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Ma D, Chen H, Liu D, Feng C, Hua Y, Gu T, Guo X, Zhou Y, Wang H, Tong G, Li H, Zhang K. Soil-derived cellulose-degrading bacteria: screening, identification, the optimization of fermentation conditions, and their whole genome sequencing. Front Microbiol 2024; 15:1409697. [PMID: 39050626 PMCID: PMC11266136 DOI: 10.3389/fmicb.2024.1409697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Straw cellulose is an abundant renewable resource in nature. In recent years, the conversion of cellulose from waste straw into biofuel by specific microorganisms' fragmentation has attracted extensive attention. Although many bacteria with the ability to degrade cellulose have been identified, comprehensive bioinformatics analyses of these bacteria remain limited, and research exploring optimal fragmentation conditions is scarce. Our study involved the isolation and screening of bacteria from various locations in Yangzhou using carboxymethyl cellulose (CMC) media. Then, the cellulose-degrading bacteria were identified using 16S rRNA and seven candidate bacterial strains with cellulose degrading ability were identified in Yangzhou city for the first time. The cellulase activity was determined by the 3,5-dinitrosalicylic acid (DNS) method in different fragmentation conditions, and finally two bacteria strains with the strongest cellulose degradation ability were selected for whole genome sequencing analysis. Sequencing results revealed that the genome sizes of Rhodococcus wratislaviensis YZ02 and Pseudomonas Xanthosomatis YZ03 were 8.51 Mb and 6.66 Mb, containing 8,466 and 5,745 genes, respectively. A large number of cellulose degradation-related genes were identified and annotated using KEGG, GO and COG analyses. In addition, genomic CAZyme analysis indicated that both R. wratislaviensis YZ02 and P. Xanthosomatis YZ03 harbor a series of glycoside hydrolase family (GH) genes and other genes related to cellulose degradation. Our finding provides new options for the development of cellulose-degrading bacteria and a theoretical basis for improving the cellulose utilization of straw.
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Affiliation(s)
- Degao Ma
- Yangzhou Environmental Monitoring Center of Jiangsu Province, Yangzhou, China
| | - Haoyu Chen
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Duxuan Liu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Chenwei Feng
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yanhong Hua
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Tianxiao Gu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiao Guo
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yuchen Zhou
- Department of Pharmacy, Medical School of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Houjun Wang
- Yangzhou Environmental Monitoring Center of Jiangsu Province, Yangzhou, China
| | - Guifeng Tong
- Yangzhou Environmental Monitoring Center of Jiangsu Province, Yangzhou, China
| | - Hua Li
- College of Engineering, Nanjing Agricultural University, Nanjing, China
| | - Kun Zhang
- College of Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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Lisov A, Belova O, Lisova Z, Nagel A, Shadrin A, Andreeva-Kovalevskaya Z, Nagornykh M, Zakharova M, Leontievsky A. Two β-glucanases from bacterium Cellulomonas flavigena: expression in Pichia pastoris, properties, biotechnological potential. Prep Biochem Biotechnol 2023; 53:1313-1321. [PMID: 37093814 DOI: 10.1080/10826068.2023.2201934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In the genome of Cellulomonas flavigena, two genes that potentially encode endoglucanases - Cfla_2912 and Cfla_2913 were identified. We cloned the genes and created Pichia pastoris-based recombinant producers of two proteins that were expressed from the AOX1 promoter. Each of the endoglucanase molecules contains a GH6 catalytic domain, CBM2 carbohydrate-binding module, and TAT signal peptide. The fermentation of the producers was carried out in a 10 L fermenter; Cfla_2912 and Cfla_2913 were purified using affinity chromatography. The yield comprised 10.3 mg/ml (430 U/ml) for Cfla_2913 and 9 mg/ml (370 U/ml) for Cfla_2912. Cfla_2912 and Cfla_2913 were found to have a high activity against barley β-glucan and lichenan, a weak activity against carboxymethyl cellulose (CMC), phosphoric-acid treated cellulose, and no activity against laminarin, xylan, soluble starch, microcrystalline cellulose, cellobiose, and cellotriose. Thus, the proteins exhibited β-glucanase activity. Both proteins had a neutral pH optimum of about 7.0 and were more stable at neutral and slightly alkaline pH ranging from 7.0 to 9.0. Cfla_2912 and Cfla_2913 showed a moderate thermal stability. The products of barley β-glucan hydrolysis by Cfla_2912 and Cfla_2913 were trisaccharide, tetrasaccharide, and cellobiose. Cfla_2912 and Cfla_2913 efficiently hydrolyzed cereal polysaccharides, which indicate that they may have biotechnological potential.
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Affiliation(s)
- Alexander Lisov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Oksana Belova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Zoya Lisova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Nagel
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Shadrin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Zhanna Andreeva-Kovalevskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Maxim Nagornykh
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Marina Zakharova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Leontievsky
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
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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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Chitin-Active Lytic Polysaccharide Monooxygenases Are Rare in Cellulomonas Species. Appl Environ Microbiol 2022; 88:e0096822. [PMID: 35862679 PMCID: PMC9361826 DOI: 10.1128/aem.00968-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cellulomonas flavigena is a saprotrophic bacterium that encodes, within its genome, four predicted lytic polysaccharide monooxygenases (LPMOs) from Auxiliary Activity family 10 (AA10). We showed previously that three of these cleave the plant polysaccharide cellulose by oxidation at carbon-1 (J. Li, L. Solhi, E.D. Goddard-Borger, Y. Mattieu et al., Biotechnol Biofuels 14:29, 2021, https://doi.org/10.1186/s13068-020-01860-3). Here, we present the biochemical characterization of the fourth C. flavigena AA10 member (CflaLPMO10D) as a chitin-active LPMO. Both the full-length CflaLPMO10D-Carbohydrate-Binding Module family 2 (CBM2) and catalytic module-only proteins were produced in Escherichia coli using the native general secretory (Sec) signal peptide. To quantify chitinolytic activity, we developed a high-performance anion-exchange chromatography-pulsed amperometric detection (HPAEC-PAD) method as an alternative to the established hydrophilic interaction liquid ion chromatography coupled with UV detection (HILIC-UV) method for separation and detection of released oxidized chito-oligosaccharides. Using this method, we demonstrated that CflaLPMO10D is strictly active on the β-allomorph of chitin, with optimal activity at pH 5 to 6 and a preference for ascorbic acid as the reducing agent. We also demonstrated the importance of the CBM2 member for both mediating enzyme localization to substrates and prolonging LPMO activity. Together with previous work, the present study defines the distinct substrate specificities of the suite of C. flavigena AA10 members. Notably, a cross-genome survey of AA10 members indicated that chitinolytic LPMOs are, in fact, rare among Cellulomonas bacteria. IMPORTANCE Species from the genus Cellulomonas have a long history of study due to their roles in biomass recycling in nature and corresponding potential as sources of enzymes for biotechnological applications. Although Cellulomonas species are more commonly associated with the cleavage and utilization of plant cell wall polysaccharides, here, we show that C. flavigena produces a unique lytic polysaccharide monooxygenase with activity on β-chitin, which is found, for example, in arthropods. The limited distribution of orthologous chitinolytic LPMOs suggests adaptation of individual cellulomonads to specific nutrient niches present in soil ecosystems. This research provides new insight into the biochemical specificity of LPMOs in Cellulomonas species and related bacteria, and it raises new questions about the physiological function of these enzymes.
