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Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024; 108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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2
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Klimek D, Herold M, Calusinska M. Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes. BMC Genomics 2024; 25:523. [PMID: 38802741 PMCID: PMC11131199 DOI: 10.1186/s12864-024-10413-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats. RESULTS Our in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides - this opens new perspectives for algal biomass valorisation in biogas processes. CONCLUSIONS Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.
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Affiliation(s)
- Dominika Klimek
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg.
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 2 Avenue de l'Université, Esch-sur-Alzette, L-4365, Luxembourg.
| | - Malte Herold
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
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3
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Netherway T, Bengtsson J, Buegger F, Fritscher J, Oja J, Pritsch K, Hildebrand F, Krab EJ, Bahram M. Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe. Nat Commun 2024; 15:159. [PMID: 38167673 PMCID: PMC10761831 DOI: 10.1038/s41467-023-44172-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.
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Affiliation(s)
- Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden.
| | - Jan Bengtsson
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
| | - Franz Buegger
- Research Unit for Environmental Simulation (EUS), German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Joachim Fritscher
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Digital Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Jane Oja
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Karin Pritsch
- Research Unit for Environmental Simulation (EUS), German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Digital Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Eveline J Krab
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, 750 07, Uppsala, Sweden
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
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4
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Complete Genome Sequence and Comparative Genome Analysis of Variovorax sp. Strains PAMC28711, PAMC26660, and PAMC28562 and Trehalose Metabolic Pathways in Antarctica Isolates. Int J Microbiol 2022. [DOI: 10.1155/2022/5067074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The complete genomes of Variovorax strains were analyzed and compared along with the genomes of Variovorax strains PAMC28711, PAMC28562, and PAMC26660, Antarctic isolates. The genomic information was collected from the NCBI database and the CAZyme database, and Prokka annotation was used to find the genes that encode for the trehalose metabolic pathway. Likewise, CAZyme annotation (dbCAN2 Meta server) was performed to predict the CAZyme family responsible for trehalose biosynthesis and degradation enzymes. Trehalose has been found to respond to osmotic stress and extreme temperatures. As a result, the study of the trehalose metabolic pathway was carried out in harsh environments such as the Antarctic, where bacteria Variovorax sp. strains PAMC28711, PAMC28562, and PAMC26660 can survive in extreme environments, such as cold temperatures. The trehalose metabolic pathway was analyzed via bioinformatics tools, such as the dbCAN2 Meta server, Prokka annotation, Multiple Sequence Alignment, ANI calculator, and PATRIC database, which helped to predict trehalose biosynthesis and degradation genes’ involvement in the complete genome of Variovorax strains. Likewise, MEGA X was used for evolutionary and conserved genes. The complete genomes of Variovorax strains PAMC28711, PAMC26660, and PAMC28562 are circular chromosomes of length (4,320,000, 7,390,000, and 4,690,000) bp, respectively, with GC content of (66.00, 66.00, and 63.70)%, respectively. The GC content of these three Variovorax strains is lower than that of the other Variovorax strains with complete genomes. Strains PAMC28711 and PAMC28562 exhibit three complete trehalose biosynthetic pathways (OtsA/OtsB, TS, and TreY/TreZ), but strain PAMC26660 only possesses one (OtsA/OtsB). Despite the fact that all three strains contain trehalose, only strain PAMC28711 has two trehaloses according to CAZyme families (GH37 and GH15). Moreover, among the three Antarctica isolates, only strain PAMC28711 exhibits auxiliary activities (AAs), a CAZyme family. To date, although the Variovorax strains are studied for different purposes, the trehalose metabolic pathways in Variovorax strains have not been reported. Further, this study provides additional information regarding trehalose biosynthesis genes and degradation genes (trehalose) as one of the factors facilitating bacterial survival under extreme environments, and this enzyme has shown potential application in biotechnology fields.
