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Reichart NJ, Steiger AK, Van Fossen EM, McClure R, Overkleeft HS, Wright AT. Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing. ISME COMMUNICATIONS 2023; 3:106. [PMID: 37777628 PMCID: PMC10542759 DOI: 10.1038/s43705-023-00305-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/22/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
Multi-omic analyses can provide information on the potential for activity within a microbial community but often lack specificity to link functions to cell, primarily offer potential for function or rely on annotated databases. Functional assays are necessary for understanding in situ microbial activity to better describe and improve microbiome biology. Targeting enzyme activity through activity-based protein profiling enhances the accuracy of functional studies. Here, we introduce a pipeline of coupling activity-based probing with fluorescence-activated cell sorting, culturing, and downstream activity assays to isolate and examine viable populations of cells expressing a function of interest. We applied our approach to a soil microbiome using two activity-based probes to enrich for communities with elevated activity for lignocellulose-degradation phenotypes as determined by four fluorogenic kinetic assays. Our approach efficiently separated and identified microbial members with heightened activity for glycosyl hydrolases, and by expanding this workflow to various probes for other function, this process can be applied to unique phenotype targets of interest.
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Affiliation(s)
- Nicholas J Reichart
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Andrea K Steiger
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Elise M Van Fossen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Aaron T Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
- Department of Biology, Baylor University, Waco, TX, USA.
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA.
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2
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Paul M, Pandey NK, Banerjee A, Shroti GK, Tomer P, Gazara RK, Thatoi H, Bhaskar T, Hazra S, Ghosh D. An insight into omics analysis and metabolic pathway engineering of lignin-degrading enzymes for enhanced lignin valorization. BIORESOURCE TECHNOLOGY 2023; 379:129045. [PMID: 37044152 DOI: 10.1016/j.biortech.2023.129045] [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: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
Lignin, a highly heterogeneous polymer of lignocellulosic biomass, is intricately associated with cellulose and hemicellulose, responsible for its strength and rigidity. Lignin decomposition is carried out through certain enzymes derived from microorganisms to promote the hydrolysis of lignin. Analyzing multi-omics data helps to emphasize the probable value of fungal-produced enzymes to degrade the lignocellulosic material, which provides them an advantage in their ecological niches. This review focuses on lignin biodegrading microorganisms and associated ligninolytic enzymes, including lignin peroxidase, manganese peroxidase, versatile peroxidase, laccase, and dye-decolorizing peroxidase. Further, enzymatic catalysis, lignin biodegradation mechanisms, vital factors responsible for lignin modification and degradation, and the design and selection of practical metabolic pathways are also discussed. Highlights were made on metabolic pathway engineering, different aspects of omics analyses, and its scope and applications to ligninase enzymes. Finally, the advantages and essential steps of successfully applying metabolic engineering and its path forward have been addressed.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada, Odisha 757003, India
| | - Niteesh Kumar Pandey
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand 247667, India
| | - Ayan Banerjee
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Mohkampur, Dehradun, Uttarakhand 248005, India; Academy of Scientific and Innovative Research, CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh 201002, India
| | - Gireesh Kumar Shroti
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand 247667, India
| | - Preeti Tomer
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand 247667, India
| | - Rajesh Kumar Gazara
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand 247667, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada, Odisha 757003, India
| | - Thallada Bhaskar
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Mohkampur, Dehradun, Uttarakhand 248005, India; Academy of Scientific and Innovative Research, CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh 201002, India
| | - Saugata Hazra
- Department of Bioscience and Bioengineering, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand 247667, India; Centre for Nanotechnology, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand 247667, India.