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5
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Lewin GR, Davis NM, McDonald BR, Book AJ, Chevrette MG, Suh S, Boll A, Currie CR. Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. mSystems 2022; 7:e0151921. [PMID: 35258341 PMCID: PMC9040578 DOI: 10.1128/msystems.01519-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.
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Affiliation(s)
- Gina R. Lewin
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Nicole M. Davis
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Bradon R. McDonald
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Adam J. Book
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Marc G. Chevrette
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Steven Suh
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Ardina Boll
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cameron R. Currie
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Akermann A, Weiermüller J, Chodorski JN, Nestriepke MJ, Baclig MT, Ulber R. Optimization of bioprocesses with Brewers' spent grain and Cellulomonas uda. Eng Life Sci 2022; 22:132-151. [PMID: 35382540 PMCID: PMC8961044 DOI: 10.1002/elsc.202100053] [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: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/29/2021] [Indexed: 01/09/2023] Open
Abstract
Brewers' spent grain (BSG) is a low-value by-product of the brewing process, which is produced in large quantities every year. In this study, the lignocellulosic feedstock (solid BSG) was used to optimize fermentations with Cellulomonas uda. Under aerobic conditions, maximum cellulase activities of 0.98 nkat∙mL-1, maximum xylanase activities of 5.00 nkat∙mL-1 and cell yields of 0.22 gCells∙gBSG -1 were achieved. Under anaerobic conditions, enzyme activities and cell yields were lower, but valuable liquid products (organic acids, ethanol) were produced with a yield of 0.41 gProd∙gBSG -1. The growth phase of the organisms was monitored by measuring extracellular concentrations of two fluorophores pyridoxin (aerobic) and tryptophan (anaerobic) and by cell count. By combining reductive with anaerobic conditions, the ratio of ethanol to acetate was increased from 1.08 to 1.59 molEtOH∙molAc -1. This ratio was further improved to 9.2 molEtOH∙molAc -1 by lowering the pH from 7.4 to 5.0 without decreasing the final ethanol concentration. A fermentation in a bioreactor with 15 w% BSG instead of 5 w% BSG quadrupled the acetate concentration, whilst ethanol was removed by gas stripping. This study provides various ideas for optimizing and monitoring fermentations with solid substrates, which can support feasibility and incorporation into holistic biorefining approaches in the future.
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Affiliation(s)
- Alexander Akermann
- TU KaiserslauternDepartment of Mechanical and Process EngineeringKaiserslauternGermany
| | - Jens Weiermüller
- TU KaiserslauternDepartment of Mechanical and Process EngineeringKaiserslauternGermany
| | | | | | - Maria Teresa Baclig
- TU KaiserslauternDepartment of Mechanical and Process EngineeringKaiserslauternGermany
| | - Roland Ulber
- TU KaiserslauternDepartment of Mechanical and Process EngineeringKaiserslauternGermany
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Lee JA, Baugh AC, Shevalier NJ, Strand B, Stolyar S, Marx CJ. Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community. Microorganisms 2021; 9:321. [PMID: 33557371 PMCID: PMC7914493 DOI: 10.3390/microorganisms9020321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/25/2022] Open
Abstract
The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal "Model Lignocellulose" growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.
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Affiliation(s)
- Jessica A. Lee
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
| | - Alyssa C. Baugh
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Nicholas J. Shevalier
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Brandi Strand
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Sergey Stolyar
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (A.C.B.); (N.J.S.); (B.S.); (S.S.)
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
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Li J, Solhi L, Goddard-Borger ED, Mathieu Y, Wakarchuk WW, Withers SG, Brumer H. Four cellulose-active lytic polysaccharide monooxygenases from Cellulomonas species. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:29. [PMID: 33485381 PMCID: PMC7828015 DOI: 10.1186/s13068-020-01860-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/13/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The discovery of lytic polysaccharide monooxygenases (LPMOs) has fundamentally changed our understanding of microbial lignocellulose degradation. Cellulomonas bacteria have a rich history of study due to their ability to degrade recalcitrant cellulose, yet little is known about the predicted LPMOs that they encode from Auxiliary Activity Family 10 (AA10). RESULTS Here, we present the comprehensive biochemical characterization of three AA10 LPMOs from Cellulomonas flavigena (CflaLPMO10A, CflaLPMO10B, and CflaLPMO10C) and one LPMO from Cellulomonas fimi (CfiLPMO10). We demonstrate that these four enzymes oxidize insoluble cellulose with C1 regioselectivity and show a preference for substrates with high surface area. In addition, CflaLPMO10B, CflaLPMO10C, and CfiLPMO10 exhibit limited capacity to perform mixed C1/C4 regioselective oxidative cleavage. Thermostability analysis indicates that these LPMOs can refold spontaneously following denaturation dependent on the presence of copper coordination. Scanning and transmission electron microscopy revealed substrate-specific surface and structural morphological changes following LPMO action on Avicel and phosphoric acid-swollen cellulose (PASC). Further, we demonstrate that the LPMOs encoded by Cellulomonas flavigena exhibit synergy in cellulose degradation, which is due in part to decreased autoinactivation. CONCLUSIONS Together, these results advance understanding of the cellulose utilization machinery of historically important Cellulomonas species beyond hydrolytic enzymes to include lytic cleavage. This work also contributes to the broader mapping of enzyme activity in Auxiliary Activity Family 10 and provides new biocatalysts for potential applications in biomass modification.
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Affiliation(s)
- James Li
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Laleh Solhi
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ethan D Goddard-Borger
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephen G Withers
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Botany, University of British Columbia, 3200 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada.
