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Identification and Enzymatic Analysis of an Archaeal ATP-Dependent Serine Kinase from the Hyperthermophilic Archaeon Staphylothermus marinus. J Bacteriol 2021; 203:e0002521. [PMID: 34096778 DOI: 10.1128/jb.00025-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Serine kinase catalyzes the phosphorylation of free serine (Ser) to produce O-phosphoserine (Sep). An ADP-dependent Ser kinase in the hyperthermophilic archaeon Thermococcus kodakarensis (Tk-SerK) is involved in cysteine (Cys) biosynthesis and most likely Ser assimilation. An ATP-dependent Ser kinase in the mesophilic bacterium Staphylococcus aureus is involved in siderophore biosynthesis. Although proteins displaying various degrees of similarity with Tk-SerK are distributed in a wide range of organisms, it is unclear if they are actually Ser kinases. Here, we examined proteins from Desulfurococcales species in Crenarchaeota that display moderate similarity with Tk-SerK from Euryarchaeota (42 to 45% identical). Tk-serK homologs from Staphylothermus marinus (Smar_0555), Desulfurococcus amylolyticus (DKAM_0858), and Desulfurococcus mucosus (Desmu_0904) were expressed in Escherichia coli. All three partially purified recombinant proteins exhibited Ser kinase activity utilizing ATP rather than ADP as a phosphate donor. Purified Smar_0555 protein displayed activity for l-Ser but not other compounds, including d-Ser, l-threonine, and l-homoserine. The enzyme utilized ATP, UTP, GTP, CTP, and the inorganic polyphosphates triphosphate and tetraphosphate as phosphate donors. Kinetic analysis indicated that the Smar_0555 protein preferred nucleoside 5'-triphosphates over triphosphate as a phosphate donor. Transcript levels and Ser kinase activity in S. marinus cells grown with or without serine suggested that the Smar_0555 gene is constitutively expressed. The genes encoding Ser kinases examined here form an operon with genes most likely responsible for the conversion between Sep and 3-phosphoglycerate of central sugar metabolism, suggesting that the ATP-dependent Ser kinases from Desulfurococcales play a role in the assimilation of Ser. IMPORTANCE Homologs of the ADP-dependent Ser kinase from the archaeon Thermococcus kodakarensis (Tk-SerK) include representatives from all three domains of life. The results of this study show that even homologs from the archaeal order Desulfurococcales, which are the most structurally related to the ADP-dependent Ser kinases from the Thermococcales, are Ser kinases that utilize ATP, and in at least some cases inorganic polyphosphates, as the phosphate donor. The differences in properties between the Desulfurococcales and Thermococcales enzymes raise the possibility that Tk-SerK homologs constitute a group of kinases that phosphorylate free serine with a wide range of phosphate donors.
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Lindsay MR, Amenabar MJ, Fecteau KM, Debes RV, Fernandes Martins MC, Fristad KE, Xu H, Hoehler TM, Shock EL, Boyd ES. Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs. GEOBIOLOGY 2018; 16:674-692. [PMID: 30035368 DOI: 10.1111/gbi.12308] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/15/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
The geochemistry of hot springs and the availability of oxidants capable of supporting microbial metabolisms are influenced by subsurface processes including the separation of hydrothermal fluids into vapor and liquid phases. Here, we characterized the influence of geochemical variation and oxidant availability on the abundance, composition, and activity of hydrogen (H2 )-dependent chemoautotrophs along the outflow channels of two-paired hot springs in Yellowstone National Park. The hydrothermal fluid at Roadside East (RSE; 82.4°C, pH 3.0) is acidic due to vapor-phase input while the fluid at Roadside West (RSW; 68.1°C, pH 7.0) is circumneutral due to liquid-phase input. Most chemotrophic communities exhibited net rates of H2 oxidation, consistent with H2 support of primary productivity, with one chemotrophic community exhibiting a net rate of H2 production. Abundant H2 -oxidizing chemoautotrophs were supported by reduction in oxygen, elemental sulfur, sulfate, and nitrate in RSW and oxygen and ferric iron in RSE; O2 utilizing hydrogenotrophs increased in abundance down both outflow channels. Sequencing of 16S rRNA transcripts or genes from native sediments and dilution series incubations, respectively, suggests that members of the archaeal orders Sulfolobales, Desulfurococcales, and Thermoproteales are likely responsible for H2 oxidation in RSE, whereas members of the bacterial order Thermoflexales and the archaeal order Thermoproteales are likely responsible for H2 oxidation in RSW. These observations suggest that subsurface processes strongly influence spring chemistry and oxidant availability, which in turn select for unique assemblages of H2 oxidizing microorganisms. Therefore, these data point to the role of oxidant availability in shaping the ecology and evolution of hydrogenotrophic organisms.
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Affiliation(s)
- Melody R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana
| | | | - Kristopher M Fecteau
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona
| | - Randal V Debes
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona
| | | | | | - Huifang Xu
- Department of Geosciences, University of Wisconsin, Madison, Wisconsin
- NASA Astrobiology Institute, Mountain View, California
| | - Tori M Hoehler
- NASA Ames Research Center, Moffett Field, California
- NASA Astrobiology Institute, Mountain View, California
| | - Everett L Shock
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona
- NASA Astrobiology Institute, Mountain View, California
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana
- NASA Astrobiology Institute, Mountain View, California
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Yu Z, Ma Y, Zhong W, Qiu J, Li J. Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles. Front Microbiol 2017; 8:1278. [PMID: 28744269 PMCID: PMC5504354 DOI: 10.3389/fmicb.2017.01278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 12/22/2022] Open
Abstract
Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.
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Affiliation(s)
- Zhiliang Yu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Yunting Ma
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Weihong Zhong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Juanping Qiu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Jun Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong UniversityShanghai, China
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Karaevskaya ES, Demchenko LS, Demidov NE, Rivkina EM, Bulat SA, Gilichinsky DA. Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714040092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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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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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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Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ioanna P, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bilek Y, Hader T, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Stand Genomic Sci 2011; 4:173-82. [PMID: 21677854 PMCID: PMC3111991 DOI: 10.4056/sigs.1644004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Desulfurococcus mucosus Zillig and Stetter 1983 is the type species of the genus Desulfurococcus, which belongs to the crenarchaeal family Desulfurococcaceae. The species is of interest because of its position in the tree of life, its ability for sulfur respiration, and several biotechnologically relevant thermostable and thermoactive extracellular enzymes. This is the third completed genome sequence of a member of the genus Desulfurococcus and already the 8(th) sequence from a member the family Desulfurococcaceae. The 1,314,639 bp long genome with its 1,371 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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