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Jay ZJ, Hunt KA, Chou KJ, Schut GJ, Maness PC, Adams MWW, Carlson RP. Integrated thermodynamic analysis of electron bifurcating [FeFe]-hydrogenase to inform anaerobic metabolism and H 2 production. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148087. [PMID: 31669490 DOI: 10.1016/j.bbabio.2019.148087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/14/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022]
Abstract
Electron bifurcating, [FeFe]-hydrogenases are recently described members of the hydrogenase family and catalyze a combination of exergonic and endergonic electron exchanges between three carriers (2 ferredoxinred- + NAD(P)H + 3 H+ = 2 ferredoxinox + NAD(P)+ + 2 H2). A thermodynamic analysis of the bifurcating, [FeFe]-hydrogenase reaction, using electron path-independent variables, quantified potential biological roles of the reaction without requiring enzyme details. The bifurcating [FeFe]-hydrogenase reaction, like all bifurcating reactions, can be written as a sum of two non-bifurcating reactions. Therefore, the thermodynamic properties of the bifurcating reaction can never exceed the properties of the individual, non-bifurcating, reactions. The bifurcating [FeFe]-hydrogenase reaction has three competitive properties: 1) enabling NAD(P)H-driven proton reduction at pH2 higher than the concurrent operation of the two, non-bifurcating reactions, 2) oxidation of NAD(P)H and ferredoxin simultaneously in a 1:1 ratio, both are produced during typical glucose fermentations, and 3) enhanced energy conservation (~10 kJ mol-1 H2) relative to concurrent operation of the two, non-bifurcating reactions. Our analysis demonstrated ferredoxin E°' largely determines the sensitivity of the bifurcating reaction to pH2, modulation of the reduced/oxidized electron carrier ratios contributed less to equilibria shifts. Hydrogenase thermodynamics data were integrated with typical and non-typical glycolysis pathways to evaluate achieving the 'Thauer limit' (4 H2 per glucose) as a function of temperature and pH2. For instance, the bifurcating [FeFe]-hydrogenase reaction permits the Thauer limit at 60 °C if pH 2 ≤ ~10 mbar. The results also predict Archaea, expressing a non-typical glycolysis pathway, would not benefit from a bifurcating [FeFe]-hydrogenase reaction; interestingly, no Archaea have been observed experimentally with a [FeFe]-hydrogenase enzyme.
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Affiliation(s)
- Zackary J Jay
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - Kristopher A Hunt
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
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Kaushal G, Kumar J, Sangwan RS, Singh SP. Metagenomic analysis of geothermal water reservoir sites exploring carbohydrate-related thermozymes. Int J Biol Macromol 2018; 119:882-895. [DOI: 10.1016/j.ijbiomac.2018.07.196] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/17/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
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Jay ZJ, Inskeep WP. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales. Biol Direct 2015; 10:35. [PMID: 26156036 PMCID: PMC4496867 DOI: 10.1186/s13062-015-0065-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022] Open
Abstract
Background Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which “universal” archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Results Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. Conclusions The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different “universal” 16S rRNA primers employed in environmental microbial community analysis. Reviewers This article was reviewed by Dr. Eugene Koonin and Dr. W. Ford Doolittle. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0065-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.