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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Hengge NN, Mallinson SJB, Pason P, Lunin VV, Alahuhta M, Chung D, Himmel ME, Westpheling J, Bomble YJ. Characterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticus. Int J Mol Sci 2022; 23:ijms23116070. [PMID: 35682749 PMCID: PMC9181691 DOI: 10.3390/ijms23116070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial conversion of biomass relies on a complex combination of enzyme systems promoting synergy to overcome biomass recalcitrance. Some thermophilic bacteria have been shown to exhibit particularly high levels of cellulolytic activity, making them of particular interest for biomass conversion. These bacteria use varying combinations of CAZymes that vary in complexity from a single catalytic domain to large multi-modular and multi-functional architectures to deconstruct biomass. Since the discovery of CelA from Caldicellulosiruptor bescii which was identified as one of the most active cellulase so far identified, the search for efficient multi-modular and multi-functional CAZymes has intensified. One of these candidates, GuxA (previously Acel_0615), was recently shown to exhibit synergy with other CAZymes in C. bescii, leading to a dramatic increase in growth on biomass when expressed in this host. GuxA is a multi-modular and multi-functional enzyme from Acidothermus cellulolyticus whose catalytic domains include a xylanase/endoglucanase GH12 and an exoglucanase GH6, representing a unique combination of these two glycoside hydrolase families in a single CAZyme. These attributes make GuxA of particular interest as a potential candidate for thermophilic industrial enzyme preparations. Here, we present a more complete characterization of GuxA to understand the mechanism of its activity and substrate specificity. In addition, we demonstrate that GuxA exhibits high levels of synergism with E1, a companion endoglucanase from A. cellulolyticus. We also present a crystal structure of one of the GuxA domains and dissect the structural features that might contribute to its thermotolerance.
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Affiliation(s)
- Neal N. Hengge
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Sam J. B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand;
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, GA 30602, USA;
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA; (N.N.H.); (S.J.B.M.); (V.V.L.); (M.A.); (D.C.); (M.E.H.)
- Correspondence:
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Banu JR, Kumar G, Chattopadhyay I. Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches. 3 Biotech 2021; 11:429. [PMID: 34603908 DOI: 10.1007/s13205-021-02962-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced "omics" approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.
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Affiliation(s)
- J Rajesh Banu
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
| | - Gopalakrishnan Kumar
- Faculty of Science and Technology, Institute of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Forus, Box 8600, 4036 Stavanger, Norway
| | - Indranil Chattopadhyay
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
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Clostridium thermocellum as a Promising Source of Genetic Material for Designer Cellulosomes: An Overview. Catalysts 2021. [DOI: 10.3390/catal11080996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant biomass-based biofuels have gradually substituted for conventional energy sources thanks to their obvious advantages, such as renewability, huge quantity, wide availability, economic feasibility, and sustainability. However, to make use of the large amount of carbon sources stored in the plant cell wall, robust cellulolytic microorganisms are highly demanded to efficiently disintegrate the recalcitrant intertwined cellulose fibers to release fermentable sugars for microbial conversion. The Gram-positive, thermophilic, cellulolytic bacterium Clostridium thermocellum possesses a cellulolytic multienzyme complex termed the cellulosome, which has been widely considered to be nature’s finest cellulolytic machinery, fascinating scientists as an auspicious source of saccharolytic enzymes for biomass-based biofuel production. Owing to the supra-modular characteristics of the C. thermocellum cellulosome architecture, the cellulosomal components, including cohesin, dockerin, scaffoldin protein, and the plentiful cellulolytic and hemicellulolytic enzymes have been widely used for constructing artificial cellulosomes for basic studies and industrial applications. In addition, as the well-known microbial workhorses are naïve to biomass deconstruction, several research groups have sought to transform them from non-cellulolytic microbes into consolidated bioprocessing-enabling microbes. This review aims to update and discuss the current progress in these mentioned issues, point out their limitations, and suggest some future directions.
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Basik AA, Sanglier JJ, Yeo CT, Sudesh K. Microbial Degradation of Rubber: Actinobacteria. Polymers (Basel) 2021; 13:polym13121989. [PMID: 34204568 PMCID: PMC8235351 DOI: 10.3390/polym13121989] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/25/2023] Open
Abstract
Rubber is an essential part of our daily lives with thousands of rubber-based products being made and used. Natural rubber undergoes chemical processes and structural modifications, while synthetic rubber, mainly synthetized from petroleum by-products are difficult to degrade safely and sustainably. The most prominent group of biological rubber degraders are Actinobacteria. Rubber degrading Actinobacteria contain rubber degrading genes or rubber oxygenase known as latex clearing protein (lcp). Rubber is a polymer consisting of isoprene, each containing one double bond. The degradation of rubber first takes place when lcp enzyme cleaves the isoprene double bond, breaking them down into the sole carbon and energy source to be utilized by the bacteria. Actinobacteria grow in diverse environments, and lcp gene containing strains have been detected from various sources including soil, water, human, animal, and plant samples. This review entails the occurrence, physiology, biochemistry, and molecular characteristics of Actinobacteria with respect to its rubber degrading ability, and discusses possible technological applications based on the activity of Actinobacteria for treating rubber waste in a more environmentally responsible manner.
