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Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, Severinov K, Chen A, Lucks J. The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch. Nucleic Acids Res 2024; 52:4466-4482. [PMID: 38567721 PMCID: PMC11077080 DOI: 10.1093/nar/gkae231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/17/2024] [Accepted: 03/20/2024] [Indexed: 04/16/2024] Open
Abstract
A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of Escherichia coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37°C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65°C through Thermus aquaticus RNA polymerase in vitro transcription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.
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Affiliation(s)
- Laura M Hertz
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Elise N White
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | | | - Luyi Cheng
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Rivaan Kakkaramadam
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Alan Chen
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
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2
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Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, Severinov K, Chen A, Lucks JB. The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570056. [PMID: 38106011 PMCID: PMC10723315 DOI: 10.1101/2023.12.05.570056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of E. coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37 °C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65 °C through Thermus aquaticus RNA polymerase in vitro transcription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.
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Affiliation(s)
- Laura M Hertz
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Elise N White
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | | | - Luyi Cheng
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Rivaan Kakkaramadam
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Alan Chen
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
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Akram F, Haq IU, Shah FI, Aqeel A, Ahmed Z, Mir AS, Qureshi SS, Raja SI. Genus Thermotoga: A valuable home of multifunctional glycoside hydrolases (GHs) for industrial sustainability. Bioorg Chem 2022; 127:105942. [PMID: 35709577 DOI: 10.1016/j.bioorg.2022.105942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Nature is a dexterous and prolific chemist for cataloging a number of hostile niches that are the ideal residence of various thermophiles. Apart from having other species, these subsurface environments are considered a throne of bacterial genus Thermotoga. The genome sequence of Thermotogales encodes complex and incongruent clusters of glycoside hydrolases (GHs), which are superior to their mesophilic counterparts and play a prominent role in various applications due to their extreme intrinsic stability. They have a tremendous capacity to use a wide variety of simple and multifaceted carbohydrates through GHs, formulate fermentative hydrogen and bioethanol at extraordinary yield, and catalyze high-temperature reactions for various biotechnological applications. Nevertheless, no stringent rules exist for the thermo-stabilization of biocatalysts present in the genus Thermotoga. These enzymes endure immense attraction in fundamental aspects of how these polypeptides attain and stabilize their distinctive three-dimensional (3D) structures to accomplish their physiological roles. Moreover, numerous genome sequences from Thermotoga species have revealed a significant fraction of genes most closely related to those of archaeal species, thus firming a staunch belief of lateral gene transfer mechanism. However, the question of its magnitude is still in its infancy. In addition to GHs, this genus is a paragon of encapsulins which carry pharmacological and industrial significance in the field of life sciences. This review highlights an intricate balance between the genomic organizations, factors inducing the thermostability, and pharmacological and industrial applications of GHs isolated from genus Thermotoga.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan; Pakistan Academy of Science, Islamabad, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Azka Shahzad Mir
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Sumbal Sajid Qureshi
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Saleha Ibadat Raja
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
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Amundson KK, Borton MA, Daly RA, Hoyt DW, Wong A, Eder E, Moore J, Wunch K, Wrighton KC, Wilkins MJ. Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation. MICROBIOME 2022; 10:5. [PMID: 35034639 PMCID: PMC8762873 DOI: 10.1186/s40168-021-01194-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. RESULTS We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. CONCLUSIONS These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.
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Affiliation(s)
- Kaela K. Amundson
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - Mikayla A. Borton
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - Rebecca A. Daly
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - David W. Hoyt
- Environmental Molecular Sciences Laboratory, Richland, WA USA
| | - Allison Wong
- Environmental Molecular Sciences Laboratory, Richland, WA USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Richland, WA USA
| | | | | | - Kelly C. Wrighton
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
| | - Michael J. Wilkins
- Department of Soil & Crop Sciences, Colorado State University, Fort Collins, CO USA
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Lanzilli M, Esercizio N, Vastano M, Xu Z, Nuzzo G, Gallo C, Manzo E, Fontana A, d’Ippolito G. Effect of Cultivation Parameters on Fermentation and Hydrogen Production in the Phylum Thermotogae. Int J Mol Sci 2020; 22:ijms22010341. [PMID: 33396970 PMCID: PMC7795431 DOI: 10.3390/ijms22010341] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/19/2023] Open
Abstract
The phylum Thermotogae is composed of a single class (Thermotogae), 4 orders (Thermotogales, Kosmotogales, Petrotogales, Mesoaciditogales), 5 families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, Mesoaciditogaceae), and 13 genera. They have been isolated from extremely hot environments whose characteristics are reflected in the metabolic and phenotypic properties of the Thermotogae species. The metabolic versatility of Thermotogae members leads to a pool of high value-added products with application potentials in many industry fields. The low risk of contamination associated with their extreme culture conditions has made most species of the phylum attractive candidates in biotechnological processes. Almost all members of the phylum, especially those in the order Thermotogales, can produce bio-hydrogen from a variety of simple and complex sugars with yields close to the theoretical Thauer limit of 4 mol H2/mol consumed glucose. Acetate, lactate, and L-alanine are the major organic end products. Thermotagae fermentation processes are influenced by various factors, such as hydrogen partial pressure, agitation, gas sparging, culture/headspace ratio, inoculum, pH, temperature, nitrogen sources, sulfur sources, inorganic compounds, metal ions, etc. Optimization of these parameters will help to fully unleash the biotechnological potentials of Thermotogae and promote their applications in industry. This article gives an overview of how these operational parameters could impact Thermotogae fermentation in terms of sugar consumption, hydrogen yields, and organic acids production.
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Affiliation(s)
- Mariamichela Lanzilli
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Nunzia Esercizio
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Marco Vastano
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA;
| | - Genoveffa Nuzzo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Carmela Gallo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Emiliano Manzo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Angelo Fontana
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Giuliana d’Ippolito
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
- Correspondence: ; Tel.: +39-081-8675096
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6
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Summers ZM, Belahbib H, Pradel N, Bartoli M, Mishra P, Tamburini C, Dolla A, Ollivier B, Armougom F. A novel Thermotoga strain TFO isolated from a Californian petroleum reservoir phylogenetically related to Thermotoga petrophila and T. naphthophila, two thermophilic anaerobic isolates from a Japanese reservoir: Taxonomic and genomic considerations. Syst Appl Microbiol 2020; 43:126132. [DOI: 10.1016/j.syapm.2020.126132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
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7
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Biochemical characterization of a novel hyperthermophilic α-l-rhamnosidase from Thermotoga petrophila and its application in production of icaritin from epimedin C with a thermostable β-glucosidase. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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8
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da Silva VM, Cabral AD, Sperança MA, Squina FM, Muniz JRC, Martin L, Nicolet Y, Garcia W. High-resolution structure of a modular hyperthermostable endo-β-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140437. [PMID: 32325255 DOI: 10.1016/j.bbapap.2020.140437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/20/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022]
Abstract
The endo-β-1,4-mannanase from the hyperthermostable bacterium Thermotoga petrophila (TpMan) is an enzyme that catalyzes the hydrolysis of mannan and heteromannan polysaccharides. Of the three domains that comprise TpMan, the N-terminal GH5 catalytic domain and the C-terminal carbohydrate-binding domain are connected through a central ancillary domain of unknown structure and function. In this study, we report the partial crystal structure of the TpMan at 1.45 Å resolution, so far, the first modular hyperthermostable endo-β-1,4-mannanase structure determined. The structure exhibits two domains, a (β/α)8-barrel GH5 catalytic domain connected via a linker to the central domain with an immunoglobulin-like β-sandwich fold formed of seven β-strands. Functional analysis showed that whereas the immunoglobulin-like domain does not have the carbohydrate-binding function, it stacks on the GH5 catalytic domain acting as a thermostabilizing domain and allowing operation at hyperthermophilic conditions. The carbohydrate-binding domain is absent in the crystal structure most likely due to its high flexibility around the immunoglobulin-like domain which may act also as a pivot. These results represent new structural and functional information useful on biotechnological applications for biofuel and food industries.
