond and Aspergillus niger have been instantly recognizable sources of β-glucosidases utilized for various applications, an intricate pool of novel β-glucosidases from different sources can provide their potent replacements. Moreover, one can envisage the better efficacy of these novel candidates in biofuel and biorefinery industries facilitating efficient degradation of biomass. This article reviews properties of the novel β-glucosidases such as glucose tolerance and activation, substrate specificity, and thermostability which can be useful for their applications in lignocellulose degradation, food industry, and pharmaceutical industry in comparison with the β-glucosidases from the conventional sources. Such β-glucosidases have potential for encouraging white biotechnology.
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Oh EJ, Jin YS. Engineering of Saccharomyces cerevisiae for efficient fermentation of cellulose. FEMS Yeast Res 2021; 20:5698803. [PMID: 31917414 DOI: 10.1093/femsyr/foz089] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/08/2020] [Indexed: 12/18/2022] Open
Abstract
Conversion of lignocellulosic biomass to biofuels using microbial fermentation is an attractive option to substitute petroleum-based production economically and sustainably. The substantial efforts to design yeast strains for biomass hydrolysis have led to industrially applicable biological routes. Saccharomyces cerevisiae is a robust microbial platform widely used in biofuel production, based on its amenability to systems and synthetic biology tools. The critical challenges for the efficient microbial conversion of lignocellulosic biomass by engineered S. cerevisiae include heterologous expression of cellulolytic enzymes, co-fermentation of hexose and pentose sugars, and robustness against various stresses. Scientists developed many engineering strategies for cellulolytic S. cerevisiae strains, bringing the application of consolidated bioprocess at an industrial scale. Recent advances in the development and implementation of engineered yeast strains capable of assimilating lignocellulose will be reviewed.
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Affiliation(s)
- Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, 4001 Discovery Dr., CO 80303, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, 905 S. Goodwin Ave., IL 61801, USA.,1105 Carl R. Woese Institute for Genomic Biology, 1206 W. Gregory Dr. Urbana, IL 61801. USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr. Urbana, IL 61801, USA
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Bao Y, Dolfing J, Guo Z, Chen R, Wu M, Li Z, Lin X, Feng Y. Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils. MICROBIOME 2021; 9:84. [PMID: 33827695 PMCID: PMC8028251 DOI: 10.1186/s40168-021-01032-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria, one of the most widely distributed bacterial phyla in soils, are known for their ability to degrade plant residues in vitro. However, their in situ importance and specific activity across contrasting ecological environments are not known. Here, we conducted three field experiments with buried straw in combination with microcosm experiments with 13C-straw in paddy soils under different soil fertility levels to reveal the ecophysiological roles of Actinobacteria in plant residue decomposition. RESULTS While accounting for only 4.6% of the total bacterial abundance, the Actinobacteria encoded 16% of total abundance of carbohydrate-active enzymes (CAZymes). The taxonomic and functional compositions of the Actinobacteria were, surprisingly, relatively stable during straw decomposition. Slopes of linear regression models between straw chemical composition and Actinobacterial traits were flatter than those for other taxonomic groups at both local and regional scales due to holding genes encoding for full set of CAZymes, nitrogenases, and antibiotic synthetases. Ecological co-occurrence network and 13C-based metagenomic analyses both indicated that their importance for straw degradation increased in less fertile soils, as both links between Actinobacteria and other community members and relative abundances of their functional genes increased with decreasing soil fertility. CONCLUSIONS This study provided DNA-based evidence that non-dominant Actinobacteria plays a key ecophysiological role in plant residue decomposition as their members possess high proportions of CAZymes and as a group maintain a relatively stable presence during plant residue decomposition both in terms of taxonomic composition and functional roles. Their importance for decomposition was more pronounced in less fertile soils where their possession functional genes and interspecies interactions stood out more. Our work provides new ecophysiological angles for the understanding of the importance of Actinobacteria in global carbon cycling. Video abstract.
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Affiliation(s)
- Yuanyuan Bao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Jan Dolfing
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Zhiying Guo
- Soil Subcenter of Chinese Ecological Research Network, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
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Gharechahi J, Vahidi MF, Bahram M, Han JL, Ding XZ, Salekdeh GH. Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen. THE ISME JOURNAL 2021; 15:1108-1120. [PMID: 33262428 PMCID: PMC8114923 DOI: 10.1038/s41396-020-00837-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/08/2023]
Abstract
Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.