| | - Debashish Ghosh
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Mohkampur, Dehradun, Uttarakhand 248005, India; Academy of Scientific and Innovative Research, CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh 201002, India
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3
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Novak JK, Gardner JG. Galactomannan utilization by Cellvibrio japonicus relies on a single essential α-galactosidase encoded by the aga27A gene. Mol Microbiol 2023; 119:312-325. [PMID: 36604822 DOI: 10.1111/mmi.15024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
Plant mannans are a component of lignocellulose that can have diverse compositions in terms of its backbone and side-chain substitutions. Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides that can include mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has 10 predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential mannan-degrading components in this bacterium. The transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode carbohydrate active enzymes (CAZymes) when mannan was actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme-encoding genes in the context of mannan utilization. Growth analysis of the mutant strains found that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α-galactosidase, and mannosidase, respectively, were important for the deconstruction of galactomannan, with Aga27A being essential. Our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the complete degradation of this hemicellulose.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
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4
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Wu L, Che S, Qin X, Xu Y, Tian S, Zhu Y, Song J, Guan Y, Wang D, Wu M, Yang X, Wu Z, Yang M. Identification, characteristics and rice growth promotion of a highly efficient cellulolytic bacterial strain, Cellulomonas iranensis ZJW-6, isolated from paddy soil in central China. Front Microbiol 2023; 14:1152966. [PMID: 37032857 PMCID: PMC10073736 DOI: 10.3389/fmicb.2023.1152966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
The microbial degradation of lignocellulose is the best way to treat straw, which has a broad application prospect. It is consistent with the idea of agricultural sustainable development and has an important impact on the utilization of biomass resources. To explore and utilize the microbial resources of lignocellulose degradation, 27 lignocellulose degrading strains were screened from 13 regions in China. ZJW-6 was selected because of its 49.6% lignocellulose weight loss rate. According to the theoretical analysis of the experimental results, the following straw degradation conditions were obtained by ZJW-6: nitrogen source input of 8.45 g/L, a pH of 8.57, and a temperature of 31.63°C, the maximum weight loss rate of rice straw could reach 54.8%. It was concluded that ZJW-6 belonged to Cellulomonas iranensis according to 16S rRNA-encoding gene sequence comparison and identification. ZJW-6 is a Gram-positive bacterium that grows slowly and has a small yellowish green colony. To explain the degradation mechanism of lignocellulose, the experiment of enzymatic properties of the strain was prepared and carried out. It was discovered that ZJW-6 has an excellent ability to degrade cellulose, hemicellulose, and lignin, with cellulose and hemicellulose loss rates reaching almost 50% in 4 days and lignin loss rates reaching nearly 30%. Furthermore, ZJW-6 demonstrated lignocellulose degradation under aerobic and anaerobic conditions, indicating the strain's broad application potential. ZJW-6 was found to be more effective than ordinary humic acid in improving rice soil (available phosphorus, available nitrogen, organic matter) and promoting rice growth in a rice pot experiment (increasing root-shoot ratio, root activity, chlorophyll content and net photosynthetic rate). ZJW-6 plays an important role in promoting the development and utilization of straw resources. It has important significance for the advancement of green agriculture.
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Affiliation(s)
- Lei Wu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Songhao Che
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Xueting Qin
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yufeng Xu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Shiqi Tian
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuan Zhu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jian Song
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yunpeng Guan
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Dongchao Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Meikang Wu
- Faculty of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Xue Yang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhihai Wu
- Faculty of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Meiying Yang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- *Correspondence: Meiying Yang,
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Identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling. Commun Biol 2022; 5:1254. [DOI: 10.1038/s42003-022-04141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractActivity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.
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Rammala B, Zhou N. Looking into the world's largest elephant population in search of ligninolytic microorganisms for biorefineries: a mini-review. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:64. [PMID: 35689287 PMCID: PMC9188235 DOI: 10.1186/s13068-022-02159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022]
Abstract
Gastrointestinal tracts (GIT) of herbivores are lignin-rich environments with the potential to find ligninolytic microorganisms. The occurrence of the microorganisms in herbivore GIT is a well-documented mutualistic relationship where the former benefits from the provision of nutrients and the latter benefits from the microorganism-assisted digestion of their recalcitrant lignin diets. Elephants are one of the largest herbivores that rely on the microbial anaerobic fermentation of their bulky recalcitrant low-quality forage lignocellulosic diet given their inability to break down major components of plant cells. Tapping the potential of these mutualistic associations in the biggest population of elephants in the whole world found in Botswana is attractive in the valorisation of the bulky recalcitrant lignin waste stream generated from the pulp and paper, biofuel, and agro-industries. Despite the massive potential as a feedstock for industrial fermentations, few microorganisms have been commercialised. This review focuses on the potential of microbiota from the gastrointestinal tract and excreta of the worlds' largest population of elephants of Botswana as a potential source of extremophilic ligninolytic microorganisms. The review further discusses the recalcitrance of lignin, achievements, limitations, and challenges with its biological depolymerisation. Methods of isolation of microorganisms from elephant dung and their improvement as industrial strains are further highlighted.