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Ferry JG. Acetate Metabolism in Anaerobes from the Domain Archaea. Life (Basel) 2015; 5:1454-71. [PMID: 26068860 PMCID: PMC4500148 DOI: 10.3390/life5021454] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/01/2015] [Indexed: 01/26/2023] Open
Abstract
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth's biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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5
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Kim KM, Nasir A, Hwang K, Caetano-Anollés G. A tree of cellular life inferred from a genomic census of molecular functions. J Mol Evol 2014; 79:240-62. [PMID: 25128982 DOI: 10.1007/s00239-014-9637-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
Phylogenomics aims to describe evolutionary relatedness between organisms by analyzing genomic data. The common practice is to produce phylogenomic trees from molecular information in the sequence, order, and content of genes in genomes. These phylogenies describe the evolution of life and become valuable tools for taxonomy. The recent availability of structural and functional data for hundreds of genomes now offers the opportunity to study evolution using more deep, conserved, and reliable sets of molecular features. Here, we reconstruct trees of life from the functions of proteins. We start by inferring rooted phylogenomic trees and networks of organisms directly from Gene Ontology annotations. Phylogenies and networks yield novel insights into the emergence and evolution of cellular life. The ancestor of Archaea originated earlier than the ancestors of Bacteria and Eukarya and was thermophilic. In contrast, basal bacterial lineages were non-thermophilic. A close relationship between Plants and Metazoa was also identified that disagrees with the traditional Fungi-Metazoa grouping. While measures of evolutionary reticulation were minimum in Eukarya and maximum in Bacteria, the massive role of horizontal gene transfer in microbes did not materialize in phylogenomic networks. Phylogenies and networks also showed that the best reconstructions were recovered when problematic taxa (i.e., parasitic/symbiotic organisms) and horizontally transferred characters were excluded from analysis. Our results indicate that functionomic data represent a useful addition to the set of molecular characters used for tree reconstruction and that trees of cellular life carry in deep branches considerable predictive power to explain the evolution of living organisms.
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Affiliation(s)
- Kyung Mo Kim
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
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6
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Al Ashhab A, Herzberg M, Gillor O. Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition. WATER RESEARCH 2014; 50:341-349. [PMID: 24231030 DOI: 10.1016/j.watres.2013.10.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 06/02/2023]
Abstract
Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community.
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Affiliation(s)
- Ashraf Al Ashhab
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede-Boqer Campus, 84990, Israel.
| | - Moshe Herzberg
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede-Boqer Campus, 84990, Israel.
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede-Boqer Campus, 84990, Israel.
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Lebedinsky AV, Mardanov AV, Kublanov IV, Gumerov VM, Beletsky AV, Perevalova AA, Bidzhieva SK, Bonch-Osmolovskaya EA, Skryabin KG, Ravin NV. Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function. Extremophiles 2013; 18:295-309. [DOI: 10.1007/s00792-013-0616-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/05/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-let Oktyabrya, 7/2, Moscow, 117312, Russia,
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Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Appl Environ Microbiol 2013; 80:294-305. [PMID: 24162572 DOI: 10.1128/aem.02860-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.
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9
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Mardanov AV, Ravin NV. The impact of genomics on research in diversity and evolution of archaea. BIOCHEMISTRY (MOSCOW) 2013; 77:799-812. [PMID: 22860902 DOI: 10.1134/s0006297912080019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.
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Affiliation(s)
- A V Mardanov
- Laboratory of Molecular Cloning, Centre Bioengineering, Russian Academy of Sciences, pr. 60-let Oktyabrya 7-1, 117312 Moscow, Russia
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10
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Identification of the first archaeal arylsulfatase from Pyrococcus furiosus and its application to desulfatation of agar. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0228-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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An extremely thermostable amylopullulanase from Staphylothermus marinus displays both pullulan- and cyclodextrin-degrading activities. Appl Microbiol Biotechnol 2012; 97:5359-69. [DOI: 10.1007/s00253-012-4397-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/23/2012] [Accepted: 08/27/2012] [Indexed: 11/26/2022]
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12
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Schut GJ, Nixon WJ, Lipscomb GL, Scott RA, Adams MWW. Mutational Analyses of the Enzymes Involved in the Metabolism of Hydrogen by the Hyperthermophilic Archaeon Pyrococcus furiosus. Front Microbiol 2012; 3:163. [PMID: 22557999 PMCID: PMC3341082 DOI: 10.3389/fmicb.2012.00163] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/12/2012] [Indexed: 11/21/2022] Open
Abstract
Pyrococcus furiosus grows optimally near 100°C by fermenting carbohydrates to produce hydrogen (H2) or, if elemental sulfur (S0) is present, hydrogen sulfide instead. It contains two cytoplasmic hydrogenases, SHI and SHII, that use NADP(H) as an electron carrier and a membrane-bound hydrogenase (MBH) that utilizes the redox protein ferredoxin. We previously constructed deletion strains lacking SHI and/or SHII and showed that they exhibited no obvious phenotype. This study has now been extended to include biochemical analyses and growth studies using the ΔSHI and ΔSHII deletion strains together with strains lacking a functional MBH (ΔmbhL). Hydrogenase activity in cytoplasmic extracts of various strains demonstrate that SHI is responsible for most of the cytoplasmic hydrogenase activity. The ΔmbhL strain showed no growth in the absence of S0, confirming the hypothesis that, in the absence of S0, MBH is the only enzyme that can dispose of reductant (in the form of H2) generated during sugar oxidation. Under conditions of limiting sulfur, a small but significant amount of H2 was produced by the ΔmbhL strain, showing that SHI can produce H2 from NADPH in vivo, although this does not enable growth of ΔmbhL in the absence of S0. We propose that the physiological function of SHI is to recycle H2 and provide a link between external H2 and the intracellular pool of NADPH needed for biosynthesis. This likely has a distinct energetic advantage in the environment, but it is clearly not required for growth of the organism under the usual laboratory conditions. The function of SHII, however, remains unknown.