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Affiliation(s)
- Javad Gharechahi
- grid.411521.20000 0000 9975 294XHuman Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Mohammad Bahram
- grid.6341.00000 0000 8578 2742Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden ,grid.10939.320000 0001 0943 7661Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
| | - Jian-Lin Han
- grid.419369.00000 0000 9378 4481Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100 Nairobi, Kenya ,grid.410727.70000 0001 0526 1937CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193 Beijing, China
| | - Xue-Zhi Ding
- grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), 730050 Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran ,grid.1004.50000 0001 2158 5405Department of Molecular Sciences, Macquarie University, North Ryde, NSW Australia
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A Systemic Review on Microalgal Peptides: Bioprocess and Sustainable Applications. SUSTAINABILITY 2021. [DOI: 10.3390/su13063262] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nowadays, microalgal research is predominantly centered on an industrial scale. In general, multipotent bioactive peptides are the advantages over focal points over utilitarian nourishment as well as nutraceuticals. Microalgal peptides are now profoundly connected with biological properties rather than nutritive. Numerous techniques are employed to purify active peptides from algal protein using enzymatic hydrolysis; it is broadly used for numerous favorable circumstances. There is a chance to utilize microalgal peptides for human well-being as nutritive enhancements. This exhaustive survey details the utilization of microalgal peptides as antioxidant, anti-cancerous, anti-hypersensitive, anti-atherosclerotic, and nutritional functional foods. It is also exploring the novel technologies for the production of active peptides, for instance, the use of algal peptides as food for human health discovered restrictions, where peptides are sensitive to hydrolysis protease degradation. This review emphasizes the issue of active peptides in gastrointestinal transit, which has to be solved in the future, and prompt impacts.
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Tamayo-Ordóñez MC, Contreras-Esquivel JC, Ayil-Gutiérrez BA, De la Cruz-Arguijo EA, Tamayo-Ordóñez FA, Ríos-González LJ, Tamayo-Ordóñez YJ. Interspecific evolutionary relationships of alpha-glucuronidase in the genus Aspergillus. Fungal Biol 2021; 125:560-575. [PMID: 34140152 DOI: 10.1016/j.funbio.2021.02.005] [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: 07/13/2020] [Revised: 02/05/2021] [Accepted: 02/21/2021] [Indexed: 12/15/2022]
Abstract
The increased availability and production of lignocellulosic agroindustrial wastes has originated proposals for their use as raw material to obtain biofuels (ethanol and biodiesel) or derived products. However, for biomass generated from lignocellulosic residues to be successfully degraded, in most cases it requires a physical (thermal), chemical, or enzymatic pretreatment before the application of microbial or enzymatic fermentation technologies (biocatalysis). In the context of enzymatic technologies, fungi have demonstrated to produce enzymes capable of degrading polysaccharides like cellulose, hemicelluloses and pectin. Because of this ability for degrading lignocellulosic material, researchers are making efforts to isolate and identify fungal enzymes that could have a better activity for the degradation of plant cell walls and agroindustrial biomass. We performed an in silico analysis of alpha-glucoronidase in 82 accessions of the genus Aspergillus. The constructed dendrograms of amino acid sequences defined the formation of 6 groups (I, II, III, IV, V, and VI), which demonstrates the high diversity of the enzyme. Despite this ample divergence between enzyme groups, our 3D structure modeling showed both conservation and differences in amino acid residues participating in enzyme-substrate binding, which indicates the possibility that some enzymes are functionally specialized for the specific degradation of a substrate depending on the genetics of each species in the genus and the condition of the habitat where they evolved. The identification of alpha-glucuronidase isoenzymes would allow future use of genetic engineering and biocatalysis technologies aimed at specific production of the enzyme for its use in biotransformation.