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Affiliation(s)
- Viviam M da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil; Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Aline D Cabral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Marcia A Sperança
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - João Renato C Muniz
- São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil.
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Hameed U, Ul-Haq I. Kinetics and thermodynamics of catalysis and thermal inactivation of a novel α-amylase (Tp-AmyS) from Thermotoga petrophila. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1736573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Uzma Hameed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Ikram Ul-Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
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10
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Yadav A, Vilcáez J, Farag IF, Johnson B, Mueller K, Youssef NH, Elshahed MS. Candidatus Mcinerneyibacterium aminivorans gen. nov., sp. nov., the first representative of the candidate phylum Mcinerneyibacteriota phyl. nov. recovered from a high temperature, high salinity tertiary oil reservoir in north central Oklahoma, USA. Syst Appl Microbiol 2020; 43:126057. [PMID: 31987701 DOI: 10.1016/j.syapm.2020.126057] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 11/17/2022]
Abstract
We report on the characterization of a novel genomic assembly (ARYD3) recovered from formation water (17.6% salinity) and crude oil enrichment amended by isolated soy proteins (0.2%), and incubated for 100 days under anaerobic conditions at 50°C. Phylogenetic and phylogenomic analysis demonstrated that the ARYD3 is unaffiliated with all currently described bacterial phyla and candidate phyla, as evident by the low AAI (34.7%), shared gene content (19.4%), and 78.9% 16S rRNA gene sequence similarity to Halothiobacillus neapolitanus, its closest cultured relative. Genomic characterization predicts a slow-growing, non-spore forming, and non-motile Gram-negative rod. Adaptation to high salinity is potentially mediated by the production of the compatible solutes cyclic 2,3-diphosphoglycerate (cDPG), α-glucosylglycerate, as well as the uptake of glycine betaine. Metabolically, the genome encodes primarily aminolytic capabilities for a wide range of amino acids and peptides. Interestingly, evidence of propionate degradation to succinate via methyl-malonyl CoA was identified, suggesting possible capability for syntrophic propionate degradation. Analysis of ARYD3 global distribution patterns identified its occurrence in a very small fraction of Earth Microbiome Project datasets examined (318/27,068), where it consistently represented an extremely rare fraction (maximum 0.28%, average 0.004%) of the overall community. We propose the Candidatus name Mcinerneyibacterium aminivorans gen. nov, sp. nov. for ARYD3T, with the genome serving as the type material for the novel family Mcinerneyibacteriaceae fam. nov., order Mcinerneyibacteriales ord. nov., class Mcinerneyibacteria class nov., and phylum Mcinerneyibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number VSIX00000000.
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MESH Headings
- Bacterial Proteins/genetics
- Culture Media
- DNA, Bacterial/genetics
- Ecosystem
- Genome, Bacterial/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/metabolism
- Oil and Gas Fields/chemistry
- Oil and Gas Fields/microbiology
- Oklahoma
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Salinity
- Sequence Analysis, DNA
- Soybean Proteins/metabolism
- Temperature
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Affiliation(s)
- Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Javier Vilcáez
- Boone Pickens School of Geology, Oklahoma State University, Stillwater, OK, United States
| | - Ibrahim F Farag
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Britny Johnson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Katherine Mueller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States.
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11
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Wang H, Lu L, Chen X, Bian Y, Ren ZJ. Geochemical and microbial characterizations of flowback and produced water in three shale oil and gas plays in the central and western United States. WATER RESEARCH 2019; 164:114942. [PMID: 31401327 DOI: 10.1016/j.watres.2019.114942] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
Limited understanding of wastewater streams produced from shale oil and gas wells impedes best practices of wastewater treatment and reuse. This study provides a comprehensive and comparative analysis of flowback and produced water from three major and newly developed shale plays (the Bakken shale, North Dakota; the Barnett shale, Texas; and the Denver-Julesburg (DJ) basin, Colorado) in central and western United States. Geochemical features that included more than 10 water quality parameters, dissolved organic matter, as well as microbial community structures were characterized and compared. Results showed that wastewater from Bakken and Barnett shales has extremely high salinity (∼295 g/L total dissolved solids (TDS)) and low organic concentration (80-252 mg/L dissolved organic carbon (DOC)). In contrast, DJ basin showed an opposite trend with low TDS (∼30 g/L) and high organic content (644 mg/L DOC). Excitation-emission matrix (EEM) fluorescence spectra demonstrated that more humic acid and fluvic acid-like organics with higher aromaticity existed in Bakken wastewater than that in Barnett and DJ basin. Microbial communities of Bakken samples were dominated by Fe (III)-reducing bacteria Geobacter, lactic acid bacteria Lactococcus and Enterococcus, and Bradyrhizobium, while DJ basin water showed higher abundance of Rhodococcus, Thermovirga, and sulfate reducing bacteria Thermotoga and Petrotoga. All these bacteria are capable of hydrocarbon degradation. Hydrogenotrophic methanogens dominated the archaeal communities in all samples.
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Affiliation(s)
- Huan Wang
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
| | - Lu Lu
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Xi Chen
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Yanhong Bian
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Zhiyong Jason Ren
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
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12
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Cloning, Purification, and Characterization of Recombinant Thermostable β-Xylanase Tnap_0700 from Thermotoga naphthophila. Appl Biochem Biotechnol 2019; 189:1274-1290. [DOI: 10.1007/s12010-019-03068-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/07/2019] [Indexed: 01/31/2023]
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13
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Zhang S, Xie J, Zhao L, Pei J, Su E, Xiao W, Wang Z. Cloning, overexpression and characterization of a thermostable β-xylosidase from Thermotoga petrophila and cooperated transformation of ginsenoside extract to ginsenoside 20(S)-Rg3 with a β-glucosidase. Bioorg Chem 2019; 85:159-167. [DOI: 10.1016/j.bioorg.2018.12.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 11/26/2022]
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14
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Dipasquale L, Pradhan N, d’Ippolito G, Fontana A. Potential of Hydrogen Fermentative Pathways in Marine Thermophilic Bacteria: Dark Fermentation and Capnophilic Lactic Fermentation in Thermotoga and Pseudothermotoga Species. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Zheng T, Cui J, Bae HR, Lynd LR, Olson DG. Expression of adhA from different organisms in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:251. [PMID: 29213311 PMCID: PMC5707802 DOI: 10.1186/s13068-017-0940-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum is a cellulolytic anaerobic thermophile that is a promising candidate for consolidated bioprocessing of lignocellulosic biomass into biofuels such as ethanol. It was previously shown that expressing Thermoanaerobacterium saccharolyticum adhA in C. thermocellum increases ethanol yield.In this study, we investigated expression of adhA genes from different organisms in Clostridium thermocellum. METHODS Based on sequence identity to T. saccharolyticum adhA, we chose adhA genes from 10 other organisms: Clostridium botulinum, Methanocaldococcus bathoardescens, Thermoanaerobacterium ethanolicus, Thermoanaerobacter mathranii, Thermococcus strain AN1, Thermoanaerobacterium thermosaccharolyticum, Caldicellulosiruptor saccharolyticus, Fervidobacterium nodosum, Marinitoga piezophila, and Thermotoga petrophila. All 11 adhA genes (including T. saccharolyticum adhA) were expressed in C. thermocellum and fermentation end products were analyzed. RESULTS All 11 adhA genes increased C. thermocellum ethanol yield compared to the empty-vector control. C. botulinum and T. ethanolicus adhA genes generated significantly higher ethanol yield than T. saccharolyticum adhA. CONCLUSION Our results indicated that expressing adhA is an effective method of increasing ethanol yield in wild-type C. thermocellum, and that this appears to be a general property of adhA genes.