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9
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Ghosh S, Godoy L, Anchang KY, Achilonu CC, Gryzenhout M. Fungal Cellulases: Current Research and Future Challenges. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Profiles of Human Milk Oligosaccharides and Their Relations to the Milk Microbiota of Breastfeeding Mothers in Dubai. Nutrients 2020; 12:nu12061727. [PMID: 32526930 PMCID: PMC7353065 DOI: 10.3390/nu12061727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
The composition of human breast milk is affected by several factors, including genetics, geographic location and maternal nutrition. This study investigated the human milk oligosaccharides (HMOs) of breastfeeding mothers living in Dubai and their relations with the milk microbiota. A total of 30 breast milk samples were collected from healthy Emirati and UAE-expatriates at Latifa Hospital. HMO profiling was performed using UHPLC-MS. Microbiota profiles were determined by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. HMO concentrations were significantly higher in Emirati, and dropped with the lactation period in both groups of mothers. The Le (a-b+)-secretor (Le+Se+) type was the most abundant in Dubai mothers (60%), followed by the Le(a-b-)-secretor (Le-Se+) type (23%). Bifidobacterium and Lactobacillus were considerably lower in Dubai-based mothers, while Pseudomonas and Delftia (Hydrogenophaga) were detected at a higher abundance compared to mothers from other countries. Atopobium was correlated with sialyl-lacto-N-tetraose c, Leptotrichia and Veillonella were correlated with 6'-sialyl-lactose, and Porphyromonas was correlated with lacto-N-hexaose. The study highlights the HMO profiles of breastfeeding mothers in Dubai and reveals few correlations with milk microbial composition. Targeted genomic analyses may help in determining whether these differences are due to genetic variations or to sociocultural and environmental factors.
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11
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Cao L, Ma Y, Deng D, Jiang H, Wang J, Liu Y. Electricity production of microbial fuel cells by degrading cellulose coupling with Cr(VI) removal. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122184. [PMID: 32092674 DOI: 10.1016/j.jhazmat.2020.122184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/18/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
A facultative exoelectrogen strain Lsc-8 belonging to the Cellulomonas genus with the ability to degrade carboxymethyl cellulose (CMC) coupled with the reduction of Cr(VI), was successfully isolated from rumen content. The maximum output power density of the microbial fuel cells (MFCs) inoculated strain Lsc-8 was 9.56 ± 0.37 mW·m-2 with CMC as the sole carbon source. From the biomass analysis it can be seen that the electricity generation of the MFCs was primarily attributed to the planktonic cells of strain Lsc-8 rather than the biofilm attached on the electrode, which was different from Geobacter sulfurreducens. Especially, during electricity generation of the MFCs using CMC as carbon source in the anode chamber, the Cr(VI) reduction were simultaneously realized. And it is also found that the Cr(VI) reduction ratio by strain Lsc-8 is directly related to the initial Cr(VI) concentration, and it increased with the increase of initial Cr(VI) concentration at first, then started to decrease when the Cr(VI) concentration was above 21 mg ·L-1. Meanwhile, the highest output power density of 3.47 ± 0.28 mW·m-2 was observed coupling with 95.22 ± 2.72 % of Cr(VI) reduction. These data suggested that the strain Lsc-8 could reduce high toxicity Cr(VI) to low toxicity Cr(III) coupled with electricity generation in MFCs with CMC as the carbon source. Our results also suggested that this study will provide a possibility to simultaneously degrade Cr(VI) and generate electricity by using cellulose as the carbon source via MFCs.
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Affiliation(s)
- Lianbin Cao
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi Province, 712100, PR China
| | - Yamei Ma
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi Province, 712100, PR China
| | - Dandan Deng
- College of Biology and Food, Shangqiu Normal University, No. 55 Pingyuan Road, Shangqiu, Henan Province, 476000, PR China
| | - Huichun Jiang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi Province, 712100, PR China
| | - Jiaxin Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi Province, 712100, PR China
| | - Ying Liu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi Province, 712100, PR China.
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12
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Low A, Zhao S, Rogers MJ, Zemb O, Lee M, He J, Manefield M. Isolation, characterization and bioaugmentation of an acidotolerant 1,2-dichloroethane respiring Desulfitobacterium species from a low pH aquifer. FEMS Microbiol Ecol 2020; 95:5454739. [PMID: 30980656 DOI: 10.1093/femsec/fiz055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/11/2019] [Indexed: 01/14/2023] Open
Abstract
A Desulfitobacterium sp. strain AusDCA of the Peptococcaceae family capable of respiring 1,2-dichloroethane (1,2-DCA) to ethene anaerobically with ethanol or hydrogen as electron donor at pH 5.0 with optimal range between pH 6.5-7.5 was isolated from an acidic aquifer near Sydney, Australia. Strain AusDCA is distant (94% nucleotide identity) from its nearest phylogenetic neighbor, D. metallireducens, and could represent a new species. Reference gene-based quantification of growth indicated a doubling time of 2 days in cultures buffered at pH 7.2, and a yield of 7.66 (± 4.0) × 106 cells µmol-1 of 1,2-DCA. A putative 1,2-DCA reductive dehalogenase was translated from a dcaAB locus and had high amino acid identity (97.3% for DcaA and 100% for DcaB) to RdhA1B1 of the 1,2-DCA respiring Dehalobacter strain WL. Proteomic analysis confirmed DcaA expression in the pure culture. Dehalogenation of 1,2-DCA (1.6 mM) was observed in batch cultures established from groundwater at pH 5.5 collected 38 days after in situ bioaugmentation but not in cultures established with groundwater collected at the same time from wells not receiving bioaugmentation. Overall, strain AusDCA can tolerate lower pH than previously characterized organohalide respiring bacteria and remained viable in groundwater at pH 5.5.