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Affiliation(s)
- M C Tamayo-Ordóñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cárdenas Valdez S/N, República, 25280, Saltillo, Coah, Mexico
| | - J C Contreras-Esquivel
- Laboratorio de Glicobiotecnologia Aplicada, Departamento de Ciencia y Tecnología de Alimentos, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing. J. Cárdenas Valdez S/N, República, 25280, Saltillo, Coah, Mexico
| | - B A Ayil-Gutiérrez
- CONACYT- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnologia Vegetal. Blvd. del Maestro, s/n, Esq. Elías Piña, Reynosa, 88710, Mexico
| | - E A De la Cruz-Arguijo
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro, s/n, Esq. Elías Piña, Reynosa, 88710, Mexico
| | - F A Tamayo-Ordóñez
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 No. 4 por Av. Concordia, Campus Principal, 24180, Ciudad del Carmen, Campeche, Mexico
| | - L J Ríos-González
- Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing Cárdenas Valdez S/N, República, 25280, Saltillo, Coah, Mexico
| | - Y J Tamayo-Ordóñez
- Estancia Posdoctoral Nacional-CONACyT, Posgrado en Ciencia y Tecnología de Alimentos, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cardenas Valdez S/N, República, 25280, Saltillo, Coah, Mexico.
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Wu Z, Nguyen D, Lam TYC, Zhuang H, Shrestha S, Raskin L, Khanal SK, Lee PH. Synergistic association between cytochrome bd-encoded Proteiniphilum and reactive oxygen species (ROS)-scavenging methanogens in microaerobic-anaerobic digestion of lignocellulosic biomass. WATER RESEARCH 2021; 190:116721. [PMID: 33326896 DOI: 10.1016/j.watres.2020.116721] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Intermittent (every other day) microaerobic [picomolar oxygen by oxidation-reduction potential (ORP) set at +25 mV above anaerobic baseline] digestion of lignocellulosic biomass showed higher digestibility and better stability at a high organic loading rate (OLR) of 5 g volatile solids (VS)/L/d than that under strict anaerobic conditions. However, the microbial mechanisms supporting the delicate balance under microaeration remain underexplored. On the basis of our previous findings that microbial communities in replicate experiments were dominated by strains of the genus Proteiniphilum but contained diverse taxa of methanogenic archaea, here we recovered related genomes and reconstructed the putative metabolic pathways using a genome-centric metagenomic approach. The highly enriched Proteiniphilum strains were identified as efficient cellulolytic facultative bacterium, which directly degraded lignocellulose to carbon dioxide, formate, and acetate via aerobic respiration and anaerobic fermentation, alternatively. Moreover, high oxygen affinity cytochromes, bd-type terminal oxidases, in Proteiniphilum strains were found to be closely associated with such picomolar oxygen conditions, which has long been overlooked in anaerobic digestion. Furthermore, hydrogenotrophic methanogenesis was the prevalent pathway for methane production while Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the dominant methanogens in the replicate experiments. Importantly, the two functional groups, namely cellulolytic facultative Proteiniphilum strains and methanogens, encoded various antioxidant enzymes. Energy-dependent reactive oxygen species (ROS) scavengers (superoxide reductase (SOR) and rubrerythrin (rbr) were ubiquitously present in different methanogenic taxa in response to replicate-specific ORP levels (-470, -450 and -475 mV). Collectively, cytochrome bd oxidase and ROS defenders may play roles in improving the digestibility and stability observed in intermittent microaerobic digestion.
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Affiliation(s)
- Zhuoying Wu
- Department of Civil and Environmental Engineering, Imperial College, London, The United Kingdom
| | - Duc Nguyen
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Theo Y C Lam
- Department of Civil and Environmental Engineering, Imperial College, London, The United Kingdom; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Huichuan Zhuang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Shilva Shrestha
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College, London, The United Kingdom.
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Dubey NC, Tripathi BP. Nature Inspired Multienzyme Immobilization: Strategies and Concepts. ACS APPLIED BIO MATERIALS 2021; 4:1077-1114. [PMID: 35014469 DOI: 10.1021/acsabm.0c01293] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.
