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Carbonaro M, Aulitto M, Mazurkewich S, Fraia AD, Contursi P, Limauro D, Larsbrink J, Fiorentino G. Genomic mining of Geobacillus stearothermophilus GF16 for xylose production from hemicellulose-rich biomasses using secreted enzymes. N Biotechnol 2024; 82:14-24. [PMID: 38688408 DOI: 10.1016/j.nbt.2024.04.002] [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: 03/15/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The valorization of lignocellulosic biomass, derived from various bio-waste materials, has received considerable attention as a sustainable approach to improve production chains while reducing environmental impact. Microbial enzymes have emerged as key players in the degradation of polysaccharides, offering versatile applications in biotechnology and industry. Among these enzymes, glycoside hydrolases (GHs) play a central role. Xylanases, in particular, are used in a wide range of applications and are essential for the production of xylose, which can be fermented into bioethanol or find use in many other industries. Currently, fungal secretomes dominate as the main reservoir of lignocellulolytic enzymes, but thermophilic microorganisms offer notable advantages in terms of enzyme stability and production efficiency. Here we present the genomic characterization of Geobacillus stearothermophilus GF16 to identify genes encoding putative enzymes involved in lignocellulose degradation. Thermostable GHs secreted by G. stearothermophilus GF16 were investigated and found to be active on different natural polysaccharides and synthetic substrates, revealing an array of inducible GH activities. In particular, the concentrated secretome possesses significant thermostable xylanase and β-xylosidase activities (5 ×103 U/L and 1.7 ×105 U/L, respectively), highlighting its potential for application in biomass valorization. We assessed the hemicellulose hydrolysis capabilities of various agri-food wastes using the concentrated secretome of the strain cultivated on xylan. An impressive 300-fold increase in xylose release compared to a commercially available cocktail was obtained with the secretome, underscoring the remarkable efficacy of this approach.
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Affiliation(s)
- Miriam Carbonaro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Alessia Di Fraia
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Patrizia Contursi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Danila Limauro
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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2
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Zhai Y, Zhang L, Yao S, Zhou X, Jiang K. Green Process for Producing Xylooligosaccharides by Using Sequential Auto-hydrolysis and Xylanase Hydrolysis. Appl Biochem Biotechnol 2024; 196:5317-5333. [PMID: 38157156 DOI: 10.1007/s12010-023-04800-7] [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] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Xylooligosaccharides (XOS), as prebiotic oligomers, are increasingly receiving attention as high value-added products produced from lignocellulosic biomass. Although the XOS contains a series of different degrees of polymerization (DP) of xylose units, DP 2 and 3 (xylobiose (X2) and xylotriose (X3)) are regarded as the main active components in food and pharmaceutical fields. Therefore, in the study, in order to achieve the maximum production of XOS with the desired DP, a combination strategy of sequential auto-hydrolysis and xylanase hydrolysis was developed with corncob as raw material. The evidences showed that the hemicellulosic xylan could be effectively decomposed into various higher DP saccharides (> 4), which were dissolved into the auto-hydrolysate; sequentially, the soluble saccharides could be rapidly hydrolyzed into XOS with desired DP by xylanase hydrolysis. Finally, a maximum XOS yield of 56.3% was achieved and the ratio of (X2 + X3)/XOS was over 80%; meanwhile, the by-products could be controlled at lower levels. Overall, this study provides solid data that support the selective and precise preparation of XOS from corncob, vigorously promoting the application of XOS as functional sugar products.
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Affiliation(s)
- Yujie Zhai
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, School of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Lei Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Shuangquan Yao
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, School of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Xin Zhou
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.
| | - Kankan Jiang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China.
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3
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Akram F, Fatima T, Ibrar R, Shabbir I, Shah FI, Haq IU. Trends in the development and current perspective of thermostable bacterial hemicellulases with their industrial endeavors: A review. Int J Biol Macromol 2024; 265:130993. [PMID: 38508567 DOI: 10.1016/j.ijbiomac.2024.130993] [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: 07/15/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Hemicellulases are enzymes that hydrolyze hemicelluloses, common polysaccharides in nature. Thermophilic hemicellulases, derived from microbial strains, are extensively studied as natural biofuel sources due to the complex structure of hemicelluloses. Recent research aims to elucidate the catalytic principles, mechanisms and specificity of hemicellulases through investigations into their high-temperature stability and structural features, which have applications in biotechnology and industry. This review article targets to serve as a comprehensive resource, highlighting the significant progress in the field and emphasizing the vital role of thermophilic hemicellulases in eco-friendly catalysis. The primary goal is to improve the reliability of hemicellulase enzymes obtained from thermophilic bacterial strains. Additionally, with their ability to break down lignocellulosic materials, hemicellulases hold immense potential for biofuel production. Despite their potential, the commercial viability is hindered by their high enzyme costs, necessitating the development of efficient bioprocesses involving waste pretreatment with microbial consortia to overcome this challenge.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan.
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ifrah Shabbir
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | | | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
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4
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Zhang J, Wang X, Wang HT, Qiao Z, Yao T, Xie M, Urbanowicz BR, Zeng W, Jawdy SS, Gunter LE, Yang X, Czarnecki O, Regan S, Seguin A, Rottmann W, Winkeler KA, Sykes R, Lipzen A, Daum C, Barry K, Lu MZ, Tuskan GA, Muchero W, Chen JG. Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus. PLANT PHYSIOLOGY 2023; 194:243-257. [PMID: 37399189 PMCID: PMC10762510 DOI: 10.1093/plphys/kiad377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan but the regulatory mechanism of RWAs is not fully understood. In this study, we demonstrate that overexpression of a Populus trichocarpa PtRWA-C gene increases the level of xylan acetylation and increases the lignin content and S/G ratio, ultimately yielding poplar woody biomass with reduced saccharification efficiency. Furthermore, through gene coexpression network and expression quantitative trait loci (eQTL) analysis, we found that PtRWA-C was regulated not only by the secondary cell wall hierarchical regulatory network but also by an AP2 family transcription factor HARDY (HRD). Specifically, HRD activates PtRWA-C expression by directly binding to the PtRWA-C promoter, which is also the cis-eQTL for PtRWA-C. Taken together, our findings provide insights into the functional roles of PtRWA-C in xylan acetylation and consequently saccharification and shed light on synthetic biology approaches to manipulate this gene and alter cell wall properties. These findings have substantial implications for genetic engineering of woody species, which could be used as a sustainable source of biofuels, valuable biochemicals, and biomaterials.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaqin Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Hsin-Tzu Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Zhenzhen Qiao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wei Zeng
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Olaf Czarnecki
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sharon Regan
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Armand Seguin
- Laurentian Forestry Center, Natural Resources Canada, Québec, Quebec G1V 4C7, Canada
| | | | | | - Robert Sykes
- Bioenergy Science and Technology, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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5
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Chen B, Zhou Y, Duan L, Gong X, Liu X, Pan K, Zeng D, Ni X, Zeng Y. Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice. Front Microbiol 2023; 14:1322910. [PMID: 38125573 PMCID: PMC10731255 DOI: 10.3389/fmicb.2023.1322910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction In recent years, a large number of studies have shown that Bacillus velezensis has the potential as an animal feed additive, and its potential probiotic properties have been gradually explored. Methods In this study, Illumina NovaSeq PE150 and Oxford Nanopore ONT sequencing platforms were used to sequence the genome of Bacillus velezensis TS5, a fiber-degrading strain isolated from Tibetan sheep. To further investigate the potential of B. velezensis TS5 as a probiotic strain, in vivo experiments were conducted using 40 five-week-old male specific pathogen-free C57BL/6J mice. The mice were randomly divided into four groups: high fiber diet control group (H group), high fiber diet probiotics group (HT group), low fiber diet control group (L group), and low fiber diet probiotics group (LT group). The H and HT groups were fed high-fiber diet (30%), while the L and LT groups were fed low-fiber diet (5%). The total bacteria amount in the vegetative forms of B. velezensis TS5 per mouse in the HT and LT groups was 1 × 109 CFU per day, mice in the H and L groups were given the same volume of sterile physiological saline daily by gavage, and the experiment period lasted for 8 weeks. Results The complete genome sequencing results of B. velezensis TS5 showed that it contained 3,929,788 nucleotides with a GC content of 46.50%. The strain encoded 3,873 genes that partially related to stress resistance, adhesion, and antioxidants, as well as the production of secondary metabolites, digestive enzymes, and other beneficial nutrients. The genes of this bacterium were mainly involved in carbohydrate metabolism, amino acid metabolism, vitamin and cofactor metabolism, biological process, and molecular function, as revealed by KEGG and GO databases. The results of mouse tests showed that B. velezensis TS5 could improve intestinal digestive enzyme activity, liver antioxidant capacity, small intestine morphology, and cecum microbiota structure in mice. Conclusion These findings confirmed the probiotic effects of B. velezensis TS5 isolated from Tibetan sheep feces and provided the theoretical basis for the clinical application and development of new feed additives.