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Affiliation(s)
- Tianyong Zheng
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Jingxuan Cui
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Hye Ri Bae
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
| | - Lee R. Lynd
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
| | - Daniel G. Olson
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
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Xu Z, Puranik R, Hu J, Xu H, Han D. Complete genome sequence of Thermotoga sp. strain RQ7. Stand Genomic Sci 2017; 12:62. [PMID: 29046741 PMCID: PMC5637354 DOI: 10.1186/s40793-017-0271-1] [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: 10/04/2016] [Accepted: 09/21/2017] [Indexed: 12/26/2022] Open
Abstract
Thermotoga sp. strain RQ7 is a member of the family Thermotogaceae in the order Thermotogales. It is a Gram negative, hyperthermophilic, and strictly anaerobic bacterium. It grows on diverse simple and complex carbohydrates and can use protons as the final electron acceptor. Its complete genome is composed of a chromosome of 1,851,618 bp and a plasmid of 846 bp. The chromosome contains 1906 putative genes, including 1853 protein coding genes and 53 RNA genes. The genetic features pertaining to various lateral gene transfer mechanisms are analyzed. The genome carries a complete set of putative competence genes, 8 loci of CRISPRs, and a deletion of a well-conserved Type II R-M system.
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Affiliation(s)
- Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Rutika Puranik
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Junxi Hu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
- School of Life Sciences, Minnan Normal University, 36 Xianqianzhi Street, Zhangzhou, Fujian 363000 China
| | - Hui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Dongmei Han
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
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Functional characterization and crystal structure of thermostable amylase from Thermotoga petrophila , reveals high thermostability and an unusual form of dimerization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [DOI: 10.1016/j.bbapap.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Progeny production in the periplasm of Thermosipho globiformans. Extremophiles 2017; 21:805-815. [PMID: 28577249 PMCID: PMC5487896 DOI: 10.1007/s00792-017-0944-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 05/08/2017] [Indexed: 02/02/2023]
Abstract
Thermotogales are rod-shaped, Gram-negative, anaerobic, (hyper) thermophiles distinguished by an outer sheath-like toga, which comprises an outer membrane (OM) and an amorphous layer (AL). Thermosipho globiformans bacteria can transform into spheroids with multiple cells concurrently with AL disintegration during early growth; the cell is defined as the cytoplasmic membrane (CM) plus the entity surrounded by the CM. Spheroids eventually produce rapidly moving periplasmic ‘progenies’ through an unknown mechanism. Here, we used high-temperature microscopy (HTM) to directly observe spheroid generation and growth. Rod OMs abruptly inflated to form ~2 μm-diameter balloons. Concurrently, multiple globular cells emerged in the balloons, suggesting their translocation and transformation from the rod state. During spheroid growth, the cells elongated and acquired a large dish shape by possible fusion. Spheroids with dish-shaped cells further enlarged to ~12 μm in diameter. HTM and epifluorescence-microscopy results collectively indicated that the nucleoids of dish-shaped cells transformed to form a ring shape, which then distorted to form a lip shape as the spheroid enlarged. HTM showed that ‘progenies’ were produced in the spheroid periplasm. Transmission electron microscopy results suggested that the ‘progenies’ represented immature progenies lacking togas, which were acquired subsequently.
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Succession in the petroleum reservoir microbiome through an oil field production lifecycle. ISME JOURNAL 2017; 11:2141-2154. [PMID: 28524866 PMCID: PMC5563965 DOI: 10.1038/ismej.2017.78] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 04/19/2017] [Accepted: 04/25/2017] [Indexed: 11/08/2022]
Abstract
Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth’s surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1–15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.
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Counts JA, Zeldes BM, Lee LL, Straub CT, Adams MWW, Kelly RM. Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28206708 DOI: 10.1002/wsbm.1377] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022]
Abstract
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology-based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Laura L Lee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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Auria R, Boileau C, Davidson S, Casalot L, Christen P, Liebgott PP, Combet-Blanc Y. Hydrogen production by the hyperthermophilic bacterium Thermotoga maritima Part II: modeling and experimental approaches for hydrogen production. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:268. [PMID: 28018485 PMCID: PMC5168804 DOI: 10.1186/s13068-016-0681-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Thermotoga maritima is a hyperthermophilic bacterium known to produce hydrogen from a large variety of substrates. The aim of the present study is to propose a mathematical model incorporating kinetics of growth, consumption of substrates, product formations, and inhibition by hydrogen in order to predict hydrogen production depending on defined culture conditions. RESULTS Our mathematical model, incorporating data concerning growth, substrates, and products, was developed to predict hydrogen production from batch fermentations of the hyperthermophilic bacterium, T. maritima. It includes the inhibition by hydrogen and the liquid-to-gas mass transfer of H2, CO2, and H2S. Most kinetic parameters of the model were obtained from batch experiments without any fitting. The mathematical model is adequate for glucose, yeast extract, and thiosulfate concentrations ranging from 2.5 to 20 mmol/L, 0.2-0.5 g/L, or 0.01-0.06 mmol/L, respectively, corresponding to one of these compounds being the growth-limiting factor of T. maritima. When glucose, yeast extract, and thiosulfate concentrations are all higher than these ranges, the model overestimates all the variables. In the window of the model validity, predictions of the model show that the combination of both variables (increase in limiting factor concentration and in inlet gas stream) leads up to a twofold increase of the maximum H2-specific productivity with the lowest inhibition. CONCLUSIONS A mathematical model predicting H2 production in T. maritima was successfully designed and confirmed in this study. However, it shows the limit of validity of such mathematical models. Their limit of applicability must take into account the range of validity in which the parameters were established.
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Affiliation(s)
- Richard Auria
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, 13288 Marseille, France
| | - Céline Boileau
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, 13288 Marseille, France
| | - Sylvain Davidson
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, 13288 Marseille, France
| | - Laurence Casalot
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, 13288 Marseille, France
| | - Pierre Christen
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, 13288 Marseille, France
| | - Pierre Pol Liebgott
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, 13288 Marseille, France
| | - Yannick Combet-Blanc
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, 13288 Marseille, France
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Boucher N, Noll KM. Substrate adaptabilities of Thermotogae mannan binding proteins as a function of their evolutionary histories. Extremophiles 2016; 20:771-83. [PMID: 27457081 DOI: 10.1007/s00792-016-0866-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/12/2016] [Indexed: 12/30/2022]
Abstract
The Thermotogae possess a large number of ATP-binding cassette (ABC) transporters, including two mannan binding proteins, ManD and CelE (previously called ManE). We show that a gene encoding an ancestor of these was acquired by the Thermotogae from the archaea followed by gene duplication. To address the functional evolution of these proteins as a consequence of their evolutionary histories, we measured the binding affinities of ManD and CelE orthologs from representative Thermotogae. Both proteins bind cellobiose, cellotriose, cellotetraose, β-1,4-mannotriose, and β-1,4-mannotetraose. The CelE orthologs additionally bind β-1,4-mannobiose, laminaribiose, laminaritriose and sophorose while the ManD orthologs additionally only weakly bind β-1,4-mannobiose. The CelE orthologs have higher unfolding temperatures than the ManD orthologs. An examination of codon sites under positive selection revealed that many of these encode residues located near or in the binding site, suggesting that the proteins experienced selective pressures in regions that might have changed their functions. The gene arrangement, phylogeny, binding properties, and putative regulatory networks suggest that the ancestral mannan binding protein was a CelE ortholog which gave rise to the ManD orthologs. This study provides a window on how one class of proteins adapted to new functions and temperatures to fit the physiologies of their new hosts.
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Affiliation(s)
- Nathalie Boucher
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, 91 N. Eagleville Rd., Storrs, CT, 06269-3125, USA
- New York State Department of Health, Wadsworth Center, Albany, NY, 12201, USA
| | - Kenneth M Noll
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, 91 N. Eagleville Rd., Storrs, CT, 06269-3125, USA.