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Affiliation(s)
- Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, GA, USA
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13
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Anderson I, Wirth R, Lucas S, Copeland A, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Davenport K, Detter JC, Han C, Tapia R, Land M, Hauser L, Pati A, Mikhailova N, Woyke T, Klenk HP, Kyrpides N, Ivanova N. Complete genome sequence of Staphylothermus hellenicus P8. Stand Genomic Sci 2011; 5:12-20. [PMID: 22180806 PMCID: PMC3236042 DOI: 10.4056/sigs.2054696] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. Strain P8(T) is the type strain of the species and was isolated from a shallow hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein-coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) Laboratory Sequencing Program (LSP) project.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Reinhard Wirth
- University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Samuel Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Karen Davenport
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Miriam Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hans-Peter Klenk
- DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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Mavromatis K, Sikorski J, Pabst E, Teshima H, Lapidus A, Lucas S, Nolan M, Glavina Del Rio T, Cheng JF, Bruce D, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). Stand Genomic Sci 2010; 3:117-25. [PMID: 21304741 PMCID: PMC3035369 DOI: 10.4056/sigs.1113067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteriaand Archaea project.
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Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Stand Genomic Sci 2010; 3:66-75. [PMID: 21304693 PMCID: PMC3035270 DOI: 10.4056/sigs.1072907] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus Ignisphaera. This archaeal species is characterized by a coccoid-shape and is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral, boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed genome sequence of the genus Ignisphaera and the fifth genome (fourth type strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Molecular signatures for the Crenarchaeota and the Thaumarchaeota. Antonie van Leeuwenhoek 2010; 99:133-57. [PMID: 20711675 DOI: 10.1007/s10482-010-9488-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 07/26/2010] [Indexed: 10/19/2022]
Abstract
Crenarchaeotes found in mesophilic marine environments were recently placed into a new phylum of Archaea called the Thaumarchaeota. However, very few molecular characteristics of this new phylum are currently known which can be used to distinguish them from the Crenarchaeota. In addition, their relationships to deep-branching archaeal lineages are unclear. We report here detailed analyses of protein sequences from Crenarchaeota and Thaumarchaeota that have identified many conserved signature indels (CSIs) and signature proteins (SPs) (i.e., proteins for which all significant blast hits are from these groups) that are specific for these archaeal groups. Of the identified signatures 6 CSIs and 13 SPs are specific for the Crenarchaeota phylum; 6 CSIs and >250 SPs are uniquely found in various Thaumarchaeota (viz. Cenarchaeum symbiosum, Nitrosopumilus maritimus and a number of uncultured marine crenarchaeotes) and 3 CSIs and ~10 SPs are found in both Thaumarchaeota and Crenarchaeota species. Some of the molecular signatures are also present in Korarchaeum cryptofilum, which forms the independent phylum Korarchaeota. Although some of these molecular signatures suggest a distant shared ancestry between Thaumarchaeota and Crenarchaeota, our identification of large numbers of Thaumarchaeota-specific proteins and their deep branching between the Crenarchaeota and Euryarchaeota phyla in phylogenetic trees shows that they are distinct from both Crenarchaeota and Euryarchaeota in both genetic and phylogenetic terms. These observations support the placement of marine mesophilic archaea into the separate phylum Thaumarchaeota. Additionally, many CSIs and SPs have been found that are specific for different orders within Crenarchaeota (viz. Sulfolobales-3 CSIs and 169 SPs, Thermoproteales-5 CSIs and 25 SPs, Desulfurococcales-4 SPs, and Sulfolobales and Desulfurococcales-2 CSIs and 18 SPs). The signatures described here provide novel means for distinguishing the Crenarchaeota and the Thaumarchaeota and for the classification of related and novel species in different environments. Functional studies on these signature proteins could lead to discovery of novel biochemical properties that are unique to these groups of archaea.