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Affiliation(s)
- Bame Rammala
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
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7
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Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [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: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
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Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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8
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Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies. Int J Mol Sci 2021; 22:ijms222212249. [PMID: 34830131 PMCID: PMC8624197 DOI: 10.3390/ijms222212249] [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: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 01/14/2023] Open
Abstract
Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.
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Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N. A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:6001. [PMID: 34204975 PMCID: PMC8199887 DOI: 10.3390/ijerph18116001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.
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Affiliation(s)
| | - Mohd Rafatullah
- Division of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (O.B.C.); (H.A.T.); (N.I.)
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Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N. Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential. Life (Basel) 2021; 11:493. [PMID: 34071172 PMCID: PMC8228822 DOI: 10.3390/life11060493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022] Open
Abstract
Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes. The bacterial diversity of Municipal Solid Waste sediments was determined using the illumina MiSeq system after DNA extraction and Polymerase chain reactions. Data analysis was used to determine the community's richness, diversity, and correlation with environmental factors. Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline pH values. Temperature and moisture content showed the highest correlation with the bacteria community. The bacterial analysis of the community DNA revealed 357,030 effective sequences and 1891 operational taxonomic units (OTUs) assigned. Forty phyla were found, with the dominant phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota, while Aerococcus, Stenotrophomonas, and Sporosarcina were the dominant species. PICRUSt provided insight on community's metabolic function, which was narrowed down to search for lignocellulolytic enzymes' function. Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data. This article reports on the first phylogenetic analysis of the Pulau Burung landfill bacterial community. These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.
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Affiliation(s)
| | - Mohd Rafatullah
- School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia; (O.B.C.); (H.A.T.); (N.I.)
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11
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Bacterial valorization of pulp and paper industry process streams and waste. Appl Microbiol Biotechnol 2021; 105:1345-1363. [PMID: 33481067 DOI: 10.1007/s00253-021-11107-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
The pulp and paper industry is a major source of lignocellulose-containing streams. The components of lignocellulose material are lignin, hemicellulose, and cellulose that may be hydrolyzed into their smaller components and used as feedstocks for valorization efforts. Much of this material is contained in underutilized streams and waste products, such as black liquor, pulp and paper sludge, and wastewater. Bacterial fermentation strategies have suitable potential to upgrade lignocellulosic biomass contained in these streams to value-added chemicals. Bacterial conversion allows for a sustainable and economically feasible approach to valorizing these streams, which can bolster and expand applications of the pulp and paper industry. This review discusses the composition of pulp and paper streams, bacterial isolates from process streams that can be used for lignocellulose biotransformations, and technological approaches for improving valorization efforts. KEY POINTS: • Reviews the conversion of pulp and paper industry waste by bacterial isolates. • Metabolic pathways for the breakdown of lignocellulose components. • Methods for isolating bacteria, determining value-added products, and increasing product yields.
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12
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Chettri D, Verma AK, Verma AK. Innovations in CAZyme gene diversity and its modification for biorefinery applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00525. [PMID: 32963975 PMCID: PMC7490808 DOI: 10.1016/j.btre.2020.e00525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.