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Affiliation(s)
- Ann Anni Basik
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Jean-Jacques Sanglier
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Chia Tiong Yeo
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Correspondence: ; Tel.: +60-4-6534367; Fax: +60-4-6565125
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Li G, Zhou X, Li Z, Liu Y, Liu D, Miao Y, Wan Q, Zhang R. Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design. Appl Microbiol Biotechnol 2021; 105:4561-4576. [PMID: 34014347 DOI: 10.1007/s00253-021-11340-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 05/09/2021] [Indexed: 11/28/2022]
Abstract
Xylanases have a broad range of applications in industrial biotechnologies, which require the enzymes to resist the high-temperature environments. The majority of xylanases have maximum activity at moderate temperatures, which limited their potential applications in industries. In this study, a thermophilic GH10 family xylanase XynAF1 from the high-temperature composting strain Aspergillus fumigatus Z5 was characterized and engineered to further improve its thermostability. XynAF1 has the optimal reaction temperature of 90 °C. The crystal structure of XynAF1 was obtained by X-ray diffraction after heterologous expression, purification, and crystallization. The high-resolution X-ray crystallographic structure of the protein-product complex was obtained by soaking the apo-state crystal with xylotetraose. Structure analysis indicated that XynAF1 has a rigid skeleton, which helps to maintain the hyperthermophilic characteristic. The homologous structure analysis and the catalytic center mutant construction of XynAF1 indicated the conserved catalytic center contributed to the high optimum catalytic temperature. The amino acids in the surface of xylanase XynAF1 which might influence the enzyme thermostability were identified by the structure analysis. Combining the rational design with the saturation mutation at the high B-value regions, the integrative mutant XynAF1-AC with a 6-fold increase of thermostability was finally obtained. This study efficiently improved the thermostability of a GH10 family xylanase by semi-rational design, which provided a new biocatalyst for high-temperature biotechnological applications. KEY POINTS: • Obtained the crystal structure of GH10 family hyperthermophilic xylanase XynAF1. • Shed light on the understanding of the GH10 family xylanase thermophilic mechanism. • Constructed a 6-fold increased thermostability recombinant xylanase.
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Affiliation(s)
- Guangqi Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xuan Zhou
- National Agricultural Technology Extension and Service Center, Beijing, 100125, People's Republic of China
| | - Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. .,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. .,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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11
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Complete genome sequencing and comparative CAZyme analysis of Rhodococcus sp. PAMC28705 and PAMC28707 provide insight into their biotechnological and phytopathogenic potential. Arch Microbiol 2021; 203:1731-1742. [PMID: 33459813 DOI: 10.1007/s00203-020-02177-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/27/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Study of carbohydrate-active enzymes (CAZymes) can reveal information about the lifestyle and behavior of an organism. Rhodococcus species is well known for xenobiotic metabolism; however, their carbohydrate utilization ability has been less discussed till date. This study aimed to present the CAZyme analysis of two Rhodococcus strains, PAMC28705 and PAMC28707, isolated from lichens in Antarctica, and compare them with other Rhodococcus, Mycobacterium, and Corynebacterium strains. Genome-wide computational analysis was performed using various tools. Results showed similarities in CAZymes across all the studied genera. All three genera showed potential for significant polysaccharide utilization, including starch, cellulose, and pectin referring their biotechnological potential. Keeping in mind the pathogenic strains listed across all three genera, CAZymes associated to pathogenicity were analyzed too. Cutinase enzyme, which has been associated with phytopathogenicity, was abundant in all the studied organisms. CAZyme gene cluster of Rhodococcus sp. PAMC28705 and Rhodococcus sp. PAMC28707 showed the insertion of cutinase in the cluster, further supporting their possible phytopathogenic properties.
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Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli DK, Puri M. Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion. Int J Biol Macromol 2020; 168:572-590. [PMID: 33309672 DOI: 10.1016/j.ijbiomac.2020.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022]
Abstract
Economic production of lignocellulose degrading enzymes for biofuel industries is of considerable interest to the biotechnology community. While these enzymes are widely distributed in fungi, their industrial production from other sources, particularly by thermophilic anaerobic bacteria (growth Topt ≥ 60 °C), is an emerging field. Thermophilic anaerobic bacteria produce a large number of lignocellulolytic enzymes having unique structural features and employ different schemes for biomass degradation, which can be classified into four systems namely; 'free enzyme system', 'cell anchored enzymes', 'complex cellulosome system', and 'multifunctional multimodular enzyme system'. Such enzymes exhibit high specific activity and have a natural ability to withstand harsh bioprocessing conditions. However, achieving a higher production of these thermostable enzymes at current bioprocessing targets is challenging. In this review, the research opportunities for these distinct enzyme systems in the biofuel industry and the associated technological challenges are discussed. The current status of research findings is highlighted along with a detailed description of the categorization of the different enzyme production schemes. It is anticipated that high temperature-based bioprocessing will become an integral part of sustainable bioenergy production in the near future.
