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The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.

ABSTRACT: Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.

SUBMITTER: Scott KM

PROVIDER: S-EPMC1635747 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature

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The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.

Scott Kathleen M KM Sievert Stefan M SM Abril Fereniki N FN Ball Lois A LA Barrett Chantell J CJ Blake Rodrigo A RA Boller Amanda J AJ Chain Patrick S G PS Clark Justine A JA Davis Carisa R CR Detter Chris C Do Kimberly F KF Dobrinski Kimberly P KP Faza Brandon I BI Fitzpatrick Kelly A KA Freyermuth Sharyn K SK Harmer Tara L TL Hauser Loren J LJ Hügler Michael M Kerfeld Cheryl A CA Klotz Martin G MG Kong William W WW Land Miriam M Lapidus Alla A Larimer Frank W FW Longo Dana L DL Lucas Susan S Malfatti Stephanie A SA Massey Steven E SE Martin Darlene D DD McCuddin Zoe Z Meyer Folker F Moore Jessica L JL Ocampo Luis H LH Paul John H JH Paulsen Ian T IT Reep Douglas K DK Ren Qinghu Q Ross Rachel L RL Sato Priscila Y PY Thomas Phaedra P Tinkham Lance E LE Zeruth Gary T GT

PLoS biology 20061101 12

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A ...[more]

PMID: 17105352

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Project description:Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO2 + HCO3- + CO32-) with CO2 concentrating mechanisms (CCM) that actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has been well studied among cyanobacteria and microalgae only. The deep-sea vent gammaproteobacterial chemolithoautotroph Thiomicrospira crunogena has a low-DIC inducible CCM, though the mechanism for uptake is unclear, as homologs to cyanobacterial transporters are absent. To identify the components of this CCM, proteomes of T. crunogena cultivated under low- and high-DIC conditions were compared. Fourteen proteins, including those comprising carboxysomes, were at least 4-fold more abundant under low-DIC conditions. One of these proteins was encoded by Tcr_0854; strains carrying mutated copies of this gene, as well as the adjacent Tcr_0853, required elevated DIC for growth. Strains carrying mutated copies of Tcr_0853 and Tcr_0854 overexpressed carboxysomes and had diminished ability to accumulate intracellular DIC. Based on reverse transcription (RT)-PCR, Tcr_0853 and Tcr_0854 were cotranscribed and upregulated under low-DIC conditions. The Tcr_0853-encoded protein was predicted to have 13 transmembrane helices. Given the mutant phenotypes described above, Tcr_0853 and Tcr_0854 may encode a two-subunit DIC transporter that belongs to a previously undescribed transporter family, though it is widespread among autotrophs from multiple phyla.IMPORTANCE DIC uptake and fixation by autotrophs are the primary input of inorganic carbon into the biosphere. The mechanism for dissolved inorganic carbon uptake has been characterized only for cyanobacteria despite the importance of DIC uptake by autotrophic microorganisms from many phyla among the Bacteria and Archaea In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotroph T. crunogena were identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla in Bacteria and also in one phylum of Archaea, the Euryarchaeota Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genus Thiomicrospira.

Dataset Information

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.

Publications

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.

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