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The genome sequence of the crenarchaeon Acidilobus saccharovorans supports a new order, Acidilobales, and suggests an important ecological role in terrestrial acidic hot springs. Appl Environ Microbiol 2010; 76:5652-7. [PMID: 20581186 DOI: 10.1128/aem.00599-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acidilobus saccharovorans is an anaerobic, organotrophic, thermoacidophilic crenarchaeon isolated from a terrestrial hot spring. We report the complete genome sequence of A. saccharovorans, which has permitted the prediction of genes for Embden-Meyerhof and Entner-Doudoroff pathways and genes associated with the oxidative tricarboxylic acid cycle. The electron transfer chain is branched with two sites of proton translocation and is linked to the reduction of elemental sulfur and thiosulfate. The genomic data suggest an important role of the order Acidilobales in thermoacidophilic ecosystems whereby its members can perform a complete oxidation of organic substrates, closing the anaerobic carbon cycle.
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Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Brettin T, Detter JC, Tapia R, Han C, Heimerl T, Weikl F, Brambilla E, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Stand Genomic Sci 2010; 2:245-59. [PMID: 21304709 PMCID: PMC3035292 DOI: 10.4056/sigs.821804] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera, which comprises at the time of writing only one species. This species represents archaea with a hyperthermophilic, heterotrophic, strictly anaerobic and fermentative phenotype. The type strain M11TL(T) was isolated from a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone National Park, Wyoming). Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,316,595 bp long single replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings RD, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS One 2010; 5:e9773. [PMID: 20333304 PMCID: PMC2841643 DOI: 10.1371/journal.pone.0009773] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 02/25/2010] [Indexed: 01/07/2023] Open
Abstract
The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs.
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Affiliation(s)
- William P. Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (DBR)
| | - Douglas B. Rusch
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail: (WPI); (DBR)
| | - Zackary J. Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Mark A. Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Richard E. Macur
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Natsuko Hamamura
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Ryan deM. Jennings
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Bruce W. Fouke
- University of Illinois, Urbana, Illinois, United States of America
| | | | - Frank Roberto
- Idaho National Laboratory, Idaho Falls, Idaho, United States of America
| | - Mark Young
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Ariel Schwartz
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Eric S. Boyd
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Eric J. Mathur
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Alice C. Ortmann
- Department of Marine Science, University of South Alabama, Mobile, Alabama, United States of America
| | - Mary Bateson
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Gill Geesey
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Marvin Frazier
- J. Craig Venter Institute, Rockville, Maryland, United States of America
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Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota. Microbiology (Reading) 2010; 156:256-269. [DOI: 10.1099/mic.0.034298-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Two new autotrophic carbon fixation cycles have been recently described in Crenarchaeota. The 3-hydroxypropionate/4-hydroxybutyrate cycle using acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme has been identified for (micro)aerobic members of the Sulfolobales. The dicarboxylate/4-hydroxybutyrate cycle using oxygen-sensitive pyruvate synthase and phosphoenolpyruvate carboxylase as carboxylating enzymes has been found in members of the anaerobic Desulfurococcales and Thermoproteales. However, Sulfolobales include anaerobic and Desulfurococcales aerobic autotrophic representatives, raising the question of which of the two cycles they use. We studied the mechanisms of autotrophic CO2 fixation in the strictly anaerobic Stygiolobus azoricus (Sulfolobales) and in the facultatively aerobic Pyrolobus fumarii (Desulfurococcales). The activities of all enzymes of the 3-hydroxypropionate/4-hydroxybutyrate cycle were found in the anaerobic S. azoricus. In contrast, the aerobic or denitrifying P. fumarii possesses all enzyme activities of the dicarboxylate/4-hydroxybutyrate cycle. We conclude that autotrophic Crenarchaeota use one of the two cycles, and that their distribution correlates with the 16S rRNA-based phylogeny of this group, rather than with the aerobic or anaerobic lifestyle.