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Affiliation(s)
- Nidhi C Dubey
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science and Engineering, Indian institute of Technology Delhi, New Delhi 110016, India
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Bacterial valorization of pulp and paper industry process streams and waste. Appl Microbiol Biotechnol 2021; 105:1345-1363. [PMID: 33481067 DOI: 10.1007/s00253-021-11107-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
The pulp and paper industry is a major source of lignocellulose-containing streams. The components of lignocellulose material are lignin, hemicellulose, and cellulose that may be hydrolyzed into their smaller components and used as feedstocks for valorization efforts. Much of this material is contained in underutilized streams and waste products, such as black liquor, pulp and paper sludge, and wastewater. Bacterial fermentation strategies have suitable potential to upgrade lignocellulosic biomass contained in these streams to value-added chemicals. Bacterial conversion allows for a sustainable and economically feasible approach to valorizing these streams, which can bolster and expand applications of the pulp and paper industry. This review discusses the composition of pulp and paper streams, bacterial isolates from process streams that can be used for lignocellulose biotransformations, and technological approaches for improving valorization efforts. KEY POINTS: • Reviews the conversion of pulp and paper industry waste by bacterial isolates. • Metabolic pathways for the breakdown of lignocellulose components. • Methods for isolating bacteria, determining value-added products, and increasing product yields.
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Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. mBio 2021; 12:mBio.03099-20. [PMID: 33402535 PMCID: PMC8545098 DOI: 10.1128/mbio.03099-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.
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Ye M, Ye Y, Du Z, Chen G. Cell-surface engineering of yeasts for whole-cell biocatalysts. Bioprocess Biosyst Eng 2021; 44:1003-1019. [PMID: 33389168 DOI: 10.1007/s00449-020-02484-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/16/2020] [Indexed: 01/23/2023]
Abstract
Due to the unique advantages comparing with traditional free enzymes and chemical catalysis, whole-cell biocatalysts have been widely used to catalyze reactions effectively, simply and environment friendly. Cell-surface display technology provides a novel and effective approach for improved whole-cell biocatalysts expressing heterologous enzymes on the cell surface. They can overcome the substrate transport limitation of the intracellular expression and provide the enzymes with enhanced properties. Among all the host surface-displaying microorganisms, yeast is ideally suitable for constructing whole cell-surface-displaying biocatalyst, because of the large cell size, the generally regarded as safe (GRAS) status, and the perfect post-translational processing of secreted proteins. Yeast cell-surface display system has been a promising and powerful method for development of novel and improved engineered biocatalysts. In this review, the characterization and principles of yeast cell-surface display and the applications of yeast cell-surface display in engineered whole-cell biocatalysts as well as the improvement of the enzyme efficiency are summarized and discussed.
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Affiliation(s)
- Mengqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Yuqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Zongjun Du
- Marine College, Shandong University, Weihai, 264209, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guanjun Chen
- Marine College, Shandong University, Weihai, 264209, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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40
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Ogonda LA, Saumonneau A, Dion M, Muge EK, Wamalwa BM, Mulaa FJ, Tellier C. Characterization and engineering of two new GH9 and GH48 cellulases from a Bacillus pumilus isolated from Lake Bogoria. Biotechnol Lett 2021; 43:691-700. [PMID: 33386499 DOI: 10.1007/s10529-020-03056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To search for new alkaliphilic cellulases and to improve their efficiency on crystalline cellulose through molecular engineering RESULTS: Two novel cellulases, BpGH9 and BpGH48, from a Bacillus pumilus strain were identified, cloned and biochemically characterized. BpGH9 is a modular endocellulase belonging to the glycoside hydrolase 9 family (GH9), which contains a catalytic module (GH) and a carbohydrate-binding module belonging to class 3 and subclass c (CBM3c). This enzyme is extremely tolerant to high alkali pH and remains significantly active at pH 10. BpGH48 is an exocellulase, belonging to the glycoside hydrolase 48 family (GH48) and acts on the reducing end of oligo-β1,4 glucanes. A truncated form of BpGH9 and a chimeric fusion with an additional CBM3a module was constructed. The deletion of the CBM3c module results in a significant decline in the catalytic activity. However, fusion of CBM3a, although in a non native position, enhanced the activity of BpGH9 on crystalline cellulose. CONCLUSIONS A new alkaliphilic endocellulase BpGH9, was cloned and engineered as a fusion protein (CBM3a-BpGH9), which led to an improved activity on crystalline cellulose.
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Affiliation(s)
- Lydia A Ogonda
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France.,Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya.,Department of Medical Biochemistry, School of Medicine, Masinde Muliro University of Science and Technology, P.O BOX 190-50100, Kakamega, Kenya
| | - Amélie Saumonneau
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France
| | - Michel Dion
- Université de Nantes, IRS2, 44000, Nantes, France
| | - Edward K Muge
- Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Benson M Wamalwa
- Department of Chemistry, School of Physical Sciences, College of Biological and Physical Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Francis J Mulaa
- Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Charles Tellier
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France.