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Affiliation(s)
- Adrian Low
- Genome Structural Biology, Temasek Lifesciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Olivier Zemb
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Matthew Lee
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Mike Manefield
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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Khawdas W, Aso Y, Tanaka T, Okahisa Y, Kazama I, Ohara H. Electrical Performance of Palm Kernel Shell Utilized as Fuel for <i>Cellulomonas fimi</i> in Microbial Fuel Cells. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2020. [DOI: 10.1252/jcej.19we125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wichean Khawdas
- Department of Biobased Materials Science, Kyoto Institute of Technology
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology
| | - Tomonari Tanaka
- Department of Biobased Materials Science, Kyoto Institute of Technology
| | - Yoko Okahisa
- Department of Biobased Materials Science, Kyoto Institute of Technology
| | - Iori Kazama
- Department of Biobased Materials Science, Kyoto Institute of Technology
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology
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14
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Khawdas W, Watanabe K, Karatani H, Aso Y, Tanaka T, Ohara H. Direct electron transfer of Cellulomonas fimi and microbial fuel cells fueled by cellulose. J Biosci Bioeng 2019; 128:593-598. [PMID: 31147220 DOI: 10.1016/j.jbiosc.2019.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 04/24/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
Abstract
The strain of Cellulomonas fimi NBRC 15513 can generate electricity with cellulose as fuel without mediator using a single chamber type microbial fuel cell (MFC) which had 100 mL of chamber and 50 cm2 of the air cathode. The MFCs were operated over five days and showed the maximum current density of 10.0 ± 1.8 mA/m2, the maximum power density of 0.74 ± 0.07 mW/m2 and the ohmic resistance of 6.9 kΩ. According to the results of cyclic voltammetry, the appearance of the oxidation or reduction peak was not observed from the cell removed solution. The fact is that C. fimi does not secrete mediator-like compounds, while the oxidation peak was observed at +0.68 V from the phosphate buffer containing the washed cell. The peak appearance was caused by the electron transfer activity of which corresponds to cytochrome c, and disappeared after adding antimycin A which inhibits the electron transfer activity. The cell was alive throughout the experiment as the result of a colony forming unit on Luria-Bertani agar plates. This was thought that cytochrome c was on the membrane surface of the living cell and played a role in the direct electron transfer between the cells and anode.
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Affiliation(s)
- Wichean Khawdas
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Keigo Watanabe
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hajime Karatani
- Department of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; Kyoto Luminous Science Laboratory, Keihanna Plaza, Laboratory Wing, 1-7 Hikaridai, Seika-cho, Souraku-gum, Kyoto 619-0237, Japan
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomonari Tanaka
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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15
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Takenaka M, Lee JM, Kahar P, Ogino C, Kondo A. Efficient and Supplementary Enzyme Cocktail from Actinobacteria and Plant Biomass Induction. Biotechnol J 2018; 14:e1700744. [PMID: 29981210 DOI: 10.1002/biot.201700744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 06/28/2018] [Indexed: 11/08/2022]
Abstract
Actinobacteria plays a key role in the cycling of organic matter in soils. They secret biomass-degrading enzymes that allow it to produce the unique metabolites that originate in plant biomass. Although past studies have focused on these unique metabolites, a large-scale screening of Actinobacteria is yet to be reported to focus on their biomass-degrading ability. In the present study, a rapid and simple method is constructed for a large-scale screening, and the novel resources that form the plant biomass-degrading enzyme cocktail are identified from 850 isolates of Actinobacteria. As a result, Nonomuraea fastidiosa secretes a biomass degrading enzyme cocktail with the highest enzyme titer, although cellulase activities are lower than a commercially available enzyme. So the rich accessory enzymes are suggested to contribute to the high enzyme titer for a pretreated bagasse with a synergistic effect. Additionally, an optimized cultivation method of biomass induction caused to produce the improved enzyme cocktail indicated strong enzyme titers and a strong synergistic effect. Therefore, the novel enzyme cocktails are selected via the optimized method for large-scale screening, and then the enzyme cocktail can be improved via the optimized production with biomass-induction.
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Affiliation(s)
- Musashi Takenaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Jae M Lee
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
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16
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Leandro T, Rodriguez N, Rojas P, Sanz JL, da Costa MS, Amils R. Study of methanogenic enrichment cultures of rock cores from the deep subsurface of the Iberian Pyritic Belt. Heliyon 2018; 4:e00605. [PMID: 29862366 PMCID: PMC5968172 DOI: 10.1016/j.heliyon.2018.e00605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/15/2018] [Accepted: 04/10/2018] [Indexed: 11/26/2022] Open
Abstract
Two deep boreholes were drilled at 320 and 620 meters below surface in the Iberian Pyritic Belt (IPB) at Peña de Hierro (Huelva, Southwestern Spain). Cores were sampled and used for the establishment of enrichment cultures with methanogenic activity. The cultivable diversity of these enrichments was accessed using different cultivation techniques and several isolates were recovered in pure culture from various depths in both boreholes. Although no archaeal isolates were obtained in pure culture, strict anaerobes and facultative anaerobic bacteria belonging to the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were isolated and identified using the 16S rRNA gene sequence. Analysis of three selected enrichment cultures by amplification of both bacterial and archaeal 16S rRNA gene followed by pyrosequencing revealed further information on the populations enriched. The archaeal sequences obtained from the methanogenic enrichment cultures belonged to the orders Methanosarcinales and Methanocellales. To best of our knowledge this is the first report of enrichment in members of the Methanocellales in a deep terrestrial subsurface ecosystem. Several bacterial populations, predominantly consisting of Firmicutes and Proteobacteria, were also enriched. The prevalent microbial populations enriched as detected by pyrosequencing analysis, as well as the bacterial isolates cultivated were affiliated with known fermentative, sulfate reducing and acetogenic bacteria or methanogenic archaea. Our results show a great diversity in the microbial communities of the IPB deep subsurface.
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Affiliation(s)
- Tânia Leandro
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Nuria Rodriguez
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | - Patricia Rojas
- Department of Molecular Biology, Universidad Autónoma de Madrid, Spain
| | - Jose L. Sanz
- Department of Molecular Biology, Universidad Autónoma de Madrid, Spain
| | - Milton S. da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
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17
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Sakurai K, Kawasaki H. Genetic variation during long-term preservation of bacteria in public culture collections. Int J Syst Evol Microbiol 2018; 68:1815-1821. [PMID: 29557768 DOI: 10.1099/ijsem.0.002717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phenotypic and genetic changes during long-term preservation have been observed in microbial strains at culture collections (CCs). It is imperative to verify the effects of these changes on quality of the strains preserved at CCs. In this study, we performed genome-wide single-nucleotide polymorphism (SNP) analysis of different production lots, which had been derived from the same origin and preserved at the NITE Biological Resource Center (NBRC) for a 4-38-year period by the vacuum liquid drying method at 4 °C. The analysis was conducted for three sets of lots derived from Cellulomonas fimi NBRC 15513T, Corynebacterium glutamicum NBRC 12168T, and Saccharomonospora viridis NBRC 12207T. SNPs were found in all sets studied for comparison purposes. In sets of two or three lots, genomic SNPs were found in both non-coding sequences (non-CDSs) and in coding sequences (CDSs), and the SNPs in the CDSs resulted in non-synonymous mutations. These data indicated that genomic variation occurred during long-term preservation.