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Affiliation(s)
- Benhao Chen
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Yi Zhou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Lixiao Duan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Xuemei Gong
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Xingmei Liu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
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Yadav K, Arya M, Prakash S, Jha BS, Manchanda P, Kumar A, Deswal R. Brassica juncea leaf cuticle contains xylose and mannose (xylomannan) which inhibit ice recrystallization on the leaf surface. PLANTA 2023; 258:44. [PMID: 37460860 DOI: 10.1007/s00425-023-04203-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
MAIN CONCLUSION Conjugated sugars showed antifreeze activity in the cuticle by ice recrystallization inhibition rather than thermal hysteresis, enhancing freezing capacity at the surface of B. juncea leaves. Antifreeze biomolecules play a crucial role in mitigating the physical damage from frost by controlling extracellular ice crystal growth in plants. Antifreeze proteins (AFPs) are reported from the apoplast of different plants. Interestingly, there is no report about antifreeze properties of the cuticle. Here, we report the potential antifreeze activity in the Brassica juncea (BJ) leaf cuticle. Nano LC-MS/MS analysis of a cuticle protein enriched fraction (CPE) predicted over 30 putative AFPs using CryoProtect server and literature survey. Ice crystal morphology (ICM) and ice recrystallization inhibition (IRI) analysis of ABC supernatant showed heat and pronase-resistant, non-protein antifreeze activities as well as hexagonal ice crystals with TH of 0.17 °C and IRI 46%. The ZipTip processed ABC supernatant (without peptides) had no effect on TH activity, confirming a non-protein antifreeze molecule contributing to activity. To understand the origin and to confirm the source of antifreeze activity, cuticular membranes were isolated by pectinase and cellulase hydrolysis. FTIR analysis of the intact cuticle showed xylose, mannose, cellulose, and glucose. Xylanase and cellulase treatments of the ZipTip processed ABC supernatant led to an increase in sugar content and 50% loss in antifreeze activity. UV spectroscopy and NMR analysis supported the finding of FTIR and enzyme hydrolysis suggesting the contribution of xylose and mannose to antifreeze activity. By TLC analysis, conjugated sugars were found in the cuticle. This work has opened up a new research area where the antifreeze capacity needs to be established with regard to complete characterization and mechanism of action of the antifreeze carbohydrates (conjugated sugars) on the leaf surface.
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Affiliation(s)
- Kailash Yadav
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Meenakshi Arya
- Department of Botany, Dyal Singh College, University of Delhi, Delhi, 110003, India
| | - Satya Prakash
- Department of Botany, Acharya Narendra Dev College, University of Delhi, Delhi, 110019, India
| | - Bhavana Sharma Jha
- Department of Botany, Gargi College, University of Delhi, Delhi, 110049, India
| | - Preet Manchanda
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Abhishek Kumar
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
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7
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Costa DA, Williams TC, do Vale LHF, Filho EX. Characterization of mannanases from Clonostachys byssicola involved in the breakdown of lignocellulosic substrates. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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8
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Parra M, Libkind D, Hittinger CT, Álvarez L, Bellora N. Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation. Yeast 2023. [PMID: 37114349 DOI: 10.1002/yea.3853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/27/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Aureobasidium pullulans is a yeast-like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re-evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high-depth transcriptomic data. Our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.
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Affiliation(s)
- Micaela Parra
- Laboratorio de Genómica Computacional, Instituto de Tecnologías Nucleares para la Salud (INTECNUS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lucía Álvarez
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Nicolás Bellora
- Laboratorio de Genómica Computacional, Instituto de Tecnologías Nucleares para la Salud (INTECNUS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
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9
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Chen L, Qu Z, Yu W, Zheng L, Qiao H, Wang D, Wei B, Zhao Z. Comparative genomic and transcriptome analysis of Bacillus velezensis CL-4 fermented corn germ meal. AMB Express 2023; 13:10. [PMID: 36683079 PMCID: PMC9868226 DOI: 10.1186/s13568-023-01510-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023] Open
Abstract
Bacillus, an excellent organic-degrading agent, can degrade lignocellulose. Notably, some B. velezensis strains encode lignocellulases. However, their ability to degrade lignocellulose in fermented feed is not much appreciated. This study performed a comparative genomic analysis of twenty-three B. velezensis strains to find common carbohydrate-active enzymes (CAZymes) encoding genes and evaluated their potential to degrade lignocellulose. The comparative genomic and CAZyme database-based analyses identified several potential CAZymes genes that degrade cellulose (GH1, GH4, GH5, GH13, GH16, GH32, PL1, and PL9), hemicellulose (GH11, GH26, GH43, GH51, and CE3) and lignin (AA4, AA6, AA7, and AA10). Furthermore, Illumina RNA-seq transcriptome analysis revealed the expression of more than 1794 genes in B. velezensis CL-4 fermented corn germ meal at 48 h (FCGM 48 h). Gene ontology analysis of expressed genes revealed their enrichment in hydrolase activity (breaking the glycosyl bonds during carbohydrate metabolism), indicating the upregulation of CAZymes. In total, 58 differentially upregulated CAZymes-encoding genes were identified in FCGM 48 h compared to FCGM 0 h. The upregulated CAZymes-encoding genes were related to cellulose (6-phospho-β-galactosidase and 6-phospho-α-glucosidase), starch (α-glucosidase and α-amylase), pectin (pectin lyase), and hemicellulose (arabinan endo-1,5-α-L-arabinosidase, xylan 1,4-beta-xylosidase, α-N-arabinofuranosidase, and acetyl xylan esterase). Importantly, arabinoxylan degradation mainly occurred in FCGM 48 h, followed by partial degradation of cellulose, pectin, and starch. This study can support the development of enzymatic cocktails for the solid-state fermented feed (SFF).
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Affiliation(s)
- Long Chen
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Zihui Qu
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Wei Yu
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Lin Zheng
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Haixin Qiao
- Information Application Department, Jilin Intellectual Property Protection Center, Changchun, 130000 China
| | - Dan Wang
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Bingdong Wei
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Zijian Zhao
- grid.464388.50000 0004 1756 0215Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, No. 1366 Cai Yu Street, Changchun, 130033 Jilin Province China
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10
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Production of xylo-oligosaccharides (XOS) of tailored degree of polymerization from acetylated xylans through modelling of enzymatic hydrolysis. Food Res Int 2022; 162:112019. [DOI: 10.1016/j.foodres.2022.112019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/27/2022] [Accepted: 10/01/2022] [Indexed: 11/15/2022]
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Combining Transcriptomics and Polyphenol Profiling to Provide Insights into Phenolics Transformation of the Fermented Chinese Jujube. Foods 2022; 11:foods11172546. [PMID: 36076732 PMCID: PMC9455259 DOI: 10.3390/foods11172546] [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: 07/28/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
As an important medicine homologous food, Chinese jujube is rich in nutrition and medicinal value. To enhance the bioactive compounds level of Chinese jujube products, three kinds of fungi strains (Rhizopus oryzae, Aspergillus niger and Monascus purpureus) were firstly selected to evaluate their effects on total soluble phenolic compounds (TSPC) and total soluble flavonoids compounds (TSFC) contents during liquid state fermentation of Chinese jujube. As the best strain, the highest contents of TSPC and TSFC could increase by 102.1% (26.02 mg GAE/g DW) and 722.8% (18.76 mg RE/g DW) under M. purpureus fermentation when compared to the unfermented sample, respectively. Qualitative and quantitative analysis of individual polyphenol compounds indicated that proto-catechuic acid, p-hydroxybenzoic acid and chlorogenic acid showed the highest level in the fer-mented Chinese jujube at the 7th day, which was enhanced by 16.72-, 14.05- and 6.03-fold when compared to the control, respectively. Combining with RNA sequencing, function annotation of CAZymes database and polyphenol profiling, three potential transformation pathways of poly-phenol compounds were proposed in the fermented Chinese jujube by M. purpureus, such as the conversion of insoluble bound phenolic acids, rutin and anthocyanin degradation. These findings would be beneficial for better understanding of the biotransformation mechanism of polyphenol compounds in fungi fermentation.
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Chen L, Chen W, Zheng B, Yu W, Zheng L, Qu Z, Yan X, Wei B, Zhao Z. Fermentation of NaHCO 3-treated corn germ meal by Bacillus velezensis CL-4 promotes lignocellulose degradation and nutrient utilization. Appl Microbiol Biotechnol 2022; 106:6077-6094. [PMID: 35976426 DOI: 10.1007/s00253-022-12130-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Sodium bicarbonate pretreatment and solid-state fermentation (SSF) were used to maximize the nutritional value of corn germ meal (CGM) by inoculating it with Bacillus velezensis CL-4 (isolated from chicken cecal contents and capable of degrading lignocellulose). Based on genome sequencing, B. velezensis CL-4 has a 4,063,558 bp ring chromosome and 46.27% GC content. Furthermore, genes associated with degradation of lignocellulose degradation were detected. Pretreatment of CGM (PCGM) with sodium bicarbonate (optimized to 0.06 g/mL) neutralized low pH. Fermented and pretreated CGM (FPCGM) contained more crude protein (CP), soluble protein of trichloroacetic acid (TCA-SP), and total amino acids (aa) than CGM and PCGM. Degradation rates of cellulose and hemicellulose were reduced by 21.33 and 71.35%, respectively, after 48 h fermentation. Based on electron microscopy, FPCGM destroys the surface structure and adds small debris of the CGM substrate, due to lignocellulose breakdown. Furthermore, 2-oxoadipic acid and dimethyl sulfone were the most important metabolites during pretreatment. Concentrations of adenosine, cytidine, guanosine, S-methyl-5'-thioadenosine, and adenine decreased significantly after 48 h fermentation, whereas concentrations of probiotics, enzymes, and fatty acids (including palmitic, 16-hydroxypalmitic, and linoleic acids) were significantly improved after fermentation. In conclusion, the novel pretreatment of CGM provided a proof of concept for using B. velezensis CL-4 to degrade lignocellulose components, improve nutritional characteristics of CGM, and expand CGM lignocellulosic biological feed production. KEY POINTS: • Sodium bicarbonate (baking soda) can be used as an economical and green additive to pretreat corn germ meal; • Fermentation with B. velezensis degrades the cellulose and hemicellulose component of corn germ meal and improves its feed quality; • As a novel qualified presumption of safety (QPS) strain, B. velezensis should have broad potential applications in food and feed industries.
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Affiliation(s)
- Long Chen
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Wanying Chen
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Boyu Zheng
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Wei Yu
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Lin Zheng
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Zihui Qu
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Xiaogang Yan
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Bingdong Wei
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China.
| | - Zijian Zhao
- Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, No. 1366 Cai Yu Street, Changchun, Jilin Province, 130033, People's Republic of China.