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Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, Schlüter A. Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment. J Biotechnol 2016; 232:50-60. [PMID: 27165504 DOI: 10.1016/j.jbiotec.2016.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022]
Abstract
The genome sequence of Defluviitoga tunisiensis L3 originating from a thermophilic biogas-production plant was established and recently published as Genome Announcement by our group. The circular chromosome of D. tunisiensis L3 has a size of 2,053,097bp and a mean GC content of 31.38%. To analyze the D. tunisiensis L3 genome sequence in more detail, a phylogenetic analysis of completely sequenced Thermotogae strains based on shared core genes was performed. It appeared that Petrotoga mobilis DSM 10674(T), originally isolated from a North Sea oil-production well, is the closest relative of D. tunisiensis L3. Comparative genome analyses of P. mobilis DSM 10674(T) and D. tunisiensis L3 showed moderate similarities regarding occurrence of orthologous genes. Both genomes share a common set of 1351 core genes. Reconstruction of metabolic pathways important for the biogas production process revealed that the D. tunisiensis L3 genome encodes a large set of genes predicted to facilitate utilization of a variety of complex polysaccharides including cellulose, chitin and xylan. Ethanol, acetate, hydrogen (H2) and carbon dioxide (CO2) were found as possible end-products of the fermentation process. The latter three metabolites are considered to represent substrates for methanogenic Archaea, the key organisms in the final step of the anaerobic digestion process. To determine the degree of relatedness between D. tunisiensis L3 and dominant biogas community members within the thermophilic biogas-production plant, metagenome sequences obtained from the corresponding microbial community were mapped onto the L3 genome sequence. This fragment recruitment revealed that the D. tunisiensis L3 genome is almost completely covered with metagenome sequences featuring high matching accuracy. This result indicates that strains highly related or even identical to the reference strain D. tunisiensis L3 play a dominant role within the community of the thermophilic biogas-production plant.
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Affiliation(s)
- Irena Maus
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Katharina Gabriela Cibis
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Andreas Bremges
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Yvonne Stolze
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | | | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, 35390 Gießen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany.
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Fatima B, Aftab MN, Haq IU. Cloning, purification, and characterization of xylose isomerase fromThermotoga naphthophilaRKU-10. J Basic Microbiol 2016; 56:949-62. [DOI: 10.1002/jobm.201500589] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 03/30/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Bilqees Fatima
- Institute of Industrial Biotechnology (IIB); GC University; Lahore Pakistan
| | | | - Ikram-ul Haq
- Institute of Industrial Biotechnology (IIB); GC University; Lahore Pakistan
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Roy C, Alam M, Mandal S, Haldar PK, Bhattacharya S, Mukherjee T, Roy R, Rameez MJ, Misra AK, Chakraborty R, Nanda AK, Mukhopadhyay SK, Ghosh W. Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria. Front Microbiol 2016; 7:412. [PMID: 27065976 PMCID: PMC4814524 DOI: 10.3389/fmicb.2016.00412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
Exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 pH) mid-temperature (55-85°C) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. To gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of Gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media with 50 μg ml(-1) vancomycin. Surprisingly, this Gram-positive-specific antibiotic eliminated the entire culturable-diversity of chemoorganotrophic and sulfur-chemolithotrophic bacteria present in the tested hot water inocula. Moreover, it also killed all the Gram-negative hot-spring isolates that were obtained in vancomycin-free media. Concurrent literature search for the description of Gram-negative thermophilic bacteria revealed that at least 16 of them were reportedly vancomycin-susceptible. While these data suggested that vancomycin-susceptibility could be a global trait of thermophilic bacteria (irrespective of their taxonomy, biogeography and Gram-character), MALDI Mass Spectroscopy of the peptidoglycans of a few Gram-negative thermophilic bacteria revealed that tandem alanines were present in the fourth and fifth positions of their muropeptide precursors (MPPs). Subsequent phylogenetic analyses revealed a close affinity between the D-alanine-D-alanine ligases (Ddl) of taxonomically-diverse Gram-negative thermophiles and the thermostable Ddl protein of Thermotoga maritima, which is well-known for its high specificity for alanine over other amino acids. The Ddl tree further illustrated a divergence between the homologs of Gram-negative thermophiles and mesophiles, which broadly coincided with vancomycin-susceptibility and vancomycin-resistance respectively. It was thus hypothesized that thermophilic Ddls have been evolutionarily selected to favor a D-ala-D-ala bonding. However, preference for D-ala-D-ala-terminated MPPs does not singlehandedly guarantee vancomycin susceptibility of thermophilic bacteria as the large and relatively-hydrophilic vancomycin molecule has to cross the outer membrane before it can inhibit peptidoglycan biosynthesis. Literature shows that many mesophilic Gram-negative bacteria also have D-ala-D-ala-terminated MPPs, but they still remain resistant to vancomycin due to the relative impermeability of their membranes. But the global vancomycin-susceptibility phenotype of thermophilic bacteria itself testifies that the drug crosses the membrane in all these cases. As a corollary, it seems quite likely that the outer membranes of thermophilic bacteria have some yet-unknown characteristic feature(s) that invariably ensures the entry of vancomycin.
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Affiliation(s)
- Chayan Roy
- Department of Microbiology, Bose Institute Kolkata, India
| | - Masrure Alam
- Department of Microbiology, Bose Institute Kolkata, India
| | | | | | | | | | - Rimi Roy
- Department of Microbiology, Bose Institute Kolkata, India
| | - Moidu J Rameez
- Department of Microbiology, Bose Institute Kolkata, India
| | - Anup K Misra
- Division of Molecular Medicine, Bose Institute Kolkata, India
| | | | - Ashish K Nanda
- Department of Chemistry, University of North Bengal Siliguri, India
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Zafar A, Aftab MN, ud Din Z, Aftab S, Iqbal I, ul Haq I. Cloning, Purification and Characterization of a Highly Thermostable Amylase Gene of Thermotoga petrophila into Escherichia coli. Appl Biochem Biotechnol 2015; 178:831-48. [PMID: 26526464 DOI: 10.1007/s12010-015-1912-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/26/2015] [Indexed: 11/26/2022]
Abstract
A putative α-amylase gene of Thermotoga petrophila was cloned and expressed in Escherichia coli BL21 (DE3) using pET-21a (+), as an expression vector. The growth conditions were optimized for maximal expression of the α-amylase using various parameters, such as pH, temperature, time of induction and addition of an inducer. The optimum temperature and pH for the maximum expression of α-amylase were 22 °C and 7.0 pH units, respectively. Purification of the recombinant enzyme was carried out by heat treatment method, followed by ion exchange chromatography with 34.6-fold purification having specific activity of 126.31 U mg(-1) and a recovery of 56.25%. Molecular weight of the purified α-amylase, 70 kDa, was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The enzyme was stable at 100 °C temperature and at pH of 7.0. The enzyme activity was increased in the presence of metal ions especially Ca(+2) and decreased in the presence of EDTA indicating that the α-amylase was a metalloenzyme. However, addition of 1% Tween 20, Tween 80 and β-mercaptoethanol constrained the enzyme activity to 87, 96 and 89%, respectively. No considerable effect of organic solvents (ethanol, methanol, isopropanol, acetone and n-butanol) was observed on enzyme activity. With soluble starch as a substrate, the enzyme activity under optimized conditions was 73.8 U mg(-1). The α-amylase enzyme was active to hydrolyse starch forming maltose.