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13
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Corrêa CL, Midorikawa GEO, Filho EXF, Noronha EF, Alves GSC, Togawa RC, Silva-Junior OB, Costa MMDC, Grynberg P, Miller RNG. Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes in Aspergillus terreus Involved in Plant Biomass Degradation. Front Bioeng Biotechnol 2020; 8:564527. [PMID: 33123513 PMCID: PMC7573219 DOI: 10.3389/fbioe.2020.564527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
Given the global abundance of plant biomass residues, potential exists in biorefinery-based applications with lignocellulolytic fungi. Frequently isolated from agricultural cellulosic materials, Aspergillus terreus is a fungus efficient in secretion of commercial enzymes such as cellulases, xylanases and phytases. In the context of biomass saccharification, lignocellulolytic enzyme secretion was analyzed in a strain of A. terreus following liquid culture with sugarcane bagasse (SB) (1% w/v) and soybean hulls (SH) (1% w/v) as sole carbon source, in comparison to glucose (G) (1% w/v). Analysis of the fungal secretome revealed a maximum of 1.017 UI.mL–1 xylanases after growth in minimal medium with SB, and 1.019 UI.mL–1 after incubation with SH as carbon source. The fungal transcriptome was characterized on SB and SH, with gene expression examined in comparison to equivalent growth on G as carbon source. Over 8000 genes were identified, including numerous encoding enzymes and transcription factors involved in the degradation of the plant cell wall, with significant expression modulation according to carbon source. Eighty-nine carbohydrate-active enzyme (CAZyme)-encoding genes were identified following growth on SB, of which 77 were differentially expressed. These comprised 78% glycoside hydrolases, 8% carbohydrate esterases, 2.5% polysaccharide lyases, and 11.5% auxiliary activities. Analysis of the glycoside hydrolase family revealed significant up-regulation for genes encoding 25 different GH family proteins, with predominance for families GH3, 5, 7, 10, and 43. For SH, from a total of 91 CAZyme-encoding genes, 83 were also significantly up-regulated in comparison to G. These comprised 80% glycoside hydrolases, 7% carbohydrate esterases, 5% polysaccharide lyases, 7% auxiliary activities (AA), and 1% glycosyltransferases. Similarly, within the glycoside hydrolases, significant up-regulation was observed for genes encoding 26 different GH family proteins, with predominance again for families GH3, 5, 10, 31, and 43. A. terreus is a promising species for production of enzymes involved in the degradation of plant biomass. Given that this fungus is also able to produce thermophilic enzymes, this first global analysis of the transcriptome following cultivation on lignocellulosic carbon sources offers considerable potential for the application of candidate genes in biorefinery applications.
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Affiliation(s)
- Camila L Corrêa
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Glaucia E O Midorikawa
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | | | - Eliane Ferreira Noronha
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Gabriel S C Alves
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica - PqEB, Brasília, Brazil
| | | | | | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica - PqEB, Brasília, Brazil
| | - Robert N G Miller
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
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14
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Aliyu H, Gorte O, Zhou X, Neumann A, Ochsenreither K. In silico Proteomic Analysis Provides Insights Into Phylogenomics and Plant Biomass Deconstruction Potentials of the Tremelalles. Front Bioeng Biotechnol 2020; 8:226. [PMID: 32318549 PMCID: PMC7147457 DOI: 10.3389/fbioe.2020.00226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 01/27/2023] Open
Abstract
Basidiomycetes populate a wide range of ecological niches but unlike ascomycetes, their capabilities to decay plant polymers and their potential for biotechnological approaches receive less attention. Particularly, identification and isolation of CAZymes is of biotechnological relevance and has the potential to improve the cache of currently available commercial enzyme cocktails toward enhanced plant biomass utilization. The order Tremellales comprises phylogenetically diverse fungi living as human pathogens, mycoparasites, saprophytes or associated with insects. Here, we have employed comparative genomics approaches to highlight the phylogenomic relationships among thirty-five Tremellales and to identify putative enzymes of biotechnological interest encoded on their genomes. Evaluation of the predicted proteomes of the thirty-five Tremellales revealed 6,918 putative carbohydrate-active enzymes (CAZYmes) and 7,066 peptidases. Two soil isolates, Saitozyma podzolica DSM 27192 and Cryptococcus sp. JCM 24511, show higher numbers harboring an average of 317 compared to a range of 267-121 CAZYmes for the rest of the strains. Similarly, the proteomes of the two soil isolates along with two plant associated strains contain higher number of peptidases sharing an average of 234 peptidases compared to a range of 226-167 for the rest of the strains. Despite these huge differences and the apparent enrichment of these enzymes among the soil isolates, the data revealed a diversity of the various enzyme families that does not reflect specific habitat type. Growth experiment on various carbohydrates to validate the predictions provides support for this view. Overall, the data indicates that the Tremellales could serve as a rich source of both CAZYmes and peptidases with wide range of potential biotechnological relevance.