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Rastogi L, Chaudhari AA, Sharma R, Pawar PAM. Arabidopsis GELP7 functions as a plasma membrane-localized acetyl xylan esterase, and its overexpression improves saccharification efficiency. PLANT MOLECULAR BIOLOGY 2022; 109:781-797. [PMID: 35577991 DOI: 10.1007/s11103-022-01275-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Acetyl substitution on the xylan chain is critical for stable interaction with cellulose and other cell wall polymers in the secondary cell wall. Xylan acetylation pattern is governed by Golgi and extracellular localized acetyl xylan esterase (AXE). We investigated the role of Arabidopsis clade Id from the GDSL esterase/lipase or GELP family in polysaccharide deacetylation. The investigation of the AtGELP7 T-DNA mutant line showed a decrease in stem esterase activity and an increase in stem acetyl content. We further generated overexpressor AtGELP7 transgenic lines, and these lines showed an increase in AXE activity and a decrease in xylan acetylation compared to wild-type plants. Therefore, we have named this enzyme as AtAXE1. The subcellular localization and immunoblot studies showed that the AtAXE1 enzyme is secreted out, associated with the plasma membrane and involved in xylan de-esterification post-synthesis. The cellulose digestibility was improved in AtAXE1 overexpressor lines without pre-treatment, after alkali and xylanases pre-treatment. Furthermore, we have also established that the AtGELP7 gene is upregulated in the overexpressor line of AtMYB46, a secondary cell wall specific transcription factor. This transcriptional regulation can drive AtGELP7 or AtAXE1 to perform de-esterification of xylan in a tissue-specific manner. Overall, these data suggest that AtGELP7 overexpression in Arabidopsis reduces xylan acetylation and improves digestibility properties of polysaccharides of stem lignocellulosic biomass.
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Affiliation(s)
- Lavi Rastogi
- Laboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, NCR Biotech Science, Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Aniket Anant Chaudhari
- Laboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, NCR Biotech Science, Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Raunak Sharma
- Laboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, NCR Biotech Science, Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Prashant Anupama-Mohan Pawar
- Laboratory of Plant Cell Wall Biology, Regional Centre for Biotechnology, NCR Biotech Science, Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
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14
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Shang Z, Liu S, Duan Y, Bao C, Wang J, Dong B, Cao Y. Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig. BMC Microbiol 2022; 22:186. [PMID: 35906551 PMCID: PMC9336001 DOI: 10.1186/s12866-022-02599-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 12/05/2022] Open
Abstract
Background Cellulolytic microorganisms are considered a key player in the degradation of feed fiber. These microorganisms can be isolated from various resources, such as animal gut, plant surfaces, soil and oceans. A new strain of Bacillus amyloliquefaciens, TL106, was isolated from faeces of a healthy Tibetan pigs. This strain can produce cellulase and shows strong antimicrobial activity in mice. Thus, in this study, to better understand the strain of B. amyloliquefaciens TL106 on degradation of cellulose, the genome of the strain TL106 was completely sequenced and analyzed. In addition, we also explored the cellulose degradation ability of strain TL106 in vitro. Results TL106 was completely sequenced with the third generation high-throughput DNA sequencing. In vitro analysis with enzymatic hydrolysis identified the activity of cellulose degradation. TL106 consisted of one circular chromosome with 3,980,960 bp and one plasmid with 16,916 bp, the genome total length was 3.99 Mb and total of 4,130 genes were predicted. Several genes of cellulases and hemicellulase were blasted in Genbank, including β-glucosidase, endoglucanase, ß-glucanase and xylanase genes. Additionally, the activities of amylase (20.25 U/mL), cellulase (20.86 U/mL), xylanase (39.71 U/mL) and β-glucanase (36.13 U/mL) in the fermentation supernatant of strain TL106 were higher. In the study of degradation characteristics, we found that strain TL106 had a better degradation effect on crude fiber, neutral detergent fiber, acid detergent fiber, starch, arabinoxylan and β-glucan of wheat and highland barley . Conclusions The genome of B. amyloliquefaciens TL106 contained several genes of cellulases and hemicellulases, can produce carbohydrate-active enzymes, amylase, cellulase, xylanase and β-glucanase. The supernatant of fermented had activities of strain TL106. It could degrade the fiber fraction and non-starch polysaccharides (arabinoxylans and β-glucan) of wheat and highland barley. The present study demonstrated that the degradation activity of TL106 to crude fiber which can potentially be applied as a feed additive to potentiate the digestion of plant feed by monogastric animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02599-7.
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Affiliation(s)
- Zhenda Shang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China.,College of Animal Science, Tibet Agricultural and Animal Husbandry University, 860000, Nyingchi, People's Republic of China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, 860000, Nyingchi, People's Republic of China
| | - Yanzhen Duan
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, 860000, Nyingchi, People's Republic of China
| | - Chengling Bao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Jian Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Bing Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China.
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15
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Wang H, Chen N, Xie F, Verkasalo E, Chu J. Structural Properties and Hydrolysability of Paulownia elongate: The Effects of Pretreatment Methods Based on Acetic Acid and Its Combination with Sodium Sulfite or Sodium Sulfite. Int J Mol Sci 2022; 23:ijms23105775. [PMID: 35628579 PMCID: PMC9144951 DOI: 10.3390/ijms23105775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
The effects of CH3COOH and Na2SO3 pretreatment on the structural properties and hydrolyzability of fast-growing Paulownia elongate were investigated. Acetic acid increased cellulose’s crystallinity and hydrolyzability when combined with alkaline sodium sulfite and sodium hydroxide. The cellulose content increased by 21%, the lignin content decreased by 6%, and the product showed better enzymatic digestibility. With a cellulase dose of 30 FPU/g DM, after 72 h hydrolysis, the hydrolysis yields of glucose and xylose were 78% and 83%, respectively, which were 51% and 69% higher than those of untreated materials. When the enzyme dosage was 20 FPU/g DM, after 72 h hydrolysis, the hydrolysis yields of glucose and xylose were 74% and 79%, respectively. The high hydrolyzability, low enzyme loading, and high hydrolysis yield demonstrate the potential of the proposed system for producing platform sugars from fast-growing Paulownia elongate.
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Affiliation(s)
- Hanxing Wang
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (H.W.); (N.C.); (F.X.)
| | - Ni Chen
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (H.W.); (N.C.); (F.X.)
| | - Feifan Xie
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (H.W.); (N.C.); (F.X.)
| | - Erkki Verkasalo
- Natural Resources Institute Finland (Luke), Production Systems, Yliopistokatu 6, 80100 Joensuu, Finland;
| | - Jie Chu
- College of Forestry, Northwest A&F University, Yangling, Xianyang 712100, China; (H.W.); (N.C.); (F.X.)
- Correspondence:
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16
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Li J, Wang S, Zhao J, Dong Z, Shao T. Gut Microbiota of Ostrinia nubilalis Larvae Degrade Maize Cellulose. Front Microbiol 2022; 13:816954. [PMID: 35495661 PMCID: PMC9039043 DOI: 10.3389/fmicb.2022.816954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
Most arthropod guts harbor diverse microbiota for symbiotic digestion. The European corn borer (ECB), Ostrinia nubilalis (Hübner), is a devastating pest that feeds the lignocellulose-rich tissues of maize plants. However, the potential role of ECB gut microbes in degrading maize cellulose remains largely unexplored. Here, we investigated the gut microbiota of ECB fed with different diets and their potential function in maize lignocellulose degradation. The diversity and composition of gut bacterial communities varied dramatically between the ECB larva fed with artificial diets (ECB-D) and maize plants (ECB-M). Draft genomes of the microbial consortia from ECB-D and ECB-M showed that the principal degraders of cellulose mainly belonged to Firmicutes or Proteobacteria and they were primarily found in the midgut. The cellulolytic microbial consortia contained genes encoding various carbohydrate-active enzymes (CAZyme). Furthermore, scanning electron microscopy revealed significant breakdown of lignocellulose in maize treated by the two microbial consortia for 9 days in vitro. Metabolomic analyses show that maize particles treated by two microbial consortia generate distinctive metabolomic profiles, with enrichment for different monosaccharides (i.e., Glucose, Rhamnofuranose, Isomaltose, and Cellobiose) and amino acids (i.e., Threonine, Histidine, and Lysine). The results indicated that the diet of the host impacted the composition and function of its gut microbiota and ECB exploited specific gut microbes to digest maize lignocellulose with distinctive products. Our study provides valuable microbiota resources for lignocellulose bioconversion.
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Affiliation(s)
| | | | | | | | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
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17
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Li S, Zhao S, Hu C, Mao C, Guo L, Yu H, Yu H. Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu). J Fungi (Basel) 2022; 8:99. [PMID: 35205854 PMCID: PMC8880121 DOI: 10.3390/jof8020099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Stropharia rugosoannulata, also known as Daqiugaigu in China, is a well-known edible mushroom that has been widely cultivated in China in recent years. Many studies have focused on its nutrients, bioactive compounds, and lignin degradation capacity, although there are few molecular and genetic breeding studies due to the lack of genomic information. Here, we present the 47.9 Mb genome sequence of an S. rugosoannulata monokaryotic strain (A15), which has 20 contigs and an N50 of 3.64 Mb, which was obtained by a combination of Illumina and Nanopore sequencing platforms. Further analysis predicted 12,752 protein-coding genes, including 486 CAZyme-encoding genes. Phylogenetic analysis revealed a close evolutionary relationship between S. rugosoannulata and Hypholoma sublateritium, Psilocybe cyanescens, and Galerina marginata based on single-copy orthologous genes. Proteomic analysis revealed different protein expression profiles between the cap and the stipe of the S. rugosoannulata fruiting body. The proteins of the stipe associated with carbon metabolism, energy production, and stress-response-related biological processes had higher abundance, whereas proteins involved in fatty acid synthesis and mRNA splicing showed higher expression in the cap than in the stipe. The genome of S. rugosoannulata will provide valuable genetic resources not only for comparative genomic analyses and evolutionary studies among Basidiomycetes but also for alleviating the bottlenecks that restrict the molecular breeding of this edible mushroom.