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Affiliation(s)
- Kenta Sakurai
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shibuyaku, Tokyo 151-0066, Japan
| | - Hiroko Kawasaki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shibuyaku, Tokyo 151-0066, Japan
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18
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Characterisation of novel biomass degradation enzymes from the genome of Cellulomonas fimi. Enzyme Microb Technol 2018; 113:9-17. [PMID: 29602392 PMCID: PMC5892457 DOI: 10.1016/j.enzmictec.2018.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/11/2017] [Accepted: 02/12/2018] [Indexed: 01/06/2023]
Abstract
Identified over 90 putative polysaccharide degrading ORFs in C. fimi genome. Cloned 14 putative cellulolytic ORFs as BioBricks, screened them for activity. Partially purified AfsB, BxyF, BxyH and XynF and characterised them further. BxyH proved highly temperature and alkaline pH tolerant. BioBricks are an easy method for screening genes for specific activities.
Recent analyses of genome sequences belonging to cellulolytic bacteria have revealed many genes potentially coding for cellulosic biomass degradation enzymes. Annotation of these genes however, is based on few biochemically characterised examples. Here we present a simple strategy based on BioBricks for the rapid screening of candidate genes expressed in Escherichia coli. As proof of principle we identified over 70 putative biomass degrading genes from bacterium Cellulomonas fimi, expressing a subset of these in BioBrick format. Six novel genes showed activity in E. coli. Four interesting enzymes were characterised further. α-l-arabinofuranosidase AfsB, β-xylosidases BxyF and BxyH and multi-functional β-cellobiosidase/xylosidase XynF were partially purified to determine their optimum pH, temperature and kinetic parameters. One of these enzymes, BxyH, was unexpectedly found to be highly active at strong alkaline pH and at temperatures as high as 100 °C. This report demonstrates a simple method of quickly screening and characterising putative genes as BioBricks.
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19
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Spertino S, Boatti L, Icardi S, Manfredi M, Cattaneo C, Marengo E, Cavaletto M. Cellulomonas fimi secretomes: In vivo and in silico approaches for the lignocellulose bioconversion. J Biotechnol 2018; 270:21-29. [PMID: 29409863 DOI: 10.1016/j.jbiotec.2018.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/30/2017] [Accepted: 01/26/2018] [Indexed: 12/17/2022]
Abstract
Lignocellulose degradation is a challenging step for value added products and biofuels production. Cellulomonas fimi secretes complex mixtures of carbohydrate active enzymes (CAZymes) which synergistically degrade cellulose and hemicelluloses. Their characterization may provide new insights for enzymatic cocktails implementation. Bioinformatic analysis highlighted 1127 secreted proteins, constituting the in silico secretome, graphically represented in a 2DE map. According to Blast2GO functional annotation, many of these are involved in carbohydrates metabolism. In vivo secretomes were obtained, growing C. fimi on glucose, CMC or wheat straw for 24 h. Zymography revealed degradative activity on carbohydrates and proteomic analysis identified some CAZymes, only in secretomes obtained with CMC and wheat straw. An interaction between cellobiohydrolases is proposed as a strategy adopted by soluble multimodular cellulases. Such approach can be crucial for a better characterization and industrial exploitation of the synergism among C. fimi enzymes.
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Affiliation(s)
- Stefano Spertino
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy.
| | - Lara Boatti
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Sara Icardi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Marcello Manfredi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy; ISALIT S.r.l., Novara, Italy
| | - Chiara Cattaneo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Maria Cavaletto
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
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20
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Saxena H, Hsu B, de Asis M, Zierke M, Sim L, Withers SG, Wakarchuk W. Characterization of a thermostable endoglucanase from Cellulomonas fimi ATCC484. Biochem Cell Biol 2017; 96:68-76. [PMID: 28982013 DOI: 10.1139/bcb-2017-0150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bacteria in the genus Cellulomonas are well known as secretors of a variety of mesophilic carbohydrate degrading enzymes (e.g., cellulases and hemicellulases), active against plant cell wall polysaccharides. Recent proteomic analysis of the mesophilic bacterium Cellulomonas fimi ATCC484 revealed uncharacterized enzymes for the hydrolysis of plant cell wall biomass. Celf_1230 (CfCel6C), a secreted protein of Cellulomonas fimi ATCC484, is a novel member of the GH6 family of cellulases that could be successfully expressed in Escherichia coli. This enzyme displayed very little enzymatic/hydrolytic activity at 30 °C, but showed an optimal activity around 65 °C, and exhibited a thermal denaturation temperature of 74 °C. In addition, it also strongly bound to filter paper despite having no recognizable carbohydrate binding module. Our experiments show that CfCel6C is a thermostable endoglucanase with activity on a variety of β-glucans produced by an organism that struggles to grow above 30 °C.
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Affiliation(s)
- Hirak Saxena
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Bryan Hsu
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Marc de Asis
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Mirko Zierke
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lyann Sim
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Stephen G Withers
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Warren Wakarchuk
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
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21
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Lubbe A, Bowen BP, Northen T. Exometabolomic Analysis of Cross-Feeding Metabolites. Metabolites 2017; 7:E50. [PMID: 28976938 PMCID: PMC5746730 DOI: 10.3390/metabo7040050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 12/16/2022] Open
Abstract
Microbial consortia have the potential to perform complex, industrially important tasks. The design of microbial consortia requires knowledge of the substrate preferences and metabolic outputs of each member, to allow understanding of potential interactions such as competition and beneficial metabolic exchange. Here, we used exometabolite profiling to follow the resource processing by a microbial co-culture of two biotechnologically relevant microbes, the bacterial cellulose degrader Cellulomonas fimi, and the oleaginous yeast Yarrowia lipolytica. We characterized the substrate preferences of the two strains on compounds typically found in lignocellulose hydrolysates. This allowed prediction that specific sugars resulting from hemicellulose polysaccharide degradation by C. fimi may serve as a cross-feeding metabolites to Y. lipolytica in co-culture. We also showed that products of ionic liquid-treated switchgrass lignocellulose degradation by C. fimi were channeled to Y. lipolytica in a co-culture. Additionally, we observed metabolites, such as shikimic acid accumulating in the co-culture supernatants, suggesting the potential for producing interesting co-products. Insights gained from characterizing the exometabolite profiles of individual and co-cultures of the two strains can help to refine this interaction, and guide strategies for making this an industrially viable co-culture to produce valuable products from lignocellulose material.
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Affiliation(s)
- Andrea Lubbe
- Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley 94720, CA, USA.
| | - Benjamin P Bowen
- Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley 94720, CA, USA.
| | - Trent Northen
- Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley 94720, CA, USA.