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Affiliation(s)
- Nisha Singh
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Anshu S Mathur
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Ravi P Gupta
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Deepak K Tuli
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Munish Puri
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; Medical Biotechnology, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, Adelaide 5042, Australia.
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Deletion of a Peptidylprolyl Isomerase Gene Results in the Inability of Caldicellulosiruptor bescii To Grow on Crystalline Cellulose without Affecting Protein Glycosylation or Growth on Soluble Substrates. Appl Environ Microbiol 2020; 86:AEM.00909-20. [PMID: 32769195 DOI: 10.1128/aem.00909-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/30/2020] [Indexed: 11/20/2022] Open
Abstract
Caldicellulosiruptor bescii secretes a large number of complementary multifunctional enzymes with unique activities for biomass deconstruction. The most abundant enzymes in the C. bescii secretome are found in a unique gene cluster containing a glycosyl transferase (GT39) and a putative peptidyl prolyl cis-trans isomerase. Deletion of the glycosyl transferase in this cluster resulted in loss of detectable protein glycosylation in C. bescii, and its activity has been shown to be responsible for the glycosylation of the proline-threonine rich linkers found in many of the multifunctional cellulases. The presence of a putative peptidyl prolyl cis-trans isomerase within this gene cluster suggested that it might also play a role in cellulase modification. Here, we identify this gene as a putative prsA prolyl cis-trans isomerase. Deletion of prsA2 leads to the inability of C. bescii to grow on insoluble substrates such as Avicel, the model cellulose substrate, while exhibiting no differences in phenotype with the wild-type strain on soluble substrates. Finally, we provide evidence that the prsA2 gene is likely needed to increase solubility of multifunctional cellulases and that this unique gene cluster was likely acquired by members of the Caldicellulosiruptor genus with a group of genes to optimize the production and activity of multifunctional cellulases.IMPORTANCE Caldicellulosiruptor has the ability to digest complex plant biomass without pretreatment and have been engineered to convert biomass, a sustainable, carbon neutral substrate, to fuels. Their strategy for deconstructing plant cell walls relies on an interesting class of cellulases consisting of multiple catalytic modules connected by linker regions and carbohydrate binding modules. The best studied of these enzymes, CelA, has a unique deconstruction mechanism. CelA is located in a cluster of genes that likely allows for optimal expression, secretion, and activity. One of the genes in this cluster is a putative isomerase that modifies the CelA protein. In higher eukaryotes, these isomerases are essential for the proper folding of glycoproteins in the endoplasmic reticulum, but little is known about the role of isomerization in cellulase activity. We show that the stability and activity of CelA is dependent on the activity of this isomerase.
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Long L, Sun L, Lin Q, Ding S, St John FJ. Characterization and functional analysis of two novel thermotolerant α-L-arabinofuranosidases belonging to glycoside hydrolase family 51 from Thielavia terrestris and family 62 from Eupenicillium parvum. Appl Microbiol Biotechnol 2020; 104:8719-8733. [PMID: 32880690 PMCID: PMC7502447 DOI: 10.1007/s00253-020-10867-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 11/26/2022]
Abstract
Abstract Arabinofuranose substitutions on xylan are known to interfere with enzymatic hydrolysis of this primary hemicellulose. In this work, two novel α-l-arabinofuranosidases (ABFs), TtABF51A from Thielavia terrestris and EpABF62C from Eupenicillium parvum, were characterized and functionally analyzed. From sequences analyses, TtABF51A and EpABF62C belong to glycoside hydrolase (GH) families 51 and 62, respectively. Recombinant TtABF51A showed high activity on 4-nitrophenyl-α-l-arabinofuranoside (83.39 U/mg), low-viscosity wheat arabinoxylan (WAX, 39.66 U/mg), high-viscosity rye arabinoxylan (RAX, 32.24 U/mg), and sugarbeet arabinan (25.69 U/mg), while EpABF62C preferred to degrade arabinoxylan. For EpABF62C, the rate of hydrolysis of RAX (94.10 U/mg) was 2.1 times that of WAX (45.46 U/mg). The optimal pH and reaction temperature for the two enzymes was between 4.0 and 4.5 and 65 °C, respectively. Calcium played an important role in the thermal stability of EpABF62C. TtABF51A and EpABF62C showed the highest thermal stabilities at pH 4.5 or 5.0, respectively. At their optimal pHs, TtABF51A and EpABF62C retained greater than 80% of their initial activities after incubation at 55 °C for 96 h or 144 h, respectively. 1H NMR analysis indicated that the two enzymes selectively removed arabinose linked to C-3 of mono-substituted xylose residues in WAX. Compared with the singular application of the GH10 xylanase EpXYN1 from E. parvum, co-digestions of WAX including TtABF51A and/or EpABF62C released 2.49, 3.38, and 4.81 times xylose or 3.38, 1.65, and 2.57 times of xylobiose, respectively. Meanwhile, the amount of arabinose released from WAX by TtABF51A with EpXYN1 was 2.11 times the amount with TtABF51A alone. Key points • Two novel α-l-arabinofuranosidases (ABFs) displayed high thermal stability. • The thermal stability of GH62 family EpABF62C was dependent on calcium. • Buffer pH affects the thermal stability of the two ABFs. • Both ABFs enhance the hydrolysis of WAX by a GH10 xylanase. Electronic supplementary material The online version of this article (10.1007/s00253-020-10867-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liangkun Long
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Lu Sun
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, Nanjing, 211111, China
| | - Shaojun Ding
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
| | - Franz J St John
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Drive, Madison, WI, 53726, USA.