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Affiliation(s)
- Shuwen Li
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Shuxue Zhao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chunhui Hu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chengzhi Mao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
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Industrially Important Genes from Trichoderma. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Yang M, Guo X, Liu G, Nan Y, Zhang J, Noyazzesh H, Kuittinen S, Vepsäläinen J, Pappinen A. Effect of solvent mixture pretreatment on sugar release from short-rotation coppice Salix schwerinii for biobutanol production. BIORESOURCE TECHNOLOGY 2022; 344:126262. [PMID: 34728360 DOI: 10.1016/j.biortech.2021.126262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the effects of pretreatment using an acetone-butanol-ethanol (ABE) mixture with and without H2SO4 (H+) as a catalyst on sugar recovery from Salix schwerinii biomass. The sugar recovery was susceptible to both the temperature and the catalyst. Moreover, the relatively higher concentration of ABE (H+ABE4) at 200 °C yielded glucose recovery of 85.5% from the pretreated solid, higher than the recovery under other conditions. This result was mainly attributed to the compositional changes in the biomass, as the xylan and lignin were removed in large quantities by ABE pretreatment at 200 °C. Correspondingly, xylose recovery of 53.8% and glucose recovery of 12.1% were obtained from the liquid in which more sugar degradation products were formed. Ultimately, a fermentation broth containing a low concentration of ABE was successfully employed for pretreatment and showed great potential in producing fermentable sugars from S. schwerinii for biobutanol production.
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Affiliation(s)
- Ming Yang
- Engineering Research Center of Hebei for Agricultural Waste Resource Utilization, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Xiaojun Guo
- Engineering Research Center of Hebei for Agricultural Waste Resource Utilization, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Guozhen Liu
- Engineering Research Center of Hebei for Agricultural Waste Resource Utilization, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China; Hebei Key Laboratory of Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Yufei Nan
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junhua Zhang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hossain Noyazzesh
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI80101 Joensuu, Finland
| | - Suvi Kuittinen
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI80101 Joensuu, Finland
| | - Jouko Vepsäläinen
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, FI70211 Kuopio, Finland
| | - Ari Pappinen
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI80101 Joensuu, Finland
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20
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Álvarez C, González A, Ballesteros I, Negro MJ. Production of xylooligosaccharides, bioethanol, and lignin from structural components of barley straw pretreated with a steam explosion. BIORESOURCE TECHNOLOGY 2021; 342:125953. [PMID: 34555750 DOI: 10.1016/j.biortech.2021.125953] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Barley straw (BS) is a potential source to obtain bioethanol and value-added products such as xylooligosaccharides (XOS) and lignin for application in diverse industries. In this study, BS was submitted to steam explosion pretreatment to valorize the main components of this lignocellulose biomass. For hemicellulose fraction valorization, different combinations of endo-β-(1,4)-D-xylanase enzyme with accessory enzymes (α-L-arabinofuranosidase, feruloy -esterase and acetylxylan-esterase) have been studied to produce XOS with a low degree of polymerization. The application of accessory enzymes combined with endo-β-(1,4)-D-xylanase enzymes turned out to be the most effective strategy for the formation of XOS. The solid fraction obtained after the pretreatment was submitted to presacharification and simultaneous saccharification and fermentation process for bioethanol production. The resulting lignin-rich residue was characterized. In this integrated process, 13.0 g XOS (DP2-DP6), 12.6 g ethanol and 16.6 g lignin were obtained from 100 g of BS, achieving the goal of valorizing this agricultural residue.
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Affiliation(s)
- Cristina Álvarez
- Advanced Biofuels and Bioproducts Unit, Renewable Energies Department, CIEMAT, Madrid 28040, Spain.
| | - Alberto González
- Advanced Biofuels and Bioproducts Unit, Renewable Energies Department, CIEMAT, Madrid 28040, Spain.
| | - Ignacio Ballesteros
- Advanced Biofuels and Bioproducts Unit, Renewable Energies Department, CIEMAT, Madrid 28040, Spain.
| | - María José Negro
- Advanced Biofuels and Bioproducts Unit, Renewable Energies Department, CIEMAT, Madrid 28040, Spain.
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21
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Heeger F, Bourne EC, Wurzbacher C, Funke E, Lipzen A, He G, Ng V, Grigoriev IV, Schlosser D, Monaghan MT. Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica. J Fungi (Basel) 2021; 7:jof7100854. [PMID: 34682274 PMCID: PMC8537685 DOI: 10.3390/jof7100854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources.
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Affiliation(s)
- Felix Heeger
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Department Materials and Environment, Federal Institute for Material Research and Testing, 12203 Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Correspondence:
| | - Elizabeth C. Bourne
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany;
| | - Elisabeth Funke
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany;
| | - Michael T. Monaghan
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, 14195 Berlin, Germany
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22
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Wang J, Gao Z, Qian Y, Hu X, Li G, Fu F, Guo J, Shan Y. Citrus Segment Degradation Potential, Enzyme Safety Evaluation, and Whole Genome Sequence of Aspergillus aculeatus Strain ZC-1005. Front Microbiol 2021; 12:671200. [PMID: 34489880 PMCID: PMC8417811 DOI: 10.3389/fmicb.2021.671200] [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: 02/23/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Aspergillus aculeatus ZC-1005 (ZC-1005 was used as the abbreviation of this strain) is a hemicellulase-producing strain isolated from rotten citrus rind buried in the soil. Our previous study has shown its biochemical properties including high xylanase activity, mannanase activity, and degradation reaction with citrus mesocarp. In this study, we focused more on the enzyme safety evaluation and the genome sequencing via PacBio and Illumina platforms. High biological safety of the crude enzymes of ZC-1005 has been proven by the acute oral toxicity test, sub-chronic toxicity test, micronucleus test, and sperm malformation test. The genome of ZC-1005 had a GC content of 52.53%, with a size of 35,458,484 bp, and encoded 10,147 genes. Strain ZC-1005 harbored 269 glycosyl hydrolase (GH) genes of 64 families. The fungus produces cellulose-acting (GH3, GH5, GH12, and GH1) and hemicellulose-acting enzymes (GH16, GH31, GH2, and GH92). In genome annotation, we paid more attention to the genes encoding xylanase, such as gene 01512, gene 05833, gene 05469, gene 07781, gene 08432, gene 09042, gene 08008, and gene 09694. The collaboration between complete genome information and the degradation test confirmed that ZC-1005 could degrade cellulose and xylan. Our results showed that the citrus enzymatic decapsulation technology was efficacious and safe for canned citrus product processing, which may also solve the industrial waste problem. Therefore, ZC-1005 and the crude enzyme secreted from the strain were very promising to be used in the citrus processing industry.
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Affiliation(s)
- Jieyi Wang
- Hunan Agriculture Product Processing Institute, International Joint Laboratory on Fruits and Vegetables Processing, Quality and Safety, Hunan Key Laboratory of Fruits and Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhipeng Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yujiao Qian
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Xiao Hu
- Hunan Agriculture Product Processing Institute, International Joint Laboratory on Fruits and Vegetables Processing, Quality and Safety, Hunan Key Laboratory of Fruits and Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Gaoyang Li
- Hunan Agriculture Product Processing Institute, International Joint Laboratory on Fruits and Vegetables Processing, Quality and Safety, Hunan Key Laboratory of Fruits and Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Fuhua Fu
- Hunan Agriculture Product Processing Institute, International Joint Laboratory on Fruits and Vegetables Processing, Quality and Safety, Hunan Key Laboratory of Fruits and Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Jiajing Guo
- Hunan Agriculture Product Processing Institute, International Joint Laboratory on Fruits and Vegetables Processing, Quality and Safety, Hunan Key Laboratory of Fruits and Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Yang Shan
- Hunan Agriculture Product Processing Institute, International Joint Laboratory on Fruits and Vegetables Processing, Quality and Safety, Hunan Key Laboratory of Fruits and Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
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23
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Li H, Chen X, Wang C, Chen X, Guo H, Xiong L, Zhang H, Huang C, Chen X. Factors Affecting the Catalytic Efficiency and Synergism of Xylanase and Cellulase During Enzymatic Hydrolysis of Birch Wood. Appl Biochem Biotechnol 2021; 193:3469-3482. [PMID: 34245403 DOI: 10.1007/s12010-021-03590-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/28/2021] [Indexed: 11/25/2022]
Abstract
Understanding factors that affect the catalytic efficiency and synergism of enzymes is helpful to enhance the process of bioconversion. In this study, birch wood (BW) was sequentially treated by delignification (DL), deacetylation (DA), and decrystallization (DC) treatments. The physiochemical structures of treated BW were characterized. Moreover, the influences of sequential treatments on the catalytic efficiency and synergism of xylanase and cellulase were studied. DL treatments efficiently improved the conversion of cellulose and xylan. A high degree of synergy (DS) between xylanase and cellulase was produced during hydrolysis of DL-treated BW. DA treatments enhanced xylan conversion but reduced the DS between xylanase and cellulase for xylan hydrolysis, whereas DC treatments enhanced cellulose conversion but reduced the DS between xylanase and cellulase for cellulose hydrolysis. The cellulose conversion of lithium chloride/N,N-dimethylacetamide (LiCl/DMAc)-treated BW (89.69%) was higher than the cellulose conversion of ball milling (BM)-treated BW (81.63%), whereas the xylan conversion of LiCl/DMAc-treated BW (83.77%) was lower than the xylan conversion of BM-treated BW (87.21%). This study showed that the catalytic efficiency and synergism of xylanase and cellulase are markedly affected by lignin hindrance, hemicellulose acetylation, and cellulose crystallization.