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22
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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23
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Revealing the insoluble metasecretome of lignocellulose-degrading microbial communities. Sci Rep 2017; 7:2356. [PMID: 28539641 PMCID: PMC5443780 DOI: 10.1038/s41598-017-02506-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/13/2017] [Indexed: 01/07/2023] Open
Abstract
Microbial communities metabolize plant biomass using secreted enzymes; however, identifying extracellular proteins tightly bound to insoluble lignocellulose in these microbiomes presents a challenge, as the rigorous extraction required to elute these proteins also lyses the microbes associated with the plant biomass releasing intracellular proteins that contaminate the metasecretome. Here we describe a technique for targeting the extracellular proteome, which was used to compare the metasecretome and meta-surface-proteome of two lignocellulose-degrading communities grown on wheat straw and rice straw. A combination of mass spectrometry-based proteomics coupled with metatranscriptomics enabled the identification of a unique secretome pool from these lignocellulose-degrading communities. This method enabled us to efficiently discriminate the extracellular proteins from the intracellular proteins by improving detection of actively secreted and transmembrane proteins. In addition to the expected carbohydrate active enzymes, our new method reveals a large number of unknown proteins, supporting the notion that there are major gaps in our understanding of how microbial communities degrade lignocellulosic substrates.
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24
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Thomas L, Ram H, Singh VP. Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya. J Comput Biol 2017; 24:1029-1042. [PMID: 28177649 DOI: 10.1089/cmb.2016.0161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities. Evolutionary relatedness was also observed in phylogenetic trees among a number of cellulase sequences of diverse taxa. In cellulases, propensity for alanine, glycine, leucine, serine, and threonine was high, but low for cysteine, histidine, and methionine. Catalytic aspartic acid had a higher propensity than glutamic acid, and both were involved in regular expression patterns. Characteristic group and multigroup-specific conserved signature indels located in the catalytic domains of cellulases were observed that further clarified evolutionary relationships. These indels can be distinctive molecular tools for understanding phylogeny and identification of unknown cellulolytic species of common evolutionary descent in different environments.
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Affiliation(s)
- Lebin Thomas
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
| | - Hari Ram
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
| | - Ved Pal Singh
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
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25
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Characterization of a Cellulomonas fimi exoglucanase/xylanase-endoglucanase gene fusion which improves microbial degradation of cellulosic biomass. Enzyme Microb Technol 2016; 93-94:113-121. [DOI: 10.1016/j.enzmictec.2016.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/17/2022]
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26
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Suriya J, Bharathiraja S, Manivasagan P, Kim SK. Enzymes From Rare Actinobacterial Strains. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 79:67-98. [PMID: 27770864 DOI: 10.1016/bs.afnr.2016.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Actinobacteria constitute rich sources of novel biocatalysts and novel natural products for medical and industrial utilization. Although actinobacteria are potential source of economically important enzymes, the isolation and culturing are somewhat tough because of its extreme habitats. But now-a-days, the rate of discovery of novel compounds producing actinomycetes from soil, freshwater, and marine ecosystem has increased much through the developed culturing and genetic engineering techniques. Actinobacteria are well-known source of their bioactive compounds and they are the promising source of broad range of industrially important enzymes. The bacteria have the capability to degrade a range of pesticides, hydrocarbons, aromatic, and aliphatic compounds (Sambasiva Rao, Tripathy, Mahalaxmi, & Prakasham, 2012). Most of the enzymes are mainly derived from microorganisms because of their easy of growth, minimal nutritional requirements, and low-cost for downstream processing. The focus of this review is about the new, commercially useful enzymes from rare actinobacterial strains. Industrial requirements are now fulfilled by the novel actinobacterial enzymes which assist the effective production. Oxidative enzymes, lignocellulolytic enzymes, extremozymes, and clinically useful enzymes are often utilized in many industrial processes because of their ability to catalyze numerous reactions. Novel, extremophilic, oxidative, lignocellulolytic, and industrially important enzymes from rare Actinobacterial population are discussed in this chapter.
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Affiliation(s)
- J Suriya
- School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - S Bharathiraja
- CAS in Marine Biology, Annamalai University, Porto Novo, Tamil Nadu, India
| | - P Manivasagan
- Marine Bioprocess Research Center, Pukyong National University, Busan, Republic of Korea.
| | - S-K Kim
- Marine Bioprocess Research Center, Pukyong National University, Busan, Republic of Korea; Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, Republic of Korea.
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27
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Lakhundi SS, Duedu KO, Cain N, Nagy R, Krakowiak J, French CE. Citrobacter freundii as a test platform for recombinant cellulose degradation systems. Lett Appl Microbiol 2016; 64:35-42. [PMID: 27617802 DOI: 10.1111/lam.12668] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/27/2016] [Accepted: 09/08/2016] [Indexed: 01/03/2023]
Abstract
Cellulosic biomass represents a huge reservoir of renewable carbon, but converting it into useful products is challenging. Attempts to transfer cellulose degradation capability to industrially useful micro-organisms have met with limited success, possibly due to poorly understood synergy between multiple cellulases. This is best studied by co-expression of many combinations of cellulases and associated proteins. Here, we describe the development of a test platform based on Citrobacter freundii, a cellobiose-assimilating organism closely related to Escherichia coli. Standard E. coli cloning vectors worked well in Cit. freundii. Expression of cellulases CenA and Cex of Cellulomonas fimi in Cit. freundii gave recombinant strains which were able to grow at the expense of cellulosic filter paper or microcrystalline cellulose (Avicel) in a mineral medium supplemented with a small amount of yeast extract. Periodic physical agitation of the cultures was highly beneficial for growth at the expense of filter paper. This provides a test platform for the expression of combinations of genes encoding biomass-degrading enzymes to develop effective genetic cassettes for degradation of different biomass streams. SIGNIFICANCE AND IMPACT OF THE STUDY Biofuels have been shown to be the best sustainable and alternative source of fuel to replace fossil fuels. Of the different types of feedstocks used for producing biofuels, lignocellulosic biomass is the most abundant. Converting this biomass to useful products has met with little success. Different approaches are being used and microbial platforms are the most promising and sustainable method. This study shows that Citrobacter freundii is a better test platform than Escherichia coli for testing various combinations of cellulases for the development of microbial systems for biomass conversion.