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Comparative Genomic Study of Polar Lichen-Associated Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 Reveals the Presence of Polysaccharide-Degrading Ability Based on Habitat. Curr Microbiol 2020; 77:2940-2952. [PMID: 32681312 DOI: 10.1007/s00284-020-02120-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
The genus Hymenobacter is classified in the family Hymenobacteraceae under the phylum Bacteroidetes. They have been isolated from diverse environments, such as air, soil, and lichen, along with extreme polar environments, including the Arctic and Antarctic regions. The polar regions have attracted intense research interest for the discovery of novel microorganisms and their functions. Analysis of the polysaccharide utilization-related carbohydrate-active enzyme among the two lichen-associated polar organisms Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 was performed, along with its comparison with the complete genome of the same genus available in the NCBI database. The study was conducted relying on the AZCL screening data for the two polar lichen-associated species. While comparing with eight other complete genomes, differences in polysaccharide preferences based on the isolation environment and biosample source were discovered. All the species showed almost similar percentage of cellulose synthesis and degradation genes. However, the polar lichen-associated microorganism was found to have a high percentage of hemicellulose degradation genes, and less starch and laminarin degradation. The Hymenobacter species with higher number of hemicellulose degradation genes was found to have a lower number of starch and laminarin degradation genes and vice versa, highlighting the differences in polysaccharide utilization among the species.
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Blumer-Schuette SE. Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology. Microorganisms 2020; 8:E385. [PMID: 32164310 PMCID: PMC7142884 DOI: 10.3390/microorganisms8030385] [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: 02/01/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.
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Kahn A, Moraïs S, Chung D, Sarai NS, Hengge NN, Kahn A, Himmel ME, Bayer EA, Bomble YJ. Glycosylation of hyperthermostable designer cellulosome components yields enhanced stability and cellulose hydrolysis. FEBS J 2020; 287:4370-4388. [DOI: 10.1111/febs.15251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/06/2020] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Amaranta Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
- Faculty of Natural Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
| | - Daehwan Chung
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Nicholas S. Sarai
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Neal N. Hengge
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Audrey Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Michael E. Himmel
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Yannick J. Bomble
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
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Complementing the intrinsic repertoire of Ustilago maydis for degradation of the pectin backbone polygalacturonic acid. J Biotechnol 2020; 307:148-163. [DOI: 10.1016/j.jbiotec.2019.10.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
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Krska D, Larsbrink J. Investigation of a thermostable multi-domain xylanase-glucuronoyl esterase enzyme from Caldicellulosiruptor kristjanssonii incorporating multiple carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:68. [PMID: 32308737 PMCID: PMC7151638 DOI: 10.1186/s13068-020-01709-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/02/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Efficient degradation of lignocellulosic biomass has become a major bottleneck in industrial processes which attempt to use biomass as a carbon source for the production of biofuels and materials. To make the most effective use of the source material, both the hemicellulosic as well as cellulosic parts of the biomass should be targeted, and as such both hemicellulases and cellulases are important enzymes in biorefinery processes. Using thermostable versions of these enzymes can also prove beneficial in biomass degradation, as they can be expected to act faster than mesophilic enzymes and the process can also be improved by lower viscosities at higher temperatures, as well as prevent the introduction of microbial contamination. RESULTS This study presents the investigation of the thermostable, dual-function xylanase-glucuronoyl esterase enzyme CkXyn10C-GE15A from the hyperthermophilic bacterium Caldicellulosiruptor kristjanssonii. Biochemical characterization of the enzyme was performed, including assays for establishing the melting points for the different protein domains, activity assays for the two catalytic domains, as well as binding assays for the multiple carbohydrate-binding domains present in CkXyn10C-GE15A. Although the enzyme domains are naturally linked together, when added separately to biomass, the expected boosting of the xylanase action was not seen. This lack of intramolecular synergy might suggest, together with previous data, that increased xylose release is not the main beneficial trait given by glucuronoyl esterases. CONCLUSIONS Due to its thermostability, CkXyn10C-GE15A is a promising candidate for industrial processes, with both catalytic domains exhibiting melting temperatures over 70 °C. Of particular interest is the glucuronoyl esterase domain, as it represents the first studied thermostable enzyme displaying this activity.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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Ibarra LN, Alves AEODA, Antonino JD, Prado GS, Pinto CEM, Soccol CR, Vasconcelos ÉARD, Grossi-de-Sa MF. Enzymatic activity of a recombinant β-1,4-endoglucanase from the Cotton Boll Weevil (Anthonomus grandis) aiming second generation ethanol production. Sci Rep 2019; 9:19580. [PMID: 31862955 PMCID: PMC6925290 DOI: 10.1038/s41598-019-56070-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/20/2019] [Indexed: 01/22/2023] Open