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Affiliation(s)
- Hailong Li
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, People's Republic of China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, People's Republic of China
- R&D Center of Xuyi Attapulgite Energy and Environmental Materials, Xuyi, 211700, People's Republic of China
| | - Xindong Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Can Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, People's Republic of China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, People's Republic of China
- R&D Center of Xuyi Attapulgite Energy and Environmental Materials, Xuyi, 211700, People's Republic of China
| | - Xuefang Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, People's Republic of China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, People's Republic of China
- R&D Center of Xuyi Attapulgite Energy and Environmental Materials, Xuyi, 211700, People's Republic of China
| | - Haijun Guo
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, People's Republic of China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, People's Republic of China
- R&D Center of Xuyi Attapulgite Energy and Environmental Materials, Xuyi, 211700, People's Republic of China
| | - Lian Xiong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, People's Republic of China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, People's Republic of China
- R&D Center of Xuyi Attapulgite Energy and Environmental Materials, Xuyi, 211700, People's Republic of China
| | - Hairong Zhang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, People's Republic of China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, People's Republic of China
- R&D Center of Xuyi Attapulgite Energy and Environmental Materials, Xuyi, 211700, People's Republic of China
| | - Chao Huang
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Xinde Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, No. 2 Energy Road, Tianhe District, Guangzhou, 510640, People's Republic of China.
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, People's Republic of China.
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, People's Republic of China.
- R&D Center of Xuyi Attapulgite Energy and Environmental Materials, Xuyi, 211700, People's Republic of China.
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Gorshkov V, Tsers I, Islamov B, Ageeva M, Gogoleva N, Mikshina P, Parfirova O, Gogoleva O, Petrova O, Gorshkova T, Gogolev Y. The Modification of Plant Cell Wall Polysaccharides in Potato Plants during Pectobacterium atrosepticum-Caused Infection. PLANTS 2021; 10:plants10071407. [PMID: 34371610 PMCID: PMC8309280 DOI: 10.3390/plants10071407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/04/2021] [Accepted: 07/08/2021] [Indexed: 12/29/2022]
Abstract
Our study is the first to consider the changes in the entire set of matrix plant cell wall (PCW) polysaccharides in the course of a plant infectious disease. We compared the molecular weight distribution, monosaccharide content, and the epitope distribution of pectic compounds and cross-linking glycans in non-infected potato plants and plants infected with Pectobacterium atrosepticum at the initial and advanced stages of plant colonization by the pathogen. To predict the gene products involved in the modification of the PCW polysaccharide skeleton during the infection, the expression profiles of potato and P. atrosepticum PCW-related genes were analyzed by RNA-Seq along with phylogenetic analysis. The assemblage of P. atrosepticum biofilm-like structures—the bacterial emboli—and the accumulation of specific fragments of pectic compounds that prime the formation of these structures were demonstrated within potato plants (a natural host of P. atrosepticum). Collenchyma was shown to be the most “vulnerable” tissue to P. atrosepticum among the potato stem tissues. The infection caused by the representative of the Soft Rot Pectobacteriaceae was shown to affect not only pectic compounds but also cross-linking glycans; the content of the latter was increased in the infected plants compared to the non-infected ones.
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Affiliation(s)
- Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420111 Kazan, Russia
- Correspondence:
| | - Ivan Tsers
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420111 Kazan, Russia
| | - Bakhtiyar Islamov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
| | - Marina Ageeva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420111 Kazan, Russia
| | - Polina Mikshina
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
| | - Olga Gogoleva
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (B.I.); (M.A.); (N.G.); (P.M.); (O.P.); (O.P.); (T.G.); (Y.G.)
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (I.T.); (O.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420111 Kazan, Russia
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25
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Marasinghe SD, Jo E, Hettiarachchi SA, Lee Y, Eom TY, Gang Y, Kang YH, Oh C. Characterization of glycoside hydrolase family 11 xylanase from Streptomyces sp. strain J103; its synergetic effect with acetyl xylan esterase and enhancement of enzymatic hydrolysis of lignocellulosic biomass. Microb Cell Fact 2021; 20:129. [PMID: 34238305 PMCID: PMC8265113 DOI: 10.1186/s12934-021-01619-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Xylanase-containing enzyme cocktails are used on an industrial scale to convert xylan into value-added products, as they hydrolyse the β-1,4-glycosidic linkages between xylopyranosyl residues. In the present study, we focused on xynS1, the glycoside hydrolase (GH) 11 xylanase gene derived from the Streptomyces sp. strain J103, which can mediate XynS1 protein synthesis and lignocellulosic material hydrolysis. Results xynS1 has an open reading frame with 693 base pairs that encodes a protein with 230 amino acids. The predicted molecular weight and isoelectric point of the protein were 24.47 kDa and 7.92, respectively. The gene was cloned into the pET-11a expression vector and expressed in Escherichia coli BL21(DE3). Recombinant XynS1 (rXynS1) was purified via His-tag affinity column chromatography. rXynS1 exhibited optimal activity at a pH of 5.0 and temperature of 55 °C. Thermal stability was in the temperature range of 50–55 °C. The estimated Km and Vmax values were 51.4 mg/mL and 898.2 U/mg, respectively. One millimolar of Mn2+ and Na+ ions stimulated the activity of rXynS1 by up to 209% and 122.4%, respectively, and 1 mM Co2+ and Ni2+ acted as inhibitors of the enzyme. The mixture of rXynS1, originates from Streptomyces sp. strain J103 and acetyl xylan esterase (AXE), originating from the marine bacterium Ochrovirga pacifica, enhanced the xylan degradation by 2.27-fold, compared to the activity of rXynS1 alone when Mn2+ was used in the reaction mixture; this reflected the ability of both enzymes to hydrolyse the xylan structure. The use of an enzyme cocktail of rXynS1, AXE, and commercial cellulase (Celluclast® 1.5 L) for the hydrolysis of lignocellulosic biomass was more effective than that of commercial cellulase alone, thereby increasing the relative activity 2.3 fold. Conclusion The supplementation of rXynS1 with AXE enhanced the xylan degradation process via the de-esterification of acetyl groups in the xylan structure. Synergetic action of rXynS1 with commercial cellulase improved the hydrolysis of pre-treated lignocellulosic biomass; thus, rXynS1 could potentially be used in several industrial applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01619-x.
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Affiliation(s)
- Svini Dileepa Marasinghe
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Eunyoung Jo
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Sachithra Amarin Hettiarachchi
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - Youngdeuk Lee
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Tae-Yang Eom
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yehui Gang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Hyeok Kang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chulhong Oh
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea. .,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.
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26
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Oates NC, Abood A, Schirmacher AM, Alessi AM, Bird SM, Bennett JP, Leadbeater DR, Li Y, Dowle AA, Liu S, Tymokhin VI, Ralph J, McQueen-Mason SJ, Bruce NC. A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1. Proc Natl Acad Sci U S A 2021; 118:e2008888118. [PMID: 33903229 PMCID: PMC8106297 DOI: 10.1073/pnas.2008888118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lignocellulose, the structural component of plant cells, is a major agricultural byproduct and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities, and currently, efficient transformation requires expensive pretreatments and high loadings of enzymes. Here, we report on a fungus from the Parascedosporium genus, isolated from a wheat-straw composting community, that secretes a large and diverse array of carbohydrate-active enzymes (CAZymes) when grown on lignocellulosic substrates. We describe an oxidase activity that cleaves the major β-ether units in lignin, thereby releasing the flavonoid tricin from monocot lignin and enhancing the digestion of lignocellulose by polysaccharidase mixtures. We show that the enzyme, which holds potential for the biorefining industry, is widely distributed among lignocellulose-degrading fungi from the Sordariomycetes phylum.
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Affiliation(s)
- Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Alexandra M Schirmacher
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Anna M Alessi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Susannah M Bird
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Joseph P Bennett
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Sarah Liu
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - Vitaliy I Tymokhin
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom;
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27
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Comparative genomic and secretomic characterisation of endophytic Bacillus velezensis LC1 producing bioethanol from bamboo lignocellulose. Arch Microbiol 2021; 203:3089-3099. [PMID: 33792738 DOI: 10.1007/s00203-021-02306-6] [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: 12/14/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022]
Abstract
Bacillus is an excellent organic matter degrader, and it has exhibited various abilities required for lignocellulose degradation. Several B. velezensis strains encode lignocellulosases, however their ability to efficiently transform biomass has not been appreciated. In the present study, through the comparative genomic analysis of the whole genome sequences of 21 B. velezensis strains, CAZyome related to lignocellulose degradation was identified and their similarities and differences were compared. Subsequently, the secretome of B. velezensis LC1 by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were identified and confirmed that a considerable number of proteins were involved in lignocellulose degradation. Moreover, after 6-day treatment, the degradation efficiency of the B. velezensis LC1 toward cellulose, hemicellulose and lignin were 59.90%, 75.44% and 23.41%, respectively, the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielded 10.44 g/L ethanol after 96 h. These results indicate that B. velezensis LC1 has the ability to effectively degrade bamboo lignocellulose and has the potential to be used in bioethanol production.
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28
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Bai DP, Lin XY, Hu YQ, Chen ZZ, Chen L, Huang YF, Huang XH, Li J. Metagenomics approach to identify lignocellulose-degrading enzymes in the gut microbiota of the Chinese bamboo rat cecum. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Santibáñez L, Henríquez C, Corro-Tejeda R, Bernal S, Armijo B, Salazar O. Xylooligosaccharides from lignocellulosic biomass: A comprehensive review. Carbohydr Polym 2021; 251:117118. [DOI: 10.1016/j.carbpol.2020.117118] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/22/2020] [Accepted: 09/04/2020] [Indexed: 02/04/2023]
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Qaseem MF, Wu AM. Balanced Xylan Acetylation is the Key Regulator of Plant Growth and Development, and Cell Wall Structure and for Industrial Utilization. Int J Mol Sci 2020; 21:ijms21217875. [PMID: 33114198 PMCID: PMC7660596 DOI: 10.3390/ijms21217875] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
Xylan is the most abundant hemicellulose, constitutes about 25–35% of the dry biomass of woody and lignified tissues, and occurs up to 50% in some cereal grains. The accurate degree and position of xylan acetylation is necessary for xylan function and for plant growth and development. The post synthetic acetylation of cell wall xylan, mainly regulated by Reduced Wall Acetylation (RWA), Trichome Birefringence-Like (TBL), and Altered Xyloglucan 9 (AXY9) genes, is essential for effective bonding of xylan with cellulose. Recent studies have proven that not only xylan acetylation but also its deacetylation is vital for various plant functions. Thus, the present review focuses on the latest advances in understanding xylan acetylation and deacetylation and explores their effects on plant growth and development. Baseline knowledge about precise regulation of xylan acetylation and deacetylation is pivotal to developing plant biomass better suited for second-generation liquid biofuel production.