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Affiliation(s)
- Asma Zafar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Muhammad Nauman Aftab
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Zia ud Din
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Saima Aftab
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Irfana Iqbal
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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27
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Kanoksilapatham W, Keawram P, Gonzalez JM, Robb FT. Isolation, characterization, and survival strategies of Thermotoga sp. strain PD524, a hyperthermophile from a hot spring in Northern Thailand. Extremophiles 2015; 19:853-61. [PMID: 26101016 DOI: 10.1007/s00792-015-0761-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/26/2015] [Indexed: 11/30/2022]
Abstract
A hyperthermophilic Thermotoga sp. strain PD524 was isolated from a hot spring in Northern Thailand. Cells were long-curved rods (0.5-0.6 × 2.5-10 μm) surrounded by a typical outer membrane toga. Strain PD524 is aero-tolerant at 4 °C but is aero-sensitive at 80 °C. A heat resistant subpopulation was observed in late-stationary phase. Cells from late-stationary phase were revealed remarkably less sensitive to 0.001 % SDS treatment than cells from exponential phase. The temperature range for growth was 70-85 °C (opt. temp. 80 °C), pH range was 6-8.5 (opt. pH 7.5-8.0), and NaCl range of 0 to <10 g/L (opt. 0.5 g/L). Glucose, sucrose, maltose, fructose, xylose, mannose, arabinose, trehalose, starch, and cellobiose were utilized as growth substrates. Growth was inhibited by S(o). Growth yield was stimulated by SO 4 (=) but not by S2O 3 (=) and NO3 (-). Analysis of 16S rRNA gene sequence (KF164213) of strain PD524 revealed closest similarity (96 %) to Thermotoga maritima MSB8(T), T. neapolitana NES(T), T. petrophila RKU-1(T), and T. naphthophila RKU-10(T).
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Affiliation(s)
- Wirojne Kanoksilapatham
- Department of Microbiology, Faculty of Science, Silpakorn University, Nakhon Pathom, 73000, Thailand,
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28
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Overexpression and characterization of a Ca2+ activated thermostable β-glucosidase with high ginsenoside Rb1 to ginsenoside 20(S)-Rg3 bioconversion productivity. ACTA ACUST UNITED AC 2015; 42:839-50. [DOI: 10.1007/s10295-015-1608-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
Abstract
The thermostable β-glucosidase gene from Thermotoga petrophila DSM 13995 was cloned and overexpressed in Escherichia coli. The activity of the recombinant β-glucosidase was 21 U/mL in the LB medium. Recombinant β-glucosidase was purified, and its molecular weight was approximately 81 kDa. The optimal activity was at pH 5.0 and 90 °C, and the thermostability of the enzyme was improved by Ca2+. The β-glucosidase had high selectivity for cleaving the outer and inner glucopyranosyl moieties at the C-20 carbon of ginsenoside Rb1, which produced the pharmacologically active minor ginsenoside 20(S)-Rg3. In a reaction at 90 °C and pH 5.0, 10 g/L of ginsenoside Rb1 was transformed into 6.93 g/L of Rg3 within 90 min, with a corresponding molar conversion of 97.9 %, and Rg3 productivity of 4620 mg/L/h. This study is the first report of a GH3-family enzyme that used Ca2+ to improve its thermostability, and it is the first report on the high substrate concentration bioconversion of ginsenoside Rb1 to ginsenoside 20(S)-Rg3 by using thermostable β-glucosidase under high temperature.
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29
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de Oliveira LC, da Silva VM, Colussi F, Cabral AD, de Oliveira Neto M, Squina FM, Garcia W. Conformational changes in a hyperthermostable glycoside hydrolase: enzymatic activity is a consequence of the loop dynamics and protonation balance. PLoS One 2015; 10:e0118225. [PMID: 25723179 PMCID: PMC4344334 DOI: 10.1371/journal.pone.0118225] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 01/10/2015] [Indexed: 11/20/2022] Open
Abstract
Endo-β-1, 4-mannanase from Thermotoga petrophila (TpMan) is a modular hyperthermostable enzyme involved in the degradation of mannan-containing polysaccharides. The degradation of these polysaccharides represents a key step for several industrial applications. Here, as part of a continuing investigation of TpMan, the region corresponding to the GH5 domain (TpManGH5) was characterized as a function of pH and temperature. The results indicated that the enzymatic activity of the TpManGH5 is pH-dependent, with its optimum activity occurring at pH 6. At pH 8, the studies demonstrated that TpManGH5 is a molecule with a nearly spherical tightly packed core displaying negligible flexibility in solution, and with size and shape very similar to crystal structure. However, TpManGH5 experiences an increase in radius of gyration in acidic conditions suggesting expansion of the molecule. Furthermore, at acidic pH values, TpManGH5 showed a less globular shape, probably due to a loop region slightly more expanded and flexible in solution (residues Y88 to A105). In addition, molecular dynamics simulations indicated that conformational changes caused by pH variation did not change the core of the TpManGH5, which means that only the above mentioned loop region presents high degree of fluctuations. The results also suggested that conformational changes of the loop region may facilitate polysaccharide and enzyme interaction. Finally, at pH 6 the results indicated that TpManGH5 is slightly more flexible at 65°C when compared to the same enzyme at 20°C. The biophysical characterization presented here is well correlated with the enzymatic activity and provide new insight into the structural basis for the temperature and pH-dependent activity of the TpManGH5. Also, the data suggest a loop region that provides a starting point for a rational design of biotechnological desired features.
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Affiliation(s)
- Leandro C de Oliveira
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, UNESP-Univ Estadual Paulista, São José do Rio Preto, SP, Brazil
| | - Viviam M da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Francieli Colussi
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Aline D Cabral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências, UNESP-Univ Estadual Paulista, Botucatu, SP, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
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30
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Colussi F, da Silva VM, Miller I, Cota J, de Oliveira LC, de Oliveira Neto M, Squina FM, Garcia W. Oligomeric state and structural stability of two hyperthermophilic β-glucosidases from Thermotoga petrophila. Amino Acids 2015; 47:937-48. [PMID: 25637167 DOI: 10.1007/s00726-015-1923-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 01/15/2015] [Indexed: 01/10/2023]
Abstract
The β-glucosidases are enzymes essential for several industrial applications, especially in the field of plant structural polysaccharides conversion into bioenergy and bioproducts. In a recent study, we have provided a biochemical characterization of two hyperthermostable β-glucosidases from Thermotoga petrophila belonging to the families GH1 (TpBGL1) and GH3 (TpBGL3). Here, as part of a continuing investigation, the oligomeric state, the net charge, and the structural stability, at acidic pH, of the TpBGL1 and TpBGL3 were characterized and compared. Enzymatic activity is directly related to the balance between protonation and conformational changes. Interestingly, our results indicated that there were no significant changes in the secondary, tertiary and quaternary structures of the β-glucosidases at temperatures below 80 °C. Furthermore, the results indicated that both the enzymes are stable homodimers in solution. Therefore, the observed changes in the enzymatic activities are due to variations in pH that modify protonation of the enzymes residues and the net charge, directly affecting the interactions with ligands. Finally, the results showed that the two β-glucosidases displayed different pH dependence of thermostability at temperatures above 80 °C. TpBGL1 showed higher stability at pH 6 than at pH 4, while TpBGL3 showed similar stability at both pH values. This study provides a useful comparison of the structural stability, at acidic pH, of two different hyperthermostable β-glucosidases and how it correlates with the activity of the enzymes. The information described here can be useful for biotechnological applications in the biofuel and food industries.
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Affiliation(s)
- Francieli Colussi
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
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31
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Nesbø CL, S Swithers K, Dahle H, Haverkamp THA, Birkeland NK, Sokolova T, Kublanov I, Zhaxybayeva O. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments. ISME JOURNAL 2014; 9:1532-42. [PMID: 25500512 DOI: 10.1038/ismej.2014.238] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 11/09/2022]
Abstract
Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the 'burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development.