Abstract
In the last years, the production of ethanol fuel has started to change with the introduction of second-generation ethanol (2 G Ethanol) in the energy sector. However, in Brazil, the process of obtaining 2 G ethanol did not reach a basic standard to achieve relevant and economically viable results. Several studies have currently been addressed to solve these issues. A critical stage in the bioethanol production is the deployment of efficient and stable enzymes to catalyze the saccharification step into the process of biomass conversion. The present study comprises a screening for genes coding for plant biomass degradation enzymes, followed by cloning a selected gene, addressing its heterologous expression, and characterizing enzymatic activity towards cellulose derived substrates, with a view to second-generation ethanol production. A cDNA database of the Cotton Boll Weevil, Anthonomus grandis (Coleoptera: Curculionidae), an insect that feeds on cotton plant biomass, was used as a source of plant biomass degradation enzyme genes. A larva and adult midgut-specific β-1,4-Endoglucanase-coding gene (AgraGH45-1) was cloned and expressed in the yeast Pichia pastoris. Its amino acid sequence, including the two catalytic domains, shares high identity with other Coleoptera Glycosyl Hydrolases from family 45 (GH45). AgraGH45-1 activity was detected in a Carboxymethylcellulose (CMC) and Hydroxyethylcellulose (HEC) degradation assay and the optimal conditions for enzymatic activity was pH 5.0 at 50 °C. When compared to commercial cellulase from Aspergillus niger, Agra GH45-1 was 1.3-fold more efficient to degrade HEC substrate. Together, these results show that AgraGH45-1 is a valid candidate to be engineered and be tested for 2 G ethanol production.
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Affiliation(s)
- Liz Nathalia Ibarra
- Universidade Federal do Paraná - UFPR, Curitiba, PR, 81530-980, Brazil.,Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil
| | - Ana Elizabeth Oliveira de Araújo Alves
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil.,Universidade de Brasília - UnB, Biology Institute, Brasília, DF, 70910-900, Brazil
| | - José Dijair Antonino
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil.,Universidade Federal Rural de Pernambuco - UFRPE, Recife-PE, 52171-900, Brazil
| | - Guilherme Souza Prado
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil.,Universidade Católica de Brasília - UCB, Brasília, DF, 70790-160, Brazil
| | - Clidia Eduarda Moreira Pinto
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil.,Universidade de Brasília - UnB, Biology Institute, Brasília, DF, 70910-900, Brazil
| | | | | | - Maria Fátima Grossi-de-Sa
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil.,Universidade Católica de Brasília - UCB, Brasília, DF, 70790-160, Brazil
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Chu Y, Hao Z, Wang K, Tu T, Huang H, Wang Y, Bai YG, Wang Y, Luo H, Yao B, Su X. The GH10 and GH48 dual-functional catalytic domains from a multimodular glycoside hydrolase synergize in hydrolyzing both cellulose and xylan. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:279. [PMID: 31827607 PMCID: PMC6892212 DOI: 10.1186/s13068-019-1617-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Regarding plant cell wall polysaccharides degradation, multimodular glycoside hydrolases (GHs) with two catalytic domains separated by one or multiple carbohydrate-binding domains are rare in nature. This special mode of domain organization endows the Caldicellulosiruptor bescii CelA (GH9-CBM3c-CBM3b-CBM3b-GH48) remarkably high efficiency in hydrolyzing cellulose. CbXyn10C/Cel48B from the same bacterium is also such an enzyme which has, however, evolved to target both xylan and cellulose. Intriguingly, the GH10 endoxylanase and GH48 cellobiohydrolase domains are both dual functional, raising the question if they can act synergistically in hydrolyzing cellulose and xylan, the two major components of plant cell wall. RESULTS In this study, we discovered that CbXyn10C and CbCel48B, which stood for the N- and C-terminal catalytic domains, respectively, cooperatively released much more cellobiose and cellotriose from cellulose. In addition, they displayed intramolecular synergy but only at the early stage of xylan hydrolysis by generating higher amounts of xylooligosaccharides including xylotriose, xylotetraose, and xylobiose. When complex lignocellulose corn straw was used as the substrate, the synergy was found only for cellulose but not xylan hydrolysis. CONCLUSION This is the first report to reveal the synergy between a GH10 and a GH48 domain. The synergy discovered in this study is helpful for understanding how C. bescii captures energy from these recalcitrant plant cell wall polysaccharides. The insight also sheds light on designing robust and multi-functional enzymes for plant cell wall polysaccharides degradation.