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Abstract
Cellulosomes are elaborate multienzyme complexes capable of efficiently deconstructing lignocellulosic substrates, produced by cellulolytic anaerobic microorganisms, colonizing a large variety of ecological niches. These macromolecular structures have a modular architecture and are composed of two main elements: the cohesin-bearing scaffoldins, which are non-catalytic structural proteins, and the various dockerin-bearing enzymes that tenaciously bind to the scaffoldins. Cellulosome assembly is mediated by strong and highly specific interactions between the cohesin modules, present in the scaffoldins, and the dockerin modules, present in the catalytic units. Cellulosomal architecture and composition varies between species and can even change within the same organism. These differences seem to be largely influenced by external factors, including the nature of the available carbon-source. Even though cellulosome producing organisms are relatively few, the development of new genomic and proteomic technologies has allowed the identification of cellulosomal components in many archea, bacteria and even some primitive eukaryotes. This reflects the importance of this cellulolytic strategy and suggests that cohesin-dockerin interactions could be involved in other non-cellulolytic processes. Due to their building-block nature and highly cellulolytic capabilities, cellulosomes hold many potential biotechnological applications, such as the conversion of lignocellulosic biomass in the production of biofuels or the development of affinity based technologies.
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Affiliation(s)
- Victor D Alves
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Carlos M G A Fontes
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal
| | - Pedro Bule
- CIISA, Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal.
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Gharechahi J, Vahidi MF, Ding XZ, Han JL, Salekdeh GH. Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in cattle rumen. FEMS Microbiol Ecol 2020; 96:5822058. [PMID: 32304321 DOI: 10.1093/femsec/fiaa069] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/15/2020] [Indexed: 01/22/2023] Open
Abstract
The attachment of rumen microbes to feed particles is critical to feed fermentation, degradation and digestion. However, the extent to which the physicochemical properties of feeds influence the colonization by rumen microbes is still unclear. We hypothesized that rumen microbial communities may have differential preferences for attachments to feeds with varying lignocellulose properties. To this end, the structure and composition of microbial communities attached to six common forages with different lignocellulosic compositions were analyzed following in situ rumen incubation in male Taleshi cattle. The results showed that differences in lignocellulosic compositions significantly affected the inter-sample diversity of forage-attached microbial communities in the first 24 h of rumen incubation, during which the highest dry matter degradation was achieved. However, extension of the incubation to 96 h resulted in the development of more uniform microbial communities across the forages. Fibrobacteres were significantly overrepresented in the bacterial communities attached to the forages with the highest neutral detergent fiber contents. Ruminococcus tended to attach to the forages with low acid detergent lignin contents. The extent of dry matter fermentation was significantly correlated with the populations of Fibrobacteraceae, unclassified Bacteroidales, Ruminococcaceae and Spirochaetacea. Our findings suggested that lignocellulosic compositions, and more specifically the cellulose components, significantly affected the microbial attachment to and thus the final digestion of the forages.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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Kumar K, Singh S, Sharma K, Goyal A. Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405. J Mol Graph Model 2020; 103:107808. [PMID: 33248343 DOI: 10.1016/j.jmgm.2020.107808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022]
Abstract
The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (α/α)6 barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed β-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% α-helices and 11.0% β-strands which was validated through circular dichroism analysis that showed the presence of 42.6% α-helices and 14.5% β-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50 ± 0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.
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Affiliation(s)
- Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shubha Singh
- Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, Delhi, 110078, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Laboratory of Small Molecules & Macro Molecular Crystallography, Department of Bioengineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Cheawchanlertfa P, Sutheeworapong S, Jenjaroenpun P, Wongsurawat T, Nookaew I, Cheevadhanarak S, Kosugi A, Pason P, Waeonukul R, Ratanakhanokchai K, Tachaapaikoon C. Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes. PeerJ 2020; 8:e10343. [PMID: 33240652 PMCID: PMC7676355 DOI: 10.7717/peerj.10343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/20/2020] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. METHODS A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. RESULTS Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).