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Affiliation(s)
- S S Lakhundi
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - K O Duedu
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,School of Basic & Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - N Cain
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - R Nagy
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J Krakowiak
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - C E French
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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28
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Poulsen HV, Willink FW, Ingvorsen K. Aerobic and anaerobic cellulase production by Cellulomonas uda. Arch Microbiol 2016; 198:725-35. [PMID: 27154570 PMCID: PMC4995238 DOI: 10.1007/s00203-016-1230-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/08/2016] [Accepted: 04/25/2016] [Indexed: 10/29/2022]
Abstract
Cellulomonas uda (DSM 20108/ATCC 21399) is one of the few described cellulolytic facultative anaerobes. Based on these characteristics, we initiated a physiological study of C. uda with the aim to exploit it for cellulase production in simple bioreactors with no or sporadic aeration. Growth, cellulase activity and fermentation product formation were evaluated in different media under both aerobic and anaerobic conditions and in experiments where C. uda was exposed to alternating aerobic/anaerobic growth conditions. Here we show that C. uda behaves as a true facultative anaerobe when cultivated on soluble substrates such as glucose and cellobiose, but for reasons unknown cellulase activity is only induced under aerobic conditions on insoluble cellulosic substrates and not under anaerobic conditions. These findings enhance knowledge on the limited number of described facultative cellulolytic anaerobes, and in addition it greatly limits the utility of C. uda as an 'easy to handle' cellulase producer with low aeration demands.
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Affiliation(s)
- Henrik Vestergaard Poulsen
- Department of Bioscience, Section for Microbiology, Aarhus University, Ny Munkegade 116, 8000, Aarhus C, Denmark
| | - Fillip Wolfgang Willink
- Department of Bioscience, Section for Microbiology, Aarhus University, Ny Munkegade 116, 8000, Aarhus C, Denmark
| | - Kjeld Ingvorsen
- Department of Bioscience, Section for Microbiology, Aarhus University, Ny Munkegade 116, 8000, Aarhus C, Denmark.
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29
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Wakarchuk WW, Brochu D, Foote S, Robotham A, Saxena H, Erak T, Kelly J. Proteomic Analysis of the Secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482. PLoS One 2016; 11:e0151186. [PMID: 26950732 PMCID: PMC4780727 DOI: 10.1371/journal.pone.0151186] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/24/2016] [Indexed: 12/19/2022] Open
Abstract
The bacteria in the genus Cellulomonas are known for their ability to degrade plant cell wall biomass. Cellulomonas fimi ATCC 484 and C. flavigena ATCC 482 have been the subject of much research into secreted cellulases and hemicellulases. Recently the genome sequences of both C. fimi ATCC 484 and C. flavigena ATCC 482 were published, and a genome comparison has revealed their full spectrum of possible carbohydrate-active enzymes (CAZymes). Using mass spectrometry, we have compared the proteins secreted by C. fimi and C. flavigena during growth on the soluble cellulose substrate, carboxymethylcellulose (CMC), as well as a soluble xylan fraction. Many known C. fimi CAZymes were detected, which validated our analysis, as were a number of new CAZymes and other proteins that, though identified in the genome, have not previously been observed in the secretome of either organism. Our data also shows that many of these are co-expressed on growth of either CMC or xylan. This analysis provides a new perspective on Cellulomonas enzymes and provides many new CAZyme targets for characterization.
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Affiliation(s)
- Warren W. Wakarchuk
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
- * E-mail:
| | - Denis Brochu
- Human Health Therapeutics Program, National Research Council Canada, Ottawa, Ontario, Canada
| | - Simon Foote
- Human Health Therapeutics Program, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anna Robotham
- Human Health Therapeutics Program, National Research Council Canada, Ottawa, Ontario, Canada
| | - Hirak Saxena
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Tamara Erak
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - John Kelly
- Human Health Therapeutics Program, National Research Council Canada, Ottawa, Ontario, Canada
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30
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Saini A, Aggarwal NK, Sharma A, Yadav A. Actinomycetes: A Source of Lignocellulolytic Enzymes. Enzyme Res 2015; 2015:279381. [PMID: 26793393 PMCID: PMC4697097 DOI: 10.1155/2015/279381] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023] Open
Abstract
Lignocellulose is the most abundant biomass on earth. Agricultural, forest, and agroindustrial activities generate tons of lignocellulosic wastes annually, which present readily procurable, economically affordable, and renewable feedstock for various lignocelluloses based applications. Lignocelluloses are the focus of present decade researchers globally, in an attempt to develop technologies based on natural biomass for reducing dependence on expensive and exhaustible substrates. Lignocellulolytic enzymes, that is, cellulases, hemicellulases, and lignolytic enzymes, play very important role in the processing of lignocelluloses which is prerequisite for their utilization in various processes. These enzymes are obtained from microorganisms distributed in both prokaryotic and eukaryotic domains including bacteria, fungi, and actinomycetes. Actinomycetes are an attractive microbial group for production of lignocellulose degrading enzymes. Various studies have evaluated the lignocellulose degrading ability of actinomycetes, which can be potentially implemented in the production of different value added products. This paper is an overview of the diversity of cellulolytic, hemicellulolytic, and lignolytic actinomycetes along with brief discussion of their hydrolytic enzyme systems involved in biomass modification.
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Affiliation(s)
- Anita Saini
- Department of Microbiology, Kurukshetra University, Kurukshetra, Haryana 136119, India
| | - Neeraj K. Aggarwal
- Department of Microbiology, Kurukshetra University, Kurukshetra, Haryana 136119, India
| | - Anuja Sharma
- Department of Microbiology, Kurukshetra University, Kurukshetra, Haryana 136119, India
| | - Anita Yadav
- Department of Biotechnology, Kurukshetra University, Kurukshetra, Haryana 136119, India
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31
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Zhuang W, Zhang S, Xia X, Wang G. Draft genome sequence of Cellulomonas carbonis T26(T) and comparative analysis of six Cellulomonas genomes. Stand Genomic Sci 2015; 10:104. [PMID: 26587181 PMCID: PMC4652355 DOI: 10.1186/s40793-015-0096-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/09/2015] [Indexed: 11/28/2022] Open
Abstract
Most Cellulomonas strains are cellulolytic and this feature may be applied in straw degradation and bioremediation. In this study, Cellulomonas carbonis T26T, Cellulomonas bogoriensis DSM 16987T and Cellulomonas cellasea 20108T were sequenced. Here we described the draft genomic information of C. carbonis T26T and compared it to the related Cellulomonas genomes. Strain T26T has a 3,990,666 bp genome size with a G + C content of 73.4 %, containing 3418 protein-coding genes and 59 RNA genes. The results showed good correlation between the genotypes and the physiological phenotypes. The information are useful for the better application of the Cellulomonas strains.