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Affiliation(s)
- Yindi Chu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, 5# Dong Dan San Tiao, Beijing, 100005 China
| | - Zhenzhen Hao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Kaikai Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Ying Guo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Yaru Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
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22
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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Genomic and physiological analyses reveal that extremely thermophilic Caldicellulosiruptor changbaiensis deploys uncommon cellulose attachment mechanisms. J Ind Microbiol Biotechnol 2019; 46:1251-1263. [PMID: 31392469 DOI: 10.1007/s10295-019-02222-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
The genus Caldicellulosiruptor is comprised of extremely thermophilic, heterotrophic anaerobes that degrade plant biomass using modular, multifunctional enzymes. Prior pangenome analyses determined that this genus is genetically diverse, with the current pangenome remaining open, meaning that new genes are expected with each additional genome sequence added. Given the high biodiversity observed among the genus Caldicellulosiruptor, we have sequenced and added a 14th species, Caldicellulosiruptor changbaiensis, to the pangenome. The pangenome now includes 3791 ortholog clusters, 120 of which are unique to C. changbaiensis and may be involved in plant biomass degradation. Comparisons between C. changbaiensis and Caldicellulosiruptor bescii on the basis of growth kinetics, cellulose solubilization and cell attachment to polysaccharides highlighted physiological differences between the two species which are supported by their respective gene inventories. Most significantly, these comparisons indicated that C. changbaiensis possesses uncommon cellulose attachment mechanisms not observed among the other strongly cellulolytic members of the genus Caldicellulosiruptor.
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Kahn A, Moraïs S, Galanopoulou AP, Chung D, Sarai NS, Hengge N, Hatzinikolaou DG, Himmel ME, Bomble YJ, Bayer EA. Creation of a functional hyperthermostable designer cellulosome. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:44. [PMID: 30858881 PMCID: PMC6394049 DOI: 10.1186/s13068-019-1386-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/20/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Renewable energy has become a field of high interest over the past decade, and production of biofuels from cellulosic substrates has a particularly high potential as an alternative source of energy. Industrial deconstruction of biomass, however, is an onerous, exothermic process, the cost of which could be decreased significantly by use of hyperthermophilic enzymes. An efficient way of breaking down cellulosic substrates can also be achieved by highly efficient enzymatic complexes called cellulosomes. The modular architecture of these multi-enzyme complexes results in substrate targeting and proximity-based synergy among the resident enzymes. However, cellulosomes have not been observed in hyperthermophilic bacteria. RESULTS Here, we report the design and function of a novel hyperthermostable "designer cellulosome" system, which is stable and active at 75 °C. Enzymes from Caldicellulosiruptor bescii, a highly cellulolytic hyperthermophilic anaerobic bacterium, were selected and successfully converted to the cellulosomal mode by grafting onto them divergent dockerin modules that can be inserted in a precise manner into a thermostable chimaeric scaffoldin by virtue of their matching cohesins. Three pairs of cohesins and dockerins, selected from thermophilic microbes, were examined for their stability at extreme temperatures and were determined stable at 75 °C for at least 72 h. The resultant hyperthermostable cellulosome complex exhibited the highest levels of enzymatic activity on microcrystalline cellulose at 75 °C, compared to those of previously reported designer cellulosome systems and the native cellulosome from Clostridium thermocellum. CONCLUSION The functional hyperthermophilic platform fulfills the appropriate physico-chemical properties required for exothermic processes. This system can thus be adapted for other types of thermostable enzyme systems and could serve as a basis for a variety of cellulolytic and non-cellulolytic industrial objectives at high temperatures.