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Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Olga Gorte
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xinhai Zhou
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Anke Neumann
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katrin Ochsenreither
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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15
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McGregor NGS, Artola M, Nin-Hill A, Linzel D, Haon M, Reijngoud J, Ram A, Rosso MN, van der Marel GA, Codée JDC, van Wezel GP, Berrin JG, Rovira C, Overkleeft HS, Davies GJ. Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining α-l-Arabinofuranosidases. J Am Chem Soc 2020; 142:4648-4662. [PMID: 32053363 PMCID: PMC7068720 DOI: 10.1021/jacs.9b11351] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Identifying
and characterizing the enzymes responsible for an observed
activity within a complex eukaryotic catabolic system remains one
of the most significant challenges in the study of biomass-degrading
systems. The debranching of both complex hemicellulosic and pectinaceous
polysaccharides requires the production of α-l-arabinofuranosidases
among a wide variety of coexpressed carbohydrate-active enzymes. To
selectively detect and identify α-l-arabinofuranosidases
produced by fungi grown on complex biomass, potential covalent inhibitors
and probes which mimic α-l-arabinofuranosides were
sought. The conformational free energy landscapes of free α-l-arabinofuranose and several rationally designed covalent α-l-arabinofuranosidase inhibitors were analyzed. A synthetic
route to these inhibitors was subsequently developed based on a key
Wittig–Still rearrangement. Through a combination of kinetic
measurements, intact mass spectrometry, and structural experiments,
the designed inhibitors were shown to efficiently label the catalytic
nucleophiles of retaining GH51 and GH54 α-l-arabinofuranosidases.
Activity-based probes elaborated from an inhibitor with an aziridine
warhead were applied to the identification and characterization of
α-l-arabinofuranosidases within the secretome of A. niger grown on arabinan. This method was extended to
the detection and identification of α-l-arabinofuranosidases
produced by eight biomass-degrading basidiomycete fungi grown on complex
biomass. The broad applicability of the cyclophellitol-derived activity-based
probes and inhibitors presented here make them a valuable new tool
in the characterization of complex eukaryotic carbohydrate-degrading
systems and in the high-throughput discovery of α-l-arabinofuranosidases.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, U.K
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Alba Nin-Hill
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Daniël Linzel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Mireille Haon
- INRA, Aix Marseille University, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, F-13009 Marseille, France
| | - Jos Reijngoud
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Arthur Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Marie-Noëlle Rosso
- INRA, Aix Marseille University, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, F-13009 Marseille, France
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jean-Guy Berrin
- INRA, Aix Marseille University, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, F-13009 Marseille, France
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, U.K
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16
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Chauhan PS. Role of various bacterial enzymes in complete depolymerization of lignin: A review. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101498] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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17
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Feng JM, Jiang CQ, Sun ZY, Hua CJ, Wen JF, Miao W, Xiong J. Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment. Mol Phylogenet Evol 2019; 143:106687. [PMID: 31740334 DOI: 10.1016/j.ympev.2019.106687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/26/2023]
Abstract
Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.
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Affiliation(s)
- Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Chuan-Qi Jiang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen 518120, China; Shenzhen Dapeng New District Science and Technology Innovation Service Center, Shenzhen 518119, China; Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zong-Yi Sun
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Cong-Jie Hua
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan 430072, China; CAS Center for Excellence in Animal Evolution and Genetics, Kunming 650223, China.