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Affiliation(s)
- Pattsarun Cheawchanlertfa
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
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Lupinus albus γ-Conglutin, a Protein Structurally Related to GH12 Xyloglucan-Specific Endo-Glucanase Inhibitor Proteins (XEGIPs), Shows Inhibitory Activity against GH2 β-Mannosidase. Int J Mol Sci 2020; 21:ijms21197305. [PMID: 33022933 PMCID: PMC7583008 DOI: 10.3390/ijms21197305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
γ-conglutin (γC) is a major protein of Lupinus albus seeds, but its function is still unknown. It shares high structural similarity with xyloglucan-specific endo-glucanase inhibitor proteins (XEGIPs) and, to a lesser extent, with Triticum aestivum endoxylanase inhibitors (TAXI-I), active against fungal glycoside hydrolases GH12 and GH11, respectively. However, γC lacks both these inhibitory activities. Since β-galactomannans are major components of the cell walls of endosperm in several legume plants, we tested the inhibitory activity of γC against a GH2 β-mannosidase (EC 3.2.1.25). γC was actually able to inhibit the enzyme, and this effect was enhanced by the presence of zinc ions. The stoichiometry of the γC/enzyme interaction was 1:1, and the calculated Ki was 1.55 μM. To obtain further insights into the interaction between γC and β-mannosidase, an in silico structural bioinformatic approach was followed, including some docking analyses. By and large, this work describes experimental findings that highlight new scenarios for understanding the natural role of γC. Although structural predictions can leave space for speculative interpretations, the full complexity of the data reported in this work allows one to hypothesize mechanisms of action for the basis of inhibition. At least two mechanisms seem plausible, both involving lupin-γC-peculiar structures.
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Whole grain cereal fibers and their support of the gut commensal Clostridia for health. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.bcdf.2020.100245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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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48
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Eibinger M, Ganner T, Plank H, Nidetzky B. A Biological Nanomachine at Work: Watching the Cellulosome Degrade Crystalline Cellulose. ACS CENTRAL SCIENCE 2020; 6:739-746. [PMID: 32490190 PMCID: PMC7256933 DOI: 10.1021/acscentsci.0c00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 05/14/2023]
Abstract
The cellulosome is a supramolecular multienzymatic protein complex that functions as a biological nanomachine of cellulosic biomass degradation. How the megadalton-size cellulosome adapts to a solid substrate is central to its mechanism of action and is also key for its efficient use in bioconversion applications. We report time-lapse visualization of crystalline cellulose degradation by individual cellulosomes from Clostridium thermocellum by atomic force microscopy. Upon binding to cellulose, the cellulosomes switch to elongated, even filamentous shapes and morph these dynamically at below 1 min time scale according to requirements of the substrate surface under attack. Compared with noncomplexed cellulases that peel off material while sliding along crystalline cellulose surfaces, the cellulosomes remain bound locally for minutes and remove the material lying underneath. The consequent roughening up of the surface leads to an efficient deconstruction of cellulose nanocrystals both from the ends and through fissions within. Distinct modes of cellulose nanocrystal deconstruction by nature's major cellulase systems are thus revealed.
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Affiliation(s)
- Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Thomas Ganner
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- Institute
for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz
Centre of Electron Microscopy, Steyrergasse 17, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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49
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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50
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Isolation and subunit compositions of the xylanosome complexes produced by Cellulosimicrobium species. Enzyme Microb Technol 2020; 133:109445. [PMID: 31874683 DOI: 10.1016/j.enzmictec.2019.109445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/28/2019] [Accepted: 10/06/2019] [Indexed: 01/10/2023]
Abstract
Cellulosimicrobium cellulans, which is type species of the genus Cellulosimicrobium, produces xylanase predominant nanoscale multienzyme complexes, i.e., xylanosomes, when grown on water-insoluble polysaccharides. Here, we report on the isolation of similar multienzyme complexes (MECs) produced by two other species in genus Cellulosimicrobium (Cellulosimicrobium funkei and Cellulosimicrobium terreum). Functional studies and subunit structure identifications using genomic sequencing and proteomic techniques were also performed. When compared with the xylanosomes produced by C. cellulans F16, the isolated MECs showed a larger particle size and shared at least three conserved multidomain proteins. In addition, they also exhibited different enzymatic activities and subunit compositions, which indicates diverse capability and strategies in degrading hemicelluloses.
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