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Affiliation(s)
- Camilla L Nesbø
- 1] Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway [2] Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Kristen S Swithers
- 1] Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, USA [2] Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Håkon Dahle
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway
| | - Nils-Kåre Birkeland
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Tatiana Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Zhaxybayeva
- 1] Department of Biological Sciences, Dartmouth College, Hanover, NH, USA [2] Department of Computer Science, Dartmouth College, Hanover, NH, USA
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32
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Hidese R, Inoue T, Imanaka T, Fujiwara S. Cysteine desulphurase plays an important role in environmental adaptation of the hyperthermophilic archaeon Thermococcus kodakarensis. Mol Microbiol 2014; 93:331-45. [PMID: 24893566 DOI: 10.1111/mmi.12662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2014] [Indexed: 11/29/2022]
Abstract
The sulphur atoms of sulphur-containing cofactors that are essential for numerous cellular functions in living organisms originate from L-cysteine via cysteine desulphurase (CSD) activity. However, many (hyper)thermophilic archaea, which thrive in solfataric fields and are positioned near the root of the evolutionary tree of life, lack CSD orthologues. The existence of CSD orthologues in a subset of (hyper)thermophilic archaea is of interest with respect to the evolution of sulphur-trafficking systems for the cofactors. This study demonstrates that the disruption of the csd gene of Thermococcus kodakarensis, a facultative elemental sulphur (S(0))-reducing hyperthermophilic archaeon, encoding Tk-CSD, conferred a growth defect evident only in the absence of S(0), and that growth can be restored by the addition of S(0), but not sulphide. We show that the csd gene is not required for biosynthesis of thiamine pyrophosphate or molybdopterin, irrespective of the presence or absence of S(0), but is necessary for iron-sulphur cluster biosynthesis in the absence of S(0). Recombinant form of Tk-CSD expressed in Escherichia coli was obtained and it was found to catalyse the desulphuration of L-cysteine. The obtained data suggest that hyperthermophiles might benefit from a capacity for CSD-dependent iron-sulphur cluster biogenesis, which allows them to thrive outside solfataric environments.
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Affiliation(s)
- Ryota Hidese
- Research Center for Environmental Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, 669-1337, Japan
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Mori K, Yamazoe A, Hosoyama A, Ohji S, Fujita N, Ishibashi JI, Kimura H, Suzuki KI. Thermotoga
profunda sp. nov. and Thermotoga
caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs. Int J Syst Evol Microbiol 2014; 64:2128-2136. [DOI: 10.1099/ijs.0.060137-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus
Thermotoga
. The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of
Thermotoga lettingae
(96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and
Thermotoga hypogea
(98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and
T. lettingae
TMOT and 76.6 % when comparing strain AZM44c09T and
T. hypogea
NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus
Thermotoga
within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Atsushi Yamazoe
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Akira Hosoyama
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shoko Ohji
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Nobuyuki Fujita
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | | | - Hiroyuki Kimura
- Department of Geosciences, Graduate School of Science, Shizuoka University, 836 Oya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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da Silva VM, Colussi F, de Oliveira Neto M, Braz ASK, Squina FM, Oliveira CLP, Garcia W. Modular hyperthermostable bacterial endo-β-1,4-mannanase: molecular shape, flexibility and temperature-dependent conformational changes. PLoS One 2014; 9:e92996. [PMID: 24671161 PMCID: PMC3966859 DOI: 10.1371/journal.pone.0092996] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/27/2014] [Indexed: 11/28/2022] Open
Abstract
Endo-β-1,4-mannanase from Thermotoga petrophila (TpMan) is a hyperthermostable enzyme that catalyzes the hydrolysis of β-1,4-mannoside linkages in various mannan-containing polysaccharides. A recent study reported that TpMan is composed of a GH5 catalytic domain joined by a linker to a carbohydrate-binding domain. However, at this moment, there is no three-dimensional structure determined for TpMan. Little is known about the conformation of the TpMan as well as the role of the length and flexibility of the linker on the spatial arrangement of the constitutive domains. In this study, we report the first structural characterization of the entire TpMan by small-angle X-ray scattering combined with the three-dimensional structures of the individual domains in order to shed light on the low-resolution model, overall dimensions, and flexibility of this modular enzyme at different temperatures. The results are consistent with a linker with a compact structure and that occupies a small volume with respect to its large number of amino acids. Furthermore, at 20°C the results are consistent with a model where TpMan is a molecule composed of three distinct domains and that presents some level of molecular flexibility in solution. Even though the full enzyme has some degree of molecular flexibility, there might be a preferable conformation, which could be described by the rigid-body modeling procedure. Finally, the results indicate that TpMan undergoes a temperature-driven transition between conformational states without a significant disruption of its secondary structure. Our results suggest that the linker can optimize the geometry between the other two domains with respect to the substrate at high temperatures. These studies should provide a useful basis for future biophysical studies of entire TpMan.
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Affiliation(s)
- Viviam M. da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Francieli Colussi
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Antonio S. K. Braz
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | | | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
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Members of the Order Thermotogales: From Microbiology to Hydrogen Production. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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36
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Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants. PLoS One 2013; 8:e84300. [PMID: 24391933 PMCID: PMC3877268 DOI: 10.1371/journal.pone.0084300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/19/2013] [Indexed: 01/06/2023] Open
Abstract
The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS). These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT) of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.
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37
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Devi S, Sharma N, Savitri, Bhalla TC. Comparative analysis of amino acid sequences from mesophiles and thermophiles in respective of carbon-nitrogen hydrolase family. 3 Biotech 2013; 3:491-507. [PMID: 28324422 PMCID: PMC3824785 DOI: 10.1007/s13205-012-0111-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/17/2012] [Indexed: 12/27/2022] Open
Abstract
A comparative study of amino acid sequence and physicochemical properties indicates the affiliation of protein from the nitrilase/cyanide hydratase family. This family contains nitrilases that break carbon-nitrogen bonds and appear to be involved in the reduction of organic nitrogen compounds and ammonia production. They all have distinct substrate specificity and include nitrilase, cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function. These sequences were analyzed for different physical and chemical properties and to relate these observed differences to the thermostability properties, phylogenetic tree construction and the evolutionary relationship among them. In this work, in silico analysis of amino acid sequences of mesophilic (15) and thermophilic (archaea, 15 and bacteria, 15) proteins has been done. The physiochemical properties of these three groups of nitrilase/cyanide hydratase family also differ in number of amino acids, molecular weight, pI values, positively charged ions, i.e. Arg + Lys, aliphatic index and grand average of hydropathacity (GRAVY). The amino acid Ala (1.37-fold) was found to be higher in mesophilic bacteria as compared to thermophilic bacteria but Lys and Phe were found to be significantly high (1.43 and 1.39-fold, respectively) in case of thermophilic bacteria. The amino acids Ala, Cys, Gln, His and Thr were found to be significantly higher (1.41, 1.6, 1.77, 1.44 and 1.29-fold, respectively) in mesophilic bacteria as compared to thermophilic archaea, where Glu, Leu and Val were found significantly high (1.22, 1.19 and 1.26-fold, respectively).
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Affiliation(s)
- Sarita Devi
- Bioinformatics Centre (Sub-Distributed Information Centre), Himachal Pradesh University, Shimla, Summer Hill, 171005, India
| | - Nikhil Sharma
- Bioinformatics Centre (Sub-Distributed Information Centre), Himachal Pradesh University, Shimla, Summer Hill, 171005, India
| | - Savitri
- Department of Biotechnology, Himachal Pradesh University, Shimla, Summer Hill, 171005, India
| | - Tek Chand Bhalla
- Bioinformatics Centre (Sub-Distributed Information Centre), Himachal Pradesh University, Shimla, Summer Hill, 171005, India.
- Department of Biotechnology, Himachal Pradesh University, Shimla, Summer Hill, 171005, India.