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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18
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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19
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Schröder S, de Boer C, McGregor NGS, Rowland RJ, Moroz O, Blagova E, Reijngoud J, Arentshorst M, Osborn D, Morant MD, Abbate E, Stringer MA, Krogh KBRM, Raich L, Rovira C, Berrin JG, van Wezel GP, Ram AFJ, Florea BI, van der Marel GA, Codée JDC, Wilson KS, Wu L, Davies GJ, Overkleeft HS. Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes. ACS CENTRAL SCIENCE 2019; 5:1067-1078. [PMID: 31263766 PMCID: PMC6598175 DOI: 10.1021/acscentsci.9b00221] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Indexed: 06/01/2023]
Abstract
Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions. Activity-based protein profiling provides a route for the functional discovery of such enzymes in complex mixtures and under industrially relevant conditions. Here, we show the detection and identification of β-xylosidases and endo-β-1,4-xylanases in the secretomes of Aspergillus niger, by the use of chemical probes inspired by the β-glucosidase inhibitor cyclophellitol. Furthermore, we demonstrate the use of these activity-based probes (ABPs) to assess enzyme-substrate specificities, thermal stabilities, and other biotechnologically relevant parameters. Our experiments highlight the utility of ABPs as promising tools for the discovery of relevant enzymes useful for biomass breakdown.
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Affiliation(s)
- Sybrin
P. Schröder
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Casper de Boer
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Nicholas G. S. McGregor
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.
| | - Rhianna J. Rowland
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.
| | - Olga Moroz
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.
| | - Elena Blagova
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.
| | - Jos Reijngoud
- Molecular
Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Mark Arentshorst
- Molecular
Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - David Osborn
- Novozymes
Inc., 1445 Drew Avenue, Davis, California 95618, United States
| | | | - Eric Abbate
- Novozymes
Inc., 1445 Drew Avenue, Davis, California 95618, United States
| | | | | | - Lluís Raich
- Departament
de Quımica Inorgànica i Orgànica (Secció
de Química Orgànica) & Institut de Quimica Teòrica
i Computacional (IQTCUB), Universitat de
Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Quımica Inorgànica i Orgànica (Secció
de Química Orgànica) & Institut de Quimica Teòrica
i Computacional (IQTCUB), Universitat de
Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Jean-Guy Berrin
- Biodiversité
et Biotechnologie Fongiques (BBF), UMR1163, INRA, Aix Marseille University, F-13009 Marseille, France
| | - Gilles P. van Wezel
- Molecular
Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Arthur F. J. Ram
- Molecular
Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Bogdan I. Florea
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | | | - Jeroen D. C. Codée
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Keith S. Wilson
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.
| | - Liang Wu
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K.
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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20
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Fractionation of DMSO-Extracted and NaOH-Extracted Hemicelluloses by Gradient Ethanol Precipitation from Neosinocalamus affinis. INT J POLYM SCI 2018. [DOI: 10.1155/2018/9587042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Neosinocalamus affinis hemicelluloses were extracted with pure DMSO and 3% NaOH in sequence. The DMSO- and NaOH-extracted hemicelluloses were then successively fractionated by gradient ethanol precipitation. NaOH-extracted hemicellulosic fractions with different branch degree could be separated by gradient ethanol precipitation, while DMSO-extracted hemicellulosic fractions could not. FT-IR spectra showed that DMSO-extracted fractions have more complete structure, while NaOH-extracted fractions have no acetyl at all. The FT-IR and NMR revealed that the DMSO-extracted Neosinocalamus affinis hemicelluloses were 4-O-methyl-glucuronoarabinoxylans consisting of a linear (1→4)-β-D-xylopyranosyl backbone with branches at O-2,3 of acetyl, O-2 of 4-O-methyl-a-D glucuronic acid, and O-3 of arabinose.
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21
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Orellana R, Chaput G, Markillie LM, Mitchell H, Gaffrey M, Orr G, DeAngelis KM. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium. PLoS One 2017; 12:e0186440. [PMID: 29049419 PMCID: PMC5648182 DOI: 10.1371/journal.pone.0186440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/02/2017] [Indexed: 12/11/2022] Open
Abstract
The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.