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Affiliation(s)
- Mirza Faisal Qaseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China;
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China;
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence:
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Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation. Microorganisms 2020; 8:microorganisms8091357. [PMID: 32899798 PMCID: PMC7564440 DOI: 10.3390/microorganisms8091357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/02/2023] Open
Abstract
A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 protein-coding genes were predicted. Clusters of orthologous groups (COG) analysis revealed various genes with functions in polymeric substrate degradation, especially for Carbohydrate Active enZymes (CAZymes), such as glycoside hydrolases (GHs) and glycosyl transferases (GTs). Furthermore, the transcriptional responses of B5 at different temperatures—with rice straw provided as the sole carbon source—were analyzed. The results revealed that B5 could resist high temperature by upregulating heat shock proteins (HSPs), enhancing protein synthesis, and decreasing carbon catabolism. Briefly, B5 possesses the ability of lignocellulose degradation, and might be considered a potential inoculant for improving composting efficiency.
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Jiménez DJ, Wang Y, Chaib de Mares M, Cortes-Tolalpa L, Mertens JA, Hector RE, Lin J, Johnson J, Lipzen A, Barry K, Mondo SJ, Grigoriev IV, Nichols NN, van Elsas JD. Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium. FEMS Microbiol Ecol 2020; 96:5643886. [PMID: 31769802 DOI: 10.1093/femsec/fiz186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
Coniochaeta species are versatile ascomycetes that have great capacity to deconstruct lignocellulose. Here, we explore the transcriptome of Coniochaeta sp. strain 2T2.1 from wheat straw-driven cultures with the fungus growing alone or as a member of a synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4. The differential expression profiles of carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation by 2T2.1 during the initial 24 hours of incubation. Within the tripartite consortium, 63 transcripts of strain 2T2.1 were differentially expressed at this time point. The presence of the two bacteria significantly upregulated the expression of one galactose oxidase, one GH79-like enzyme, one multidrug transporter, one laccase-like protein (AA1 family) and two bilirubin oxidases, suggesting that inter-kingdom interactions (e.g. amensalism) take place within this microbial consortium. Overexpression of multicopper oxidases indicated that strain 2T2.1 may be involved in lignin depolymerization (a trait of enzymatic synergism), while S. multivorum and C. freundii have the metabolic potential to deconstruct arabinoxylan. Under the conditions applied, 2T2.1 appears to be a better degrader of wheat straw when the two bacteria are absent. This conclusion is supported by the observed suppression of its (hemi)cellulolytic arsenal and lower degradation percentages within the microbial consortium.
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Affiliation(s)
- Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá, Colombia
| | - Yanfang Wang
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Maryam Chaib de Mares
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Larisa Cortes-Tolalpa
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
| | - Jeffrey A Mertens
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Ronald E Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Junyan Lin
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jenifer Johnson
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stephen J Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, Colorado 80521, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720-3102, USA
| | - Nancy N Nichols
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois 61604, USA
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7 9747AG, Groningen, The Netherlands
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Improving the fermentable sugar yields of wheat straw by high-temperature pre-hydrolysis with thermophilic enzymes of Malbranchea cinnamomea. Microb Cell Fact 2020; 19:149. [PMID: 32711527 PMCID: PMC7382850 DOI: 10.1186/s12934-020-01408-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
Background Enzymatic hydrolysis is a key step in the conversion of lignocellulosic polysaccharides to fermentable sugars for the production of biofuels and high-value chemicals. However, current enzyme preparations from mesophilic fungi are deficient in their thermostability and biomass-hydrolyzing efficiency at high temperatures. Thermophilic fungi represent promising sources of thermostable and highly active enzymes for improving the biomass-to-sugar conversion process. Here we present a comprehensive study on the lignocellulosic biomass-degrading ability and enzyme system of thermophilic fungus Malbranchea cinnamomea N12 and the application of its enzymes in the synergistic hydrolysis of lignocellulosic biomass. Results Malbranchea cinnamomea N12 was capable of utilizing untreated wheat straw to produce high levels of xylanases and efficiently degrading lignocellulose under thermophilic conditions. Temporal analysis of the wheat straw-induced secretome revealed that M. cinnamomea N12 successively degraded the lignocellulosic polysaccharides through sequential secretion of enzymes targeting xylan and cellulose. Xylanase-enriched cocktail from M. cinnamomea N12 was more active on native and alkali‑pretreated wheat straw than the commercial xylanases from Trichoderma reesei over temperatures ranging from 40 to 75 °C. Integration of M. cinnamomea N12 enzymes with the commercial cellulase preparation increased the glucose and xylose yields of alkali‑pretreated wheat straw by 32 and 166%, respectively, with pronounced effects at elevated temperature. Conclusions This study demonstrated the remarkable xylanase-producing ability and strategy of sequential lignocellulose breakdown of M. cinnamomea N12. A new process for the hydrolysis of lignocellulosic biomass was proposed, comprising thermophilic enzymolysis by enzymes of M. cinnamomea N12 followed with mesophilic enzymolysis by commercial cellulases. Developing M. cinnamomea N12 as platforms for thermophilic enzyme mixture production will provide new perspectives for improved conversion yields for current biomass saccharification schemes.
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Enhanced Enzymatic Saccharification of Wheat Flour Arabinoxylan and Barley Straw Using Recombinant Hemicellulases. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0231-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Tesei D, Quartinello F, Guebitz GM, Ribitsch D, Nöbauer K, Razzazi-Fazeli E, Sterflinger K. Shotgun proteomics reveals putative polyesterases in the secretome of the rock-inhabiting fungus Knufia chersonesos. Sci Rep 2020; 10:9770. [PMID: 32555357 PMCID: PMC7299934 DOI: 10.1038/s41598-020-66256-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
Knufia chersonesos is an ascomycotal representative of black fungi, a morphological group of polyextremotolerant melanotic fungi, whose ability to resort to recalcitrant carbon sources makes it an interesting candidate for degradation purposes. A secretome screening towards polyesterases was carried out for the fungus and its non-melanized mutant, grown in presence of the synthetic copolyester Polybutylene adipate terephthalate (PBAT) as additional or sole carbon source, and resulted in the identification of 37 esterolytic and lipolytic enzymes across the established cultivation conditions. Quantitative proteomics allowed to unveil 9 proteins being constitutively expressed at all conditions and 7 which were instead detected as up-regulated by PBAT exposure. Protein functional analysis and structure prediction indicated similarity of these enzymes to microbial polyesterases of known biotechnological use such as MHETase from Ideonella sakaiensis and CalA from Candida albicans. For both strains, PBAT hydrolysis was recorded at all cultivation conditions and primarily the corresponding monomers were released, which suggests degradation to the polymer's smallest building block. The work presented here aims to demonstrate how investigations of the secretome can provide new insights into the eco-physiology of polymer degrading fungi and ultimately aid the identification of novel enzymes with potential application in polymer processing, recycling and degradation.
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Affiliation(s)
- Donatella Tesei
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Felice Quartinello
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - Georg M Guebitz
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
- Austrian Centre of Industrial Biotechnology, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - Doris Ribitsch
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
- Austrian Centre of Industrial Biotechnology, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - Katharina Nöbauer
- VetCore Facility for Research, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Ebrahim Razzazi-Fazeli
- VetCore Facility for Research, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Katja Sterflinger
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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36
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Poria V, Saini JK, Singh S, Nain L, Kuhad RC. Arabinofuranosidases: Characteristics, microbial production, and potential in waste valorization and industrial applications. BIORESOURCE TECHNOLOGY 2020; 304:123019. [PMID: 32089440 DOI: 10.1016/j.biortech.2020.123019] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 05/15/2023]
Abstract
Alpha-L-arabinofuranoside arabinofuranohydrolase (ARA), more commonly known as alpha-L-arabinofuranosidase (E.C. number 3.2.1.55), is a hydrolytic enzyme, catalyzing the cleavage of alpha-L-arabinose by acting on the non-reducing ends of alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linked arabinoxylans and arabinogalactans. ARA functions as debranching enzyme removing arabinose substituents from arabinoxylan and arabinoxylooligomers, thereby, boosting the hydrolysis of arabinoxylan fraction of hemicellulose and improving bioconversion of lignocellulosic biomass. Previously, comprehensive information on this enzyme has not been reviewed thoroughly. Therefore, the main aim of this review is to highlight the important properties of this interesting enzyme, microorganisms used for its production, and enhanced production using genetic engineering approach. An account on synergism with other biomass hydrolyzing enzymes and various industrial applications of this enzyme has also been provided along with an outlook on further research and development.
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Affiliation(s)
- Vikram Poria
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Jitendra Kumar Saini
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Surender Singh
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India; Division of Microbiology, Indian Agricultural Research Institute, New Delhi PIN-110012, India.