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38
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Green AG, Swithers KS, Gogarten JF, Gogarten JP. Reconstruction of ancestral 16S rRNA reveals mutation bias in the evolution of optimal growth temperature in the Thermotogae phylum. Mol Biol Evol 2013; 30:2463-74. [PMID: 23966548 DOI: 10.1093/molbev/mst145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Optimal growth temperature is a complex trait involving many cellular components, and its physiology is not yet fully understood. Evolution of continuous characters, such as optimal growth temperature, is often modeled as a one-dimensional random walk, but such a model may be an oversimplification given the complex processes underlying the evolution of continuous characters. Recent articles have used ancestral sequence reconstruction to infer the optimal growth temperature of ancient organisms from the guanine and cytosine content of the stem regions of ribosomal RNA, allowing inferences about the evolution of optimal growth temperature. Here, we investigate the optimal growth temperature of the bacterial phylum Thermotogae. Ancestral sequence reconstruction using a nonhomogeneous model was used to reconstruct the stem guanine and cytosine content of 16S rRNA sequences. We compare this sequence reconstruction method with other ancestral character reconstruction methods, and show that sequence reconstruction generates smaller confidence intervals and different ancestral values than other reconstruction methods. Unbiased random walk simulation indicates that the lower temperature members of the Thermotogales have been under directional selection; however, when a simulation is performed that takes possible mutations into account, it is the high temperature lineages that are, in fact, under directional selection. We find that the evolution of Thermotogales optimal growth temperatures is best fit by a biased random walk model. These findings suggest that it may be easier to evolve from a high optimal growth temperature to a lower one than vice versa.
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MESH Headings
- Base Composition
- Cold Temperature
- Computer Simulation
- Evolution, Molecular
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/growth & development
- Models, Biological
- Mutation
- Phylogeny
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Selection, Genetic
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Affiliation(s)
- Anna G Green
- Department of Molecular and Cell Biology, University of Connecticut
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Peacock JP, Cole JK, Murugapiran SK, Dodsworth JA, Fisher JC, Moser DP, Hedlund BP. Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS One 2013; 8:e59927. [PMID: 23555835 PMCID: PMC3612082 DOI: 10.1371/journal.pone.0059927] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 02/20/2013] [Indexed: 02/01/2023] Open
Abstract
To characterize high-temperature cellulolytic microbial communities, two lignocellulosic substrates, ammonia fiber-explosion-treated corn stover and aspen shavings, were incubated at average temperatures of 77 and 85°C in the sediment and water column of Great Boiling Spring, Nevada. Comparison of 109,941 quality-filtered 16S rRNA gene pyrosequences (pyrotags) from eight enrichments to 37,057 quality-filtered pyrotags from corresponding natural samples revealed distinct enriched communities dominated by phylotypes related to cellulolytic and hemicellulolytic Thermotoga and Dictyoglomus, cellulolytic and sugar-fermenting Desulfurococcales, and sugar-fermenting and hydrogenotrophic Archaeoglobales. Minor enriched populations included close relatives of hydrogenotrophic Thermodesulfobacteria, the candidate bacterial phylum OP9, and candidate archaeal groups C2 and DHVE3. Enrichment temperature was the major factor influencing community composition, with a negative correlation between temperature and richness, followed by lignocellulosic substrate composition. This study establishes the importance of these groups in the natural degradation of lignocellulose at high temperatures and suggests that a substantial portion of the diversity of thermophiles contributing to consortial cellulolysis may be contained within lineages that have representatives in pure culture.
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Affiliation(s)
- Joseph P Peacock
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America
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Wentzel A, Lewin A, Cervantes FJ, Valla S, Kotlar HK. Deep Subsurface Oil Reservoirs as Poly-extreme Habitats for Microbial Life. A Current Review. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Polyextremophiles and the Constraints for Terrestrial Habitability. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Carere CR, Rydzak T, Verbeke TJ, Cicek N, Levin DB, Sparling R. Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria. BMC Microbiol 2012; 12:295. [PMID: 23249097 PMCID: PMC3561251 DOI: 10.1186/1471-2180-12-295] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/12/2012] [Indexed: 12/16/2022] Open
Abstract
Background Fermentative bacteria offer the potential to convert lignocellulosic waste-streams into biofuels such as hydrogen (H2) and ethanol. Current fermentative H2 and ethanol yields, however, are below theoretical maxima, vary greatly among organisms, and depend on the extent of metabolic pathways utilized. For fermentative H2 and/or ethanol production to become practical, biofuel yields must be increased. We performed a comparative meta-analysis of (i) reported end-product yields, and (ii) genes encoding pyruvate metabolism and end-product synthesis pathways to identify suitable biomarkers for screening a microorganism’s potential of H2 and/or ethanol production, and to identify targets for metabolic engineering to improve biofuel yields. Our interest in H2 and/or ethanol optimization restricted our meta-analysis to organisms with sequenced genomes and limited branched end-product pathways. These included members of the Firmicutes, Euryarchaeota, and Thermotogae. Results Bioinformatic analysis revealed that the absence of genes encoding acetaldehyde dehydrogenase and bifunctional acetaldehyde/alcohol dehydrogenase (AdhE) in Caldicellulosiruptor, Thermococcus, Pyrococcus, and Thermotoga species coincide with high H2 yields and low ethanol production. Organisms containing genes (or activities) for both ethanol and H2 synthesis pathways (i.e. Caldanaerobacter subterraneus subsp. tengcongensis, Ethanoligenens harbinense, and Clostridium species) had relatively uniform mixed product patterns. The absence of hydrogenases in Geobacillus and Bacillus species did not confer high ethanol production, but rather high lactate production. Only Thermoanaerobacter pseudethanolicus produced relatively high ethanol and low H2 yields. This may be attributed to the presence of genes encoding proteins that promote NADH production. Lactate dehydrogenase and pyruvate:formate lyase are not conducive for ethanol and/or H2 production. While the type(s) of encoded hydrogenases appear to have little impact on H2 production in organisms that do not encode ethanol producing pathways, they do influence reduced end-product yields in those that do. Conclusions Here we show that composition of genes encoding pathways involved in pyruvate catabolism and end-product synthesis pathways can be used to approximate potential end-product distribution patterns. We have identified a number of genetic biomarkers for streamlining ethanol and H2 producing capabilities. By linking genome content, reaction thermodynamics, and end-product yields, we offer potential targets for optimization of either ethanol or H2 yields through metabolic engineering.
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Affiliation(s)
- Carlo R Carere
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada R3T 5V6
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Rittmann S, Herwig C. A comprehensive and quantitative review of dark fermentative biohydrogen production. Microb Cell Fact 2012; 11:115. [PMID: 22925149 PMCID: PMC3443015 DOI: 10.1186/1475-2859-11-115] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/03/2012] [Indexed: 01/25/2023] Open
Abstract
Biohydrogen production (BHP) can be achieved by direct or indirect biophotolysis, photo-fermentation and dark fermentation, whereof only the latter does not require the input of light energy. Our motivation to compile this review was to quantify and comprehensively report strains and process performance of dark fermentative BHP. This review summarizes the work done on pure and defined co-culture dark fermentative BHP since the year 1901. Qualitative growth characteristics and quantitative normalized results of H2 production for more than 2000 conditions are presented in a normalized and therefore comparable format to the scientific community.Statistically based evidence shows that thermophilic strains comprise high substrate conversion efficiency, but mesophilic strains achieve high volumetric productivity. Moreover, microbes of Thermoanaerobacterales (Family III) have to be preferred when aiming to achieve high substrate conversion efficiency in comparison to the families Clostridiaceae and Enterobacteriaceae. The limited number of results available on dark fermentative BHP from fed-batch cultivations indicates the yet underestimated potential of this bioprocessing application. A Design of Experiments strategy should be preferred for efficient bioprocess development and optimization of BHP aiming at improving medium, cultivation conditions and revealing inhibitory effects. This will enable comparing and optimizing strains and processes independent of initial conditions and scale.