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Affiliation(s)
- Roberto Orellana
- Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Gina Chaput
- Microbiology Department, University of Massachusetts Amherst, Amherst, United States of America
| | - Lye Meng Markillie
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Hugh Mitchell
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Matt Gaffrey
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Galya Orr
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kristen M. DeAngelis
- Microbiology Department, University of Massachusetts Amherst, Amherst, United States of America
- * E-mail:
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22
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Zhou M, Wu J, Wang T, Gao L, Yin H, Lü X. The purification and characterization of a novel alkali-stable pectate lyase produced by Bacillus subtilis PB1. World J Microbiol Biotechnol 2017; 33:190. [PMID: 28975516 DOI: 10.1007/s11274-017-2357-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 09/23/2017] [Indexed: 10/18/2022]
Abstract
Pectinase is an important kind of enzyme with many industrial applications, among which pectinases produced by bacteria were scarce compared with fungal sources. In this study, a novel bacterium which produced extracellular pectinase was firstly isolated from flue-cured tobacco leaves and identified as Bacillus subtilis PB1 according to its 16S rRNA gene. The pectinolytic enzyme was purified by ammonium sulfate precipitation, ion-exchange and gel filtration chromatography, after which molecular weight was determined as 43.1 ± 0.5 kDa by SDS-PAGE. Peptide mass fingerprinting of the pectinase by MALDI-TOF MS showed that the purified enzyme shared homology with pectate lyase and was designated as BsPel-PB1. The optimal temperature for BsPel-PB1 was 50 °C. The optimal pH was pH 9.5 for BsPel-PB1 while it had a broad pH stability from 5 to 11. The values of K m and V max were 0.312 mg/mL and 1248 U/mL, respectively. Accordingly, the BsPel-PB1 was a novel alkaline pectate lyase which could find potential application as a commercial candidate in the pectinolytic related industries.
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Affiliation(s)
- Man Zhou
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Jingli Wu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Tao Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Lina Gao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Huijun Yin
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China.
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23
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Chauhan PS, Goradia B, Saxena A. Bacterial laccase: recent update on production, properties and industrial applications. 3 Biotech 2017; 7:323. [PMID: 28955620 PMCID: PMC5602783 DOI: 10.1007/s13205-017-0955-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/07/2017] [Indexed: 01/17/2023] Open
Abstract
Laccases (benzenediol: oxygen oxidoreductase, EC 1.10.3.2) are multi-copper enzymes which catalyze the oxidation of a wide range of phenolic and non-phenolic aromatic compounds in the presence or absence of a mediator. Till date, laccases have mostly been isolated from fungi and plants, whereas laccase from bacteria has not been well studied. Bacterial laccases have several unique properties that are not characteristics of fungal laccases such as stability at high temperature and high pH. Bacteria produce these enzymes either extracellularly or intracellularly and their activity is in a wide range of temperature and pH. It has application in pulp biobleaching, bioremediation, textile dye decolorization, pollutant degradation, biosensors, etc. Hence, comprehensive information including sources, production conditions, characterization, cloning and biotechnological applications is needed for the effective understanding and application of these enzymes at the industrial level. The present review provides exhaustive information of bacterial laccases reported till date.