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Affiliation(s)
- Weiping Zhuang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Shengzhe Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Xian Xia
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
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32
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Brumm PJ, De Maayer P, Mead DA, Cowan DA. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. Front Microbiol 2015; 6:430. [PMID: 26029180 PMCID: PMC4428132 DOI: 10.3389/fmicb.2015.00430] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/22/2015] [Indexed: 11/13/2022] Open
Abstract
In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.
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Affiliation(s)
- Phillip J. Brumm
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
| | - Pieter De Maayer
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
- Department of Microbiology and Plant Pathology, University of PretoriaPretoria, South Africa
| | - David A. Mead
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
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33
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Youngblut ND, Buckley DH. Intra-genomic variation in G + C content and its implications for DNA stable isotope probing. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:767-775. [PMID: 25139123 DOI: 10.1111/1758-2229.12201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Abstract
Combining deoxyribonucleic acid (DNA-based) stable isotope probing (DNA-SIP) with high-throughput sequencing provides a powerful culture-independent means to link microbial metabolic function to genomic information and taxonomic identity. DNA buoyant density (BD) in isopycnic gradients is dependent on both isotope incorporation and G + C content. G + C content varies across a genome but is constrained at rrn operons; hence, the ability to resolve isotopically labelled DNA from unlabelled DNA in SIP may vary between small subunit-ribosomal nucleic acid (SSU rRNA) amplicon and shotgun-read sequencing applications. We tested this hypothesis by evaluating the G + C content of genomic DNA fragments that encompassed either an SSU rRNA template ('amplicon-fragments') or a shotgun read template ('shotgun-fragments'). We find that, contrary to expectations, the BD distribution of amplicon-fragments is non-normal and can be highly skewed. Furthermore, the BD distribution of amplicon-fragments can differ substantially from that of shotgun-fragments from the same genome. Our findings demonstrate the impact of G + C content on the downstream applications of DNA-SIP, which will aid in proper experimental design and the development of statistical tests to accurately identify sequences derived from isotopically labelled DNA.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Crop and Soil Sciences, Cornell University, 306 Tower Road, Ithaca, NY, 14853, USA
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34
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Gao J, Wakarchuk W. Characterization of five β-glycoside hydrolases from Cellulomonas fimi ATCC 484. J Bacteriol 2014; 196:4103-10. [PMID: 25225266 PMCID: PMC4248878 DOI: 10.1128/jb.02194-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 09/04/2014] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive bacterium Cellulomonas fimi produces a large array of carbohydrate-active enzymes. Analysis of the collection of carbohydrate-active enzymes from the recent genome sequence of C. fimi ATCC 484 shows a large number of uncharacterized genes for glycoside hydrolase (GH) enzymes potentially involved in biomass utilization. To investigate the enzymatic activity of potential β-glucosidases in C. fimi, genes encoding several GH3 enzymes and one GH1 enzyme were cloned and recombinant proteins were expressed in Escherichia coli. Biochemical analysis of these proteins revealed that the enzymes exhibited different substrate specificities for para-nitrophenol-linked substrates (pNP), disaccharides, and oligosaccharides. Celf_2726 encoded a bifunctional enzyme with β-d-xylopyranosidase and α-l-arabinofuranosidase activities, based on pNP-linked substrates (CfXyl3A). Celf_0140 encoded a β-d-glucosidase with activity on β-1,3- and β-1,6-linked glucosyl disaccharides as well as pNP-β-Glc (CfBgl3A). Celf_0468 encoded a β-d-glucosidase with hydrolysis of pNP-β-Glc and hydrolysis/transglycosylation activities only on β-1,6-linked glucosyl disaccharide (CfBgl3B). Celf_3372 encoded a GH3 family member with broad aryl-β-d-glycosidase substrate specificity. Celf_2783 encoded the GH1 family member (CfBgl1), which was found to hydrolyze pNP-β-Glc/Fuc/Gal, as well as cellotetraose and cellopentaose. CfBgl1 also had good activity on β-1,2- and β-1,3-linked disaccharides but had only very weak activity on β-1,4/6-linked glucose.
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Affiliation(s)
- Juan Gao
- School of Life Sciences, Northeast Normal University, Changchun, Jilin Province, People's Republic of China
| | - Warren Wakarchuk
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
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35
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TOMOTSUNE K, KASUGA K, TSUCHIDA M, SHIMURA Y, KOBAYASHI M, AGEMATSU H, IKEDA H, ISHIKAWA J, KOJIMA I. Cloning and Sequence Analysis of the Cellulase Genes Isolated from Two Cellulolytic Streptomycetes and Their Heterologous Expression in Streptomyces lividans . ACTA ACUST UNITED AC 2014. [DOI: 10.5188/ijsmer.20.213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Kano KASUGA
- Department of Biotechnology, Akita Prefectural University
| | - Miho TSUCHIDA
- Department of Biotechnology, Akita Prefectural University
| | | | | | - Hitoshi AGEMATSU
- Department of Applied Chemistry, Akita National College of Technology
| | - Haruo IKEDA
- Kitasato Institute for Life Sciences, Kitasato University
| | - Jun ISHIKAWA
- Department of Bioactive Molecules, National Institute of Infectious Diseases
| | - Ikuo KOJIMA
- Department of Biotechnology, Akita Prefectural University
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36
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Timinskas K, Balvočiūtė M, Timinskas A, Venclovas Č. Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res 2013; 42:1393-413. [PMID: 24106089 PMCID: PMC3919608 DOI: 10.1093/nar/gkt900] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The analysis of ∼2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III α-subunit (PolIIIα) homologs. Classified into C-family of DNA polymerases they come in two major forms, PolC and DnaE, related by ancient duplication. While PolC represents an evolutionary compact group, DnaE can be further subdivided into at least three groups (DnaE1-3). We performed an extensive analysis of various sequence, structure and surface properties of all four polymerase groups. Our analysis suggests a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups. Among them, DnaE1 and PolC show the highest conservation of the analyzed properties. DnaE3 polymerases apparently represent an ‘impaired’ version of DnaE1. Nonessential DnaE2 polymerases, typical for oxygen-using bacteria with large GC-rich genomes, have a number of features in common with DnaE3 polymerases. The analysis of polymerase distribution in genomes revealed three major combinations: DnaE1 either alone or accompanied by one or more DnaE2s, PolC + DnaE3 and PolC + DnaE1. The first two combinations are present in Escherichia coli and Bacillus subtilis, respectively. The third one (PolC + DnaE1), found in Clostridia, represents a novel, so far experimentally uncharacterized, set.
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Affiliation(s)
- Kestutis Timinskas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania
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