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Affiliation(s)
- Simon Rittmann
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
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Schut GJ, Boyd ES, Peters JW, Adams MWW. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol Rev 2012; 37:182-203. [PMID: 22713092 DOI: 10.1111/j.1574-6976.2012.00346.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/30/2012] [Accepted: 06/08/2012] [Indexed: 12/01/2022] Open
Abstract
Hydrogen production is a vital metabolic process for many anaerobic organisms, and the enzyme responsible, hydrogenase, has been studied since the 1930s. A novel subfamily with unique properties was recently recognized, represented by the 14-subunit membrane-bound [NiFe] hydrogenase from the archaeon Pyrococcus furiosus. This so-called energy-converting hydrogenase links the thermodynamically favorable oxidation of ferredoxin with the formation of hydrogen and conserves energy in the form of an ion gradient. It is therefore a simple respiratory system within a single complex. This hydrogenase shows a modular composition represented by a Na(+)/H(+) antiporter domain (Mrp) and a [NiFe] hydrogenase domain (Mbh). An analysis of the large number of microbial genome sequences available shows that homologs of Mbh and Mrp tend to be clustered within the genomes of a limited number of archaeal and bacterial species. In several instances, additional genes are associated with the Mbh and Mrp gene clusters that encode proteins that catalyze the oxidation of formate, CO or NAD(P)H. The Mbh complex also shows extensive homology to a number of subunits within the NADH quinone oxidoreductase or complex I family. The respiratory-type membrane-bound hydrogenase complex appears to be closely related to the common ancestor of complex I and [NiFe] hydrogenases in general.
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Affiliation(s)
- Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Nesbø CL, Bradnan DM, Adebusuyi A, Dlutek M, Petrus AK, Foght J, Doolittle WF, Noll KM. Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales. Extremophiles 2012; 16:387-93. [DOI: 10.1007/s00792-012-0437-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/24/2012] [Indexed: 11/29/2022]
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Molecular insights into substrate specificity and thermal stability of a bacterial GH5-CBM27 endo-1,4-β-d-mannanase. J Struct Biol 2012; 177:469-76. [DOI: 10.1016/j.jsb.2011.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 11/04/2011] [Accepted: 11/18/2011] [Indexed: 11/23/2022]
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Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases. Appl Environ Microbiol 2012; 78:1978-86. [PMID: 22247137 DOI: 10.1128/aem.07069-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Four hyperthermophilic members of the bacterial genus Thermotoga (T. maritima, T. neapolitana, T. petrophila, and Thermotoga sp. strain RQ2) share a core genome of 1,470 open reading frames (ORFs), or about 75% of their genomes. Nonetheless, each species exhibited certain distinguishing features during growth on simple and complex carbohydrates that correlated with genomic inventories of specific ABC sugar transporters and glycoside hydrolases. These differences were consistent with transcriptomic analysis based on a multispecies cDNA microarray. Growth on a mixture of six pentoses and hexoses showed no significant utilization of galactose or mannose by any of the four species. T. maritima and T. neapolitana exhibited similar monosaccharide utilization profiles, with a strong preference for glucose and xylose over fructose and arabinose. Thermotoga sp. strain RQ2 also used glucose and xylose, but was the only species to utilize fructose to any extent, consistent with a phosphotransferase system (PTS) specific for this sugar encoded in its genome. T. petrophila used glucose to a significantly lesser extent than the other species. In fact, the XylR regulon was triggered by growth on glucose for T. petrophila, which was attributed to the absence of a glucose transporter (XylE2F2K2), otherwise present in the other Thermotoga species. This suggested that T. petrophila acquires glucose through the XylE1F1K1 transporter, which primarily serves to transport xylose in the other three Thermotoga species. The results here show that subtle differences exist among the hyperthermophilic Thermotogales with respect to carbohydrate utilization, which supports their designation as separate species.
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Han D, Norris SM, Xu Z. Construction and transformation of a Thermotoga-E. coli shuttle vector. BMC Biotechnol 2012; 12:2. [PMID: 22225774 PMCID: PMC3398313 DOI: 10.1186/1472-6750-12-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 01/06/2012] [Indexed: 11/29/2022] Open
Abstract
Background Thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. They may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. A lack of genetic tools has hampered the investigation and application of these organisms. This study aims to develop a genetic transfer system for Thermotoga spp. Results Methods for preparing and handling Thermotoga solid cultures under aerobic conditions were optimized. A plating efficiency of ~50% was achieved when the bacterial cells were embedded in 0.3% Gelrite. A Thermotoga-E. coli shuttle vector pDH10 was constructed using pRQ7, a cryptic mini-plasmid found in T. sp. RQ7. Plasmid pDH10 was introduced to T. maritima and T. sp. RQ7 by electroporation and liposome-mediated transformation. Transformants were isolated, and the transformed kanamycin resistance gene (kan) was detected from the plasmid DNA extracts of the recombinant strains by PCR and was confirmed by restriction digestions. The transformed DNA was stably maintained in both Thermotoga and E. coli even without the selective pressure. Conclusions Thermotoga are transformable by multiple means. Recombinant Thermotoga strains have been isolated for the first time. A heterologous kan gene is functionally expressed and stably maintained in Thermotoga.
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Affiliation(s)
- Dongmei Han
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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Sano S, Yamada Y, Shinkawa T, Kato S, Okada T, Higashibata H, Fujiwara S. Mutations to create thermostable reverse transcriptase with bacterial family A DNA polymerase from Thermotoga petrophila K4. J Biosci Bioeng 2011; 113:315-21. [PMID: 22143068 DOI: 10.1016/j.jbiosc.2011.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 11/28/2022]
Abstract
Family A DNA polymerase (K4PolI) from Thermotoga petrophila K4 was obtained as a recombinant form, and the enzyme characteristics were analyzed. K4PolI showed thermostable DNA-dependent DNA polymerase activity with 3'-5' exonuclease activity but no detectable RNA-dependent DNA polymerase activity. Its tertiary structure was speculated by in silico modeling to understand the binding situation between K4PolI and template DNA. Nine amino acids in the 3'-5' exonuclease domain are predicted to be involved in DNA/RNA distinction by steric interference with the 2' hydroxy group of ribose. To allow K4PolI to accept RNA as the template, mutants were constructed focusing on the amino acids located around the 2' hydroxyl group of the bound ribose. The mutants in which Thr326, Leu329, Gln384, Phe388, Met408, or Tyr438 was replaced with Ala (designated as T326A, L329A, Q384A, F388A, M408A, or Y438A, respectively) showed RNA-dependent DNA polymerase activity. All the mutants showed reduced 3'-5' exonuclease activity, suggesting that gain of reverse transcriptase activity is correlated with loss of 3'-5' exonuclease activity. In particular, the mutants enabled direct DNA amplification in a single tube format from structured RNA that was not efficiently amplified by retroviral reverse transcriptase.
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Affiliation(s)
- Sotaro Sano
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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Struchtemeyer CG, Elshahed MS. Bacterial communities associated with hydraulic fracturing fluids in thermogenic natural gas wells in North Central Texas, USA. FEMS Microbiol Ecol 2011; 81:13-25. [PMID: 22066833 DOI: 10.1111/j.1574-6941.2011.01196.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/11/2011] [Accepted: 08/24/2011] [Indexed: 12/25/2022] Open
Abstract
Hydraulic fracturing is used to increase the permeability of shale gas formations and involves pumping large volumes of fluids into these formations. A portion of the frac fluid remains in the formation after the fracturing process is complete, which could potentially contribute to deleterious microbially induced processes in natural gas wells. Here, we report on the geochemical and microbiological properties of frac and flowback waters from two newly drilled natural gas wells in the Barnett Shale in North Central Texas. Most probable number studies showed that biocide treatments did not kill all the bacteria in the fracturing fluids. Pyrosequencing-based 16S rRNA diversity analyses indicated that the microbial communities in the flowback waters were less diverse and completely distinct from the communities in frac waters. These differences in frac and flowback water communities appeared to reflect changes in the geochemistry of fracturing fluids that occurred during the frac process. The flowback communities also appeared well adapted to survive biocide treatments and the anoxic conditions and high temperatures encountered in the Barnett Shale.
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