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Affiliation(s)
- Prakram Singh Chauhan
- School of Biological Sciences, G. B. Pant, University of Agricultural and Technology, Pantnagar, Uttarakhand 263145 India
| | - Bindi Goradia
- Marine Biotechnology and Ecology Division, Council of Scientific and Industrial Research – Central Salt & Marine Chemicals Research Institute (CSIR-CSMCRI), Bhavnagar, Gujarat 364 021 India
| | - Arunika Saxena
- Department of Chemistry, Samrat Prithviraj Chauhan Government College, Beawar Road, Ajmer, Rajasthan 305001 India
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24
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Zhou M, Guo P, Wang T, Gao L, Yin H, Cai C, Gu J, Lü X. Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:198. [PMID: 28852421 PMCID: PMC5568718 DOI: 10.1186/s13068-017-0885-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/10/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND Degradation of pectin in lignocellulosic materials is one of the key steps for biofuel production. Biological hydrolysis of pectin, i.e., degradation by pectinolytic microbes and enzymes, is an attractive paradigm because of its obvious advantages, such as environmentally friendly procedures, low in energy demand for lignin removal, and the possibility to be integrated in consolidated process. In this study, a metagenomics sequence-guided strategy coupled with enrichment culture technique was used to facilitate targeted discovery of pectinolytic microbes and enzymes. An apple pomace-adapted compost (APAC) habitat was constructed to boost the enrichment of pectinolytic microorganisms. RESULTS Analyses of 16S rDNA high-throughput sequencing revealed that microbial communities changed dramatically during composting with some bacterial populations being greatly enriched. Metagenomics data showed that apple pomace-adapted compost microbial community (APACMC) was dominated by Proteobacteria and Bacteroidetes. Functional analysis and carbohydrate-active enzyme profiles confirmed that APACMC had been successfully enriched for the targeted functions. Among the 1756 putative genes encoding pectinolytic enzymes, 129 were predicted as novel (with an identity <30% to any CAZy database entry) and only 1.92% were more than 75% identical with proteins in NCBI environmental database, demonstrating that they have not been observed in previous metagenome projects. Phylogenetic analysis showed that APACMC harbored a broad range of pectinolytic bacteria and many of them were previously unrecognized. CONCLUSIONS The immensely diverse pectinolytic microbes and enzymes found in our study will expand the arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. Our study provides a powerful approach for targeted mining microbes and enzymes in numerous industries.
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Affiliation(s)
- Man Zhou
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Peng Guo
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Tao Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Lina Gao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Huijun Yin
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Cheng Cai
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
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Wilkens C, Busk PK, Pilgaard B, Zhang WJ, Nielsen KL, Nielsen PH, Lange L. Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:158. [PMID: 28649277 PMCID: PMC5480151 DOI: 10.1186/s13068-017-0840-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Improved carbohydrate-active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals, and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs a unique niche to look for CAZymes that can potentiate the enzyme blends currently used in industry. RESULTS Enzymatic assays showed that functional CAZymes were secreted into the AD environments in four full-scale mesophilic Danish ADs fed with primary and surplus sludge from municipal wastewater treatment plants. Metagenomes from the ADs were mined for CAZymes with Homology to Peptide Patterns (HotPep). 19,335 CAZymes were identified of which 30% showed 50% or lower identity to known proteins demonstrating that ADs make up a promising pool for discovery of novel CAZymes. A function was assigned to 54% of all CAZymes identified by HotPep. Many different α-glucan-acting CAZymes were identified in the four metagenomes, and the most abundant family was glycoside hydrolase family 13, which contains α-glucan-acting CAZymes. Cellulytic and xylanolytic CAZymes were also abundant in the four metagenomes. The cellulytic enzymes were limited almost to endoglucanases and β-glucosidases, which reflect the large amount of partly degraded cellulose in the sludge. No dockerin domains were identified suggesting that the cellulytic enzymes in the ADs studied operate independently. Of xylanolytic CAZymes, especially xylanases and β-xylosidase, but also a battery of accessory enzymes, were present in the four ADs. CONCLUSIONS Our findings suggest that the ADs are a good place to look for novel plant biomass degrading and modifying enzymes that can potentiate biological processes and provide basis for production of a range of added-value products from biorefineries.
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Affiliation(s)
- Casper Wilkens
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
| | - Peter Kamp Busk
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
| | - Bo Pilgaard
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
| | - Wen-Jing Zhang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University, A. C. Meyers Vænge 15, 2450 Copenhagen, Denmark
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kåre L. Nielsen
- Center for Microbial Communities, Section for Biotechnology, Department of Chemistry and Bioscience, Aalborg University, Frederiks Bajer Vej 7, 9220 Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Section for Biotechnology, Department of Chemistry and Bioscience, Aalborg University, Frederiks Bajer Vej 7, 9220 Aalborg, Denmark
| | - Lene Lange
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
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