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Affiliation(s)
- Amaranta Kahn
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, 8499000 Beer-Sheva, Israel
| | - Anastasia P. Galanopoulou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Neal Hengge
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Dimitris G. Hatzinikolaou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
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Conway JM, Crosby JR, Hren AP, Southerland RT, Lee LL, Lunin VV, Alahuhta P, Himmel ME, Bomble YJ, Adams MWW, Kelly RM. Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic
Caldicellulosiruptor
species. AIChE J 2018. [DOI: 10.1002/aic.16354] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jonathan M. Conway
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - James R. Crosby
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - Andrew P. Hren
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - Robert T. Southerland
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - Laura L. Lee
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | | | - Petri Alahuhta
- Biosciences CenterNational Renewable Energy LaboratoryGoldenCO80401
| | | | | | - Michael W. W. Adams
- Dept. of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGA30602
| | - Robert M. Kelly
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
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Conway JM, Crosby JR, McKinley BS, Seals NL, Adams MWW, Kelly RM. Parsing in vivo and in vitro contributions to microcrystalline cellulose hydrolysis by multidomain glycoside hydrolases in theCaldicellulosiruptor besciisecretome. Biotechnol Bioeng 2018; 115:2426-2440. [DOI: 10.1002/bit.26773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/21/2018] [Accepted: 06/21/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Jonathan M. Conway
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - James R. Crosby
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - Bennett S. McKinley
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - Nathaniel L. Seals
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthens GA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleigh NC
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Russell J, Kim SK, Duma J, Nothaft H, Himmel ME, Bomble YJ, Szymanski CM, Westpheling J. Deletion of a single glycosyltransferase in Caldicellulosiruptor bescii eliminates protein glycosylation and growth on crystalline cellulose. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:259. [PMID: 30258493 PMCID: PMC6151902 DOI: 10.1186/s13068-018-1266-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/19/2018] [Indexed: 05/21/2023]
Abstract
Protein glycosylation pathways have been identified in a variety of bacteria and are best understood in pathogens and commensals in which the glycosylation targets are cell surface proteins, such as S layers, pili, and flagella. In contrast, very little is known about the glycosylation of bacterial enzymes, especially those secreted by cellulolytic bacteria. Caldicellulosiruptor bescii secretes several unique synergistic multifunctional biomass-degrading enzymes, notably cellulase A which is largely responsible for this organism's ability to grow on lignocellulosic biomass without the conventional pretreatment. It was recently discovered that extracellular CelA is heavily glycosylated. In this work, we identified an O-glycosyltransferase in the C. bescii chromosome and targeted it for deletion. The resulting mutant was unable to grow on crystalline cellulose and showed no detectable protein glycosylation. Multifunctional biomass-degrading enzymes in this strain were rapidly degraded. With the genetic tools available in C. bescii, this system represents a unique opportunity to study the role of bacterial enzyme glycosylation as well an investigation of the pathway for protein glycosylation in a non-pathogen.
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Affiliation(s)
- Jordan Russell
- Microbiology Department, University of Georgia, Athens, GA USA
- Genetics Department, University of Georgia, Athens, GA USA
- The BioEnergy Science Center and The Center for Bioenergy Innovation U.S. Department of Energy Office of Science, Oak Ridge, Tennessee USA
| | - Sun-Ki Kim
- Genetics Department, University of Georgia, Athens, GA USA
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546 Republic of Korea
- The BioEnergy Science Center and The Center for Bioenergy Innovation U.S. Department of Energy Office of Science, Oak Ridge, Tennessee USA
| | - Justin Duma
- Microbiology Department, University of Georgia, Athens, GA USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA USA
| | - Harald Nothaft
- Department of Biological Sciences, University of Alberta, Edmonton, AB Canada
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- The BioEnergy Science Center and The Center for Bioenergy Innovation U.S. Department of Energy Office of Science, Oak Ridge, Tennessee USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- The BioEnergy Science Center and The Center for Bioenergy Innovation U.S. Department of Energy Office of Science, Oak Ridge, Tennessee USA
| | - Christine M. Szymanski
- Microbiology Department, University of Georgia, Athens, GA USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA USA
| | - Janet Westpheling
- Genetics Department, University of Georgia, Athens, GA USA
- The BioEnergy Science Center and The Center for Bioenergy Innovation U.S. Department of Energy Office of Science, Oak Ridge, Tennessee USA
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28
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Poudel S, Giannone RJ, Basen M, Nookaew I, Poole FL, Kelly RM, Adams MWW, Hettich RL. The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:80. [PMID: 29588665 PMCID: PMC5865380 DOI: 10.1186/s13068-018-1076-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/09/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates. RESULTS Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs), ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. CONCLUSIONS This study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii's utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Richard J. Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Mirko Basen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Present Address: Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt Am Main, Germany
| | - Intawat Nookaew
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Present Address: Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Farris L. Poole
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Robert M. Kelly
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Michael W. W. Adams
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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