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Ulrich LE, Zhulin IB. The MiST2 database: a comprehensive genomics resource on microbial signal transduction. Nucleic Acids Res 2009; 38:D401-7. [PMID: 19900966 PMCID: PMC2808908 DOI: 10.1093/nar/gkp940] [Citation(s) in RCA: 214] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. Signal transduction systems regulate the majority of cellular activities including the metabolism, development, host-recognition, biofilm production, virulence, and antibiotic resistance of human pathogens. Thus, knowledge of the proteins and interactions that comprise these communication networks is an essential component to furthering biomedical discovery. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface. MiST2 currently contains 966 complete and 157 draft bacterial and archaeal genomes, which collectively contain more than 245 000 signal transduction proteins. The majority (66%) of these are one-component systems, followed by two-component proteins (26%), chemotaxis (6%), and finally ECF factors (2%).
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Anderson IJ, Sun H, Lapidus A, Copeland A, Glavina Del Rio T, Tice H, Dalin E, Lucas S, Barry K, Land M, Richardson P, Huber H, Kyrpides NC. Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1. Stand Genomic Sci 2009; 1:183-8. [PMID: 21304655 PMCID: PMC3035234 DOI: 10.4056/sigs.30527] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinus strain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.
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Yokobori SI, Itoh T, Yoshinari S, Nomura N, Sako Y, Yamagishi A, Oshima T, Kita K, Watanabe YI. Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene. BMC Evol Biol 2009; 9:198. [PMID: 19671140 PMCID: PMC2738675 DOI: 10.1186/1471-2148-9-198] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 08/11/2009] [Indexed: 01/13/2023] Open
Abstract
Background We previously found the first examples of splicing of archaeal pre-mRNAs for homologs of the eukaryotic CBF5 protein (also known as dyskerin in humans) in Aeropyrum pernix, Sulfolobus solfataricus, S. tokodaii, and S. acidocaldarirus, and also showed that crenarchaeal species in orders Desulfurococcales and Sulfolobales, except for Hyperthermus butylicus, Pyrodictium occultum, Pyrolobus fumarii, and Ignicoccus islandicus, contain the (putative) cbf5 intron. However, the exact timing of the intron insertion was not determined and verification of the putative secondary loss of the intron in some lineages was not performed. Results In the present study, we determined approximately two-thirds of the entire coding region of crenarchaeal Cbf5 sequences from 43 species. A phylogenetic analysis of our data and information from the available genome sequences suggested that the (putative) cbf5 intron existed in the common ancestor of the orders Desulfurococcales and Sulfolobales and that probably at least two independent lineages in the order Desulfurococcales lost the (putative) intron. Conclusion This finding is the first observation of a lineage-specific loss of a pre-mRNA intron in Archaea. As the insertion or deletion of introns in protein-coding genes in Archaea has not yet been seriously considered, our finding suggests the possible difficulty of accurately and completely predicting protein-coding genes in Archaea.
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Affiliation(s)
- Shin-ichi Yokobori
- Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. ACTA ACUST UNITED AC 2009; 25:2271-8. [PMID: 19561336 DOI: 10.1093/bioinformatics/btp393] [Citation(s) in RCA: 726] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
MOTIVATION A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. RESULTS We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.
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Affiliation(s)
- Victor M Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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