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi PIN-110012, India
| | - Ramesh Chander Kuhad
- Central University of Haryana, Mahendergarh, Haryana PIN-123031, India; Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, New Delhi PIN-110021, India
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Li Y, Lei L, Zheng L, Xiao X, Tang H, Luo C. Genome sequencing of gut symbiotic Bacillus velezensis LC1 for bioethanol production from bamboo shoots. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:34. [PMID: 32140179 PMCID: PMC7048129 DOI: 10.1186/s13068-020-1671-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Bamboo, a lignocellulosic feedstock, is considered as a potentially excellent raw material and evaluated for lignocellulose degradation and bioethanol production, with a focus on using physical and chemical pre-treatment. However, studies reporting the biodegradation of bamboo lignocellulose using microbes such as bacteria and fungi are scarce. RESULTS In the present study, Bacillus velezensis LC1 was isolated from Cyrtotrachelus buqueti, in which the symbiotic bacteria exhibited lignocellulose degradation ability and cellulase activities. We performed genome sequencing of B. velezensis LC1, which has a 3929,782-bp ring chromosome and 46.5% GC content. The total gene length was 3,502,596 bp using gene prediction, and the GC contents were 47.29% and 40.04% in the gene and intergene regions, respectively. The genome contains 4018 coding DNA sequences, and all have been assigned predicted functions. Carbohydrate-active enzyme annotation identified 136 genes annotated to CAZy families, including GH, GTs, CEs, PLs, AAs and CBMs. Genes involved in lignocellulose degradation were identified. After a 6-day treatment, the bamboo shoot cellulose degradation efficiency reached 39.32%, and the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielding 7.2 g/L of ethanol at 96 h. CONCLUSIONS These findings provide an insight for B. velezensis strains in converting lignocellulose into ethanol. B. velezensis LC1, a symbiotic bacteria, can potentially degrade bamboo lignocellulose components and further transformation to ethanol, and expand the bamboo lignocellulosic bioethanol production.
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Affiliation(s)
- Yuanqiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Lu Lei
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Li Zheng
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Ximeng Xiao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Hao Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Chaobing Luo
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
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38
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Zhang H, Li Q, Zhao Y, Zhang M, Xu D, Wu Z, Zhou Q. Endoglucanase activity of cellulolytic bacteria from lake sediments and its application in hydrophyte degradation. FEMS Microbiol Lett 2020; 367:6029119. [PMID: 33296466 DOI: 10.1093/femsle/fnaa200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/07/2020] [Indexed: 11/14/2022] Open
Abstract
Hydrophytes are plants that grow in or on water. Their overgrowth adversely affects the ecosystem because of crowding out other aquatic organisms and polluting the environment with plant residue. In principle, cellulolytic bacteria can be used to degrade hydrophyte biomass. We here isolated and characterized four cellulolytic bacterial strains from Lake Donghu sediments (Wuhan, China) that are rich in organic matter and plant residues. The isolates (WDHS-01 to 04) represent Bacillus, Micromonospora and Streptomyces genera. The bacteria exhibited pronounced endoglucanase activities (from 0.022 to 0.064 U mL-1). They did not extensively degrade the emerged plant Canna indica L. However, in an Hydrilla verticillata (submerged plant) degradation medium, strain WDHS-02 exhibited a high degradation rate (54.91%), endoglucanase activity of 0.35 U mL-1 and the conversion rate of cellulose to reducing sugars of 7.15%. Correlation analysis revealed that bacterial endoglucanase activity was significantly correlated with the degradation rate, and acid detergent lignin, ash and cellulose content of the residual H. verticillata powder. In conclusion, the identified bacteria efficiently decomposed submerged plants without the need for acid-base pretreatment. They expand the set of known cellulolytic bacteria and can be used for natural degradation of submerged plants.
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Affiliation(s)
- Hongpei Zhang
- College of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, No. 122 Luoshi Road, Hongshan District, Wuhan, Hubei Province, P.R. China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Qianzheng Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, No.19(A) Yuquan Road, Shijingshan District, Beijing, P.R. China
| | - Yuqing Zhao
- College of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, No. 122 Luoshi Road, Hongshan District, Wuhan, Hubei Province, P.R. China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Mingzhen Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, No.19(A) Yuquan Road, Shijingshan District, Beijing, P.R. China
| | - Dong Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Qiaohong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
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Malgas S, Mafa MS, Mkabayi L, Pletschke BI. A mini review of xylanolytic enzymes with regards to their synergistic interactions during hetero-xylan degradation. World J Microbiol Biotechnol 2019; 35:187. [PMID: 31728656 DOI: 10.1007/s11274-019-2765-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
Abstract
This review examines the recent models describing the mode of action of various xylanolytic enzymes and how these enzymes can be applied (sequentially or simultaneously) with their distinctive roles in mind to achieve efficient xylan degradation. With respect to homeosynergy, synergism appears to be as a result of β-xylanase and/or oligosaccharide reducing-end β-xylanase liberating xylo-oligomers (XOS) that are preferred substrates of the processive β-xylosidase. With regards to hetero-synergism, two cross relationships appear to exist and seem to be the reason for synergism between the enzymes during xylan degradation. These cross relations are the debranching enzymes such as α-glucuronidase or side-chain cleaving enzymes such as carbohydrate esterases (CE) removing decorations that would have hindered back-bone-cleaving enzymes, while backbone-cleaving-enzymes liberate XOS that are preferred substrates of the debranching and side-chain-cleaving enzymes. This interaction is demonstrated by high yields in co-production of xylan substituents such as arabinose, glucuronic acid and ferulic acid, and XOS. Finally, lytic polysaccharide monooxygenases (LPMO) have also been implicated in boosting whole lignocellulosic biomass or insoluble xylan degradation by glycoside hydrolases (GH) by possibly disrupting entangled xylan residues. Since it has been observed that the same enzyme (same Enzyme Commission, EC, classification) from different GH or CE and/or AA families can display different synergistic interactions with other enzymes due to different substrate specificities and properties, in this review, we propose an approach of enzyme selection (and mode of application thereof) during xylan degradation, as this can improve the economic viability of the degradation of xylan for producing precursors of value added products.
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Affiliation(s)
- Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Mpho S Mafa
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.,Protein Structure-Function Research Unit (PSFRU), School of Molecular and Cell Biology, Wits University, Johannesburg, Gauteng, 2000, South Africa
| | - Lithalethu Mkabayi
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Brett I Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.
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40
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Mondo SJ, Jiménez DJ, Hector RE, Lipzen A, Yan M, LaButti K, Barry K, van Elsas JD, Grigoriev IV, Nichols NN. Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:229. [PMID: 31572496 PMCID: PMC6757388 DOI: 10.1186/s13068-019-1569-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). RESULTS The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source. CONCLUSIONS We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.
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Affiliation(s)
- Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, CO 80521 USA
| | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá, Colombia
| | - Ronald E. Hector
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720-3102 USA
| | - Nancy N. Nichols
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604 USA
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41
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Wierzbicki MP, Christie N, Pinard D, Mansfield SD, Mizrachi E, Myburg AA. A systems genetics analysis in Eucalyptus reveals coordination of metabolic pathways associated with xylan modification in wood-forming tissues. THE NEW PHYTOLOGIST 2019; 223:1952-1972. [PMID: 31144333 DOI: 10.1111/nph.15972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
Acetyl- and methylglucuronic acid decorations of xylan, the dominant hemicellulose in secondary cell walls (SCWs) of woody dicots, affect its interaction with cellulose and lignin to determine SCW structure and extractability. Genes and pathways involved in these modifications may be targets for genetic engineering; however, little is known about the regulation of xylan modifications in woody plants. To address this, we assessed genetic and gene expression variation associated with xylan modification in developing xylem of Eucalyptus grandis × Eucalyptus urophylla interspecific hybrids. Expression quantitative trait locus (eQTL) mapping identified potential regulatory polymorphisms affecting gene expression modules associated with xylan modification. We identified 14 putative xylan modification genes that are members of five expression modules sharing seven trans-eQTL hotspots. The xylan modification genes are prevalent in two expression modules. The first comprises nucleotide sugar interconversion pathways supplying the essential precursors for cellulose and xylan biosynthesis. The second contains genes responsible for phenylalanine biosynthesis and S-adenosylmethionine biosynthesis required for glucuronic acid and monolignol methylation. Co-expression and co-regulation analyses also identified four metabolic sources of acetyl coenxyme A that appear to be transcriptionally coordinated with xylan modification. Our systems genetics analysis may provide new avenues for metabolic engineering to alter wood SCW biology for enhanced biomass processability.
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Affiliation(s)
- Martin P Wierzbicki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Desré Pinard
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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Cao H, Sun L, Huang Y, Liu X, Yang D, Liu T, Jia X, Wen B, Gu T, Wang F, Xin F. Structural Insights into the Dual-Substrate Recognition and Catalytic Mechanisms of a Bifunctional Acetyl Ester–Xyloside Hydrolase from Caldicellulosiruptor lactoaceticus. ACS Catal 2019. [DOI: 10.1021/acscatal.8b03383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hao Cao
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lichao Sun
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ying Huang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dong Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Tengfei Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianyi Gu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengzhong Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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43
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Xin D, Chen X, Wen P, Zhang J. Insight into the role of α-arabinofuranosidase in biomass hydrolysis: cellulose digestibility and inhibition by xylooligomers. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:64. [PMID: 30949240 PMCID: PMC6429694 DOI: 10.1186/s13068-019-1412-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/15/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND α-l-Arabinofuranosidase (ARA), a debranching enzyme that can remove arabinose substituents from arabinoxylan and arabinoxylooligomers (AXOS), promotes the hydrolysis of the arabinoxylan fraction of biomass; however, the impact of ARA on the overall digestibility of cellulose is controversial. In this study, we investigated the effects of the addition of ARA on cellulase hydrolytic action. RESULTS We found that approximately 15% of the xylan was converted into AXOS during the hydrolysis of aqueous ammonia-pretreated corn stover and that this AXOS fraction was approximately 12% substituted with arabinose. The addition of ARA removes a portion of the arabinose decoration, but the resulting less-substituted AXOS inhibited cellulase action much more effectively; showing an increase of 45.7%. Kinetic experiments revealed that AXOS with a lower degree of arabinose substitution showed stronger affinity for the active site of cellobiohydrolase, which could be the mechanism of increased inhibition. CONCLUSIONS Our findings strongly suggest that the ratio of ARA and other xylanases should be carefully selected to avoid the strong inhibition caused by the less-substituted AXOS during the hydrolysis of arabinoxylan-containing biomass. This study advances our understanding of the inhibitory mechanism of xylooligomers and provides critical new insights into the relationship of ARA addition and cellulose digestibility.
