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Title: Proteomic and Mutant Analysis of the CO 2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena

Abstract

Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO 2+ HCO 3 -+ CO 3 2-) with CO 2 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 chemolithoautotrophThiomicrospira crunogenahas 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 ofT. crunogenacultivated 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 byTcr_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,more » though it is widespread among autotrophs from multiple phyla.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 theBacteriaandArchaea. In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotrophT. crunogenawere identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla inBacteriaand also in one phylum ofArchaea, theEuryarchaeota. Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genusThiomicrospira.« less

Authors:
 [1];  [1];  [2];  [1];  [3];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1];  [4];  [1]
  1. Univ. of South Florida, Tampa, FL (United States). Dept. of Integrative Biology
  2. Univ. of South Florida, Tampa, FL (United States). Dept. of Cell Biology, Microbiology, and Molecular Biology
  3. Richard Stockton College of New Jersey, Pomona, NJ (United States). Biology Program
  4. Univ. of Tennessee, Knoxville, TN (United States). Genome Science and Technology ; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
USF MCB4404L
OSTI Identifier:
1407731
Grant/Contract Number:
AC05-00OR22725; NSF-MCB-0643713; NSF-IOS-1257532
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Bacteriology
Additional Journal Information:
Journal Volume: 199; Journal Issue: 7; Journal ID: ISSN 0021-9193
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; autotroph; bicarbonate transporter; carbon concentrating mechanism; carbon fixation; chemolithoautotroph; hydrothermal vent

Citation Formats

Mangiapia, Mary, Brown, Terry-René W., Chaput, Dale, Haller, Edward, Harmer, Tara L., Hashemy, Zahra, Keeley, Ryan, Leonard, Juliana, Mancera, Paola, Nicholson, David, Stevens, Stanley, Wanjugi, Pauline, Zabinski, Tania, Pan, Chongle, and Scott, Kathleen M.. Proteomic and Mutant Analysis of the CO2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena. United States: N. p., 2017. Web. doi:10.1128/JB.00871-16.
Mangiapia, Mary, Brown, Terry-René W., Chaput, Dale, Haller, Edward, Harmer, Tara L., Hashemy, Zahra, Keeley, Ryan, Leonard, Juliana, Mancera, Paola, Nicholson, David, Stevens, Stanley, Wanjugi, Pauline, Zabinski, Tania, Pan, Chongle, & Scott, Kathleen M.. Proteomic and Mutant Analysis of the CO2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena. United States. doi:10.1128/JB.00871-16.
Mangiapia, Mary, Brown, Terry-René W., Chaput, Dale, Haller, Edward, Harmer, Tara L., Hashemy, Zahra, Keeley, Ryan, Leonard, Juliana, Mancera, Paola, Nicholson, David, Stevens, Stanley, Wanjugi, Pauline, Zabinski, Tania, Pan, Chongle, and Scott, Kathleen M.. Mon . "Proteomic and Mutant Analysis of the CO2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena". United States. doi:10.1128/JB.00871-16. https://www.osti.gov/servlets/purl/1407731.
@article{osti_1407731,
title = {Proteomic and Mutant Analysis of the CO2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena},
author = {Mangiapia, Mary and Brown, Terry-René W. and Chaput, Dale and Haller, Edward and Harmer, Tara L. and Hashemy, Zahra and Keeley, Ryan and Leonard, Juliana and Mancera, Paola and Nicholson, David and Stevens, Stanley and Wanjugi, Pauline and Zabinski, Tania and Pan, Chongle and Scott, Kathleen M.},
abstractNote = {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 chemolithoautotrophThiomicrospira crunogenahas 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 ofT. crunogenacultivated 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 byTcr_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.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 theBacteriaandArchaea. In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotrophT. crunogenawere identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla inBacteriaand also in one phylum ofArchaea, theEuryarchaeota. Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genusThiomicrospira.},
doi = {10.1128/JB.00871-16},
journal = {Journal of Bacteriology},
number = 7,
volume = 199,
place = {United States},
year = {Mon Jan 23 00:00:00 EST 2017},
month = {Mon Jan 23 00:00:00 EST 2017}
}

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  • 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 bp), 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 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 amore » variety of options for acquiring these substrates from the environment. T. crunogena XCL-2 is unusual among obligate sulfur oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. A 38 kb prophage is present, and a high level of prophage induction was observed, which may play a role in keeping competing populations of close relatives in check. 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.« less
  • A Chlamydomonas reinhardtii mutant has been isolated that cannot grow photoautotrophically on low CO{sub 2} concentrations but can grow on elevated CO{sub 2}. In a test cross, the high CO{sub 2}-requirement for growth showed a 2:2 segregation. This mutant, designated CIA-5, had a phenotype similar to previously identified mutants that were defective in some aspect of CO{sub 2} accumulation. Unlike previously isolated mutants, CIA-5 did not have detectable levels of the periplasmic carbonic anhydrase, an inducible protein that participates in the acquisition of CO{sub 2} by C. reinhardtii. CIA-5 also did not accumulate inorganic carbon to levels higher than couldmore » be accounted for by diffusion. This mutant strain did not synthesize any of the four polypeptides preferentially made by wild type C. reinhardtii when switched from an environment containing elevated CO{sub 2} levels to an environment low in CO{sub 2}. It is concluded that this mutant fails to induce the CO{sub 2} concentrating system and is incapable of adapting to low CO{sub 2} conditions.« less
  • Cited by 44
  • The novel thermophilic CO- and H{sub 2}-oxidizing bacterium UBT1 has been isolated from the covering soil of a burning charcoal pile. The isolate is gram positive and obligately chemolithoautotrophic and has been named Streptomyces thermoautotrophicus on the basis of G+C content (70.6 {plus minus} 0.19 mol%), a phospholipid pattern of type II, MK-9(H{sub 4}) as the major quinone, and other chemotaxonomic and morphological properties. S. thermoautotrophicus could grown with CO, H{sub 2} plus CO{sub 2}, car exhaust, or gas produced by the incomplete combustion of wood. Molybdenum was required for CO-autotrophic growth. For growth with H{sub 2}, nickel was notmore » necessary. The optimum growth temperature was 65{degree}C; no growth was observed below 40{degree}C. However, CO-grown cells were able to oxidize CO at temperatures of 10 to 70{degree}C. Temperature profiles of burning charcoal piles revealed that, up to a depth of about 10 to 25 cm, the entire covering soil provides a suitable habitat for S. thermoautotrophicus.« less