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Affiliation(s)
- Donglin Xin
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Xiang Chen
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Peiyao Wen
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Junhua Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
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44
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Gao J, Zhao Y, Zhang G, Li Y, Li Q. Production optimization, purification, expression, and characterization of a novel α-l-arabinofuranosidase from Paenibacillus polymyxa. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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45
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Malik AA, Puissant J, Buckeridge KM, Goodall T, Jehmlich N, Chowdhury S, Gweon HS, Peyton JM, Mason KE, van Agtmaal M, Blaud A, Clark IM, Whitaker J, Pywell RF, Ostle N, Gleixner G, Griffiths RI. Land use driven change in soil pH affects microbial carbon cycling processes. Nat Commun 2018; 9:3591. [PMID: 30181597 PMCID: PMC6123395 DOI: 10.1038/s41467-018-05980-1] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/06/2018] [Indexed: 01/28/2023] Open
Abstract
Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates. Land use intensification could modify microbial activity and thus ecosystem function. Here, Malik et al. sample microbes and carbon-related functions across a land use gradient, demonstrating that microbial biomass and carbon use efficiency are reduced in human-impacted near-neutral pH soils.
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Affiliation(s)
- Ashish A Malik
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK. .,Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697, USA.
| | | | - Kate M Buckeridge
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Tim Goodall
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, 04318, Germany
| | - Somak Chowdhury
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, 07745, Germany
| | - Hyun Soon Gweon
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK.,School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
| | - Jodey M Peyton
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Kelly E Mason
- Centre for Ecology and Hydrology, Lancaster, LA1 4AP, UK
| | | | - Aimeric Blaud
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Ian M Clark
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | | | - Nick Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Gerd Gleixner
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, 07745, Germany
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46
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Marjamaa K, Kruus K. Enzyme biotechnology in degradation and modification of plant cell wall polymers. PHYSIOLOGIA PLANTARUM 2018; 164:106-118. [PMID: 29987848 DOI: 10.1111/ppl.12800] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 05/28/2023]
Abstract
Lignocelluloses are abundant raw materials for production of fuels, chemicals and materials. The purpose of this paper is to review the enzyme-types and enzyme-technologies studied and applied in the processing of the lignocelluloses into different products. The enzymes here are mostly glycoside hydrolases, esterases and different redox enzymes. Enzymatic hydrolysis of lignocellulosic polysaccharides to platform sugars has been widely studied leading to development of advanced commercial products for this purpose. Restricted hydrolysis or oxidation of cellulosic fibers have been applied in processing of pulps to paper products, nanocelluloses and textile fibers. Oxidation, transglycosylation and derivatization have been utilized in functionalization of fibers, cellulosic surfaces and polysaccharides. Enzymatic polymerization, depolymerization and grafting methods are being developed for lignin valorization.
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Affiliation(s)
- Kaisa Marjamaa
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, Espoo, 02044, Finland
| | - Kristiina Kruus
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, Espoo, 02044, Finland
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47
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Sista Kameshwar AK, Qin W. Understanding the structural and functional properties of carbohydrate esterases with a special focus on hemicellulose deacetylating acetyl xylan esterases. Mycology 2018; 9:273-295. [PMID: 30533253 PMCID: PMC6282417 DOI: 10.1080/21501203.2018.1492979] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/21/2018] [Indexed: 11/29/2022] Open
Abstract
Acetyl and methyl esterifications are two major naturally found substitutions in the plant cell-wall polysaccharides. The non-cellulosic plant cell-wall polysaccharides such as pectin and hemicellulose are differentially esterified by the O-acetyl and methyl groups to cease the action of various hydrolytic enzymes secreted by different fungi and bacterial species. Thus, microorganisms have emerged with a special class of enzymes known as carbohydrate esterases (CE). The CE catalyse O-de, N-deacetylation of acetylated saccharide residues (esters or amides, where sugars play the role of alcohol/amine/acid). Carbohydrate active enzyme (CAZy) database has classified CE into 16 classes, of which hemicellulose deacetylating CE were grouped into eight classes (CE-1 to CE-7 and CE-16). Various plant biomass degrading fungi and bacteria secretes acetyl xylan esterases (AcXE); however, these enzymes exhibit varied substrate specificities. AcXE and xylanases-coupled pretreatment methods exhibit significant applications, such as enhancing animal feedstock, baking industry, production of food additives, paper and pulp, xylitol production and biorefinery-based industries, respectively. Thus, understanding the structural and functional properties of acetyl xylan esterase will significantly aid in developing the efficient AcXE with wide range of industrial applications.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
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48
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Yang Y, Yang J, Liu J, Wang R, Liu L, Wang F, Yuan H. The composition of accessory enzymes of Penicillium chrysogenum P33 revealed by secretome and synergistic effects with commercial cellulase on lignocellulose hydrolysis. BIORESOURCE TECHNOLOGY 2018; 257:54-61. [PMID: 29482166 DOI: 10.1016/j.biortech.2018.02.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 05/25/2023]
Abstract
Herein, we report the secretome of Penicillium chrysogenum P33 under induction of lignocellulose for the first time. A total of 356 proteins were identified, including complete cellulases and numerous hemicellulases. Supplementing a commercial cellulase with increasing dosage of P33 enzyme cocktail from 1 to 5 mg/g substrate increased the release of reducing sugars from delignified corn stover by 21.4% to 106.8%. When 50% cellulase was replaced by P33 enzyme cocktail, release of reducing sugars was 78.6% higher than with cellulase alone. Meanwhile, glucan and xylan conversion was increased by 37% and 106%, respectively. P33 enzyme cocktail also enhanced commercial cellulase hydrolysis against four different delignified lignocellulosic biomass. These findings demonstrate that mixing appropriate amount of P33 cocktail with cellulase improves polysaccharide hydrolysis, suggesting P33 enzymes have great potential for industrial applications.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiawen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ruonan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liang Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fengqin Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
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49
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Chen L, Gu W, Xu HY, Yang GL, Shan XF, Chen G, Kang YH, Wang CF, Qian AD. Comparative genome analysis of Bacillus velezensis reveals a potential for degrading lignocellulosic biomass. 3 Biotech 2018; 8:253. [PMID: 29765811 DOI: 10.1007/s13205-018-1270-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/30/2018] [Indexed: 02/07/2023] Open
Abstract
Genomes of 24 sequenced Bacillus velezensis strains were characterized to identity shared and unique genes of lignocellulolytic enzymes and predict potential to degrade lignocellulose. All 24 strains had genes that encoded lignocellulolytic enzymes, with potential to degrade cellulose and hemicelluloses. Several lignocellulosic genes related to cellulose degradation were universally present, including one GH5 (endo-1,4-β-glucanase), one GH30 (glucan endo-1,6-β-glucosidase), two GH4 (6-phospho-β-glucosidase, 6-phospho-α-glucosidase), one GH1 (6-phospho-β-galactosidase), one GH16 (β-glucanase) and three GH32 (two sucrose-6-phosphate hydrolase and levanase). However, in the absence of gene(s) for cellobiohydrolase, it was predicted that none of the 24 strains would be able to directly hydrolyse cellulose. Regarding genes for hemicellulose degradation, four GH43 (1,4-β-xylosidase; except strain 9912D), one GH11 (endo-1,4-β-xylanase), three GH43 (two arabinan endo-1,5-α-L-arabinosidase and one arabinoxylan arabinofuranohydrolase), two GH51 (α-N-arabinofuranosidase), one GH30 (glucuronoxylanase), one GH26 (β-mannosidase) and one GH53 (arabinogalactan endo-1,4-β-galactosidase) were present. In addition, two PL1 (pectate lyase) and one PL9 (pectate lyase) with potential for pectin degradation were conserved among all 24 strains. In addition, all 24 Bacillus velezensis had limited representation of the auxiliary activities super-family, consistent with a limited ability to degrade lignin. Therefore, it was predicted that for these bacteria to degrade lignin, pretreatment of lignocellulosic substrates may be required. Finally, based on in silico studies, we inferred that Bacillus velezensis strains may degrade a range of polysaccharides in lignocellulosic biomasses.
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Affiliation(s)
- Long Chen
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Wei Gu
- Shandong BaoLai-LeeLai Bioengineering Co. Ltd, Tai'an, 271000 Shandong People's Republic of China
| | - Hai-Yan Xu
- Shandong BaoLai-LeeLai Bioengineering Co. Ltd, Tai'an, 271000 Shandong People's Republic of China
| | - Gui-Lian Yang
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 4Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 5Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Xiao-Feng Shan
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Guang Chen
- 3College of Life Sciences, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Yuan-Huan Kang
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Chun-Feng Wang
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 4Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 5Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People's Republic of China
| | - Ai-Dong Qian
- 1College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 4Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, 130118 People's Republic of China
- 5Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118 People's Republic of China
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50
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Comtet-Marre S, Chaucheyras-Durand F, Bouzid O, Mosoni P, Bayat AR, Peyret P, Forano E. FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota. Front Microbiol 2018; 9:215. [PMID: 29487591 PMCID: PMC5816793 DOI: 10.3389/fmicb.2018.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/30/2018] [Indexed: 01/22/2023] Open
Abstract
Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme) families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6) were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi) represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.
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Affiliation(s)
- Sophie Comtet-Marre
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France.,R&D Animal Nutrition, Lallemand, Blagnac, France
| | - Frédérique Chaucheyras-Durand
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France.,R&D Animal Nutrition, Lallemand, Blagnac, France
| | - Ourdia Bouzid
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pascale Mosoni
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ali R Bayat
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Pierre Peyret
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Evelyne Forano
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
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