PXD040929

PXD040929 is an original dataset announced via ProteomeXchange.

Title	Iron and thiosulfate respiration in a natronophile Dethiobacter alkaliphilus
Description	Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, representing geologically ancient ecosystems which are still widespread on Earth and supposedly harbor relict microbial communities. We compared metabolic features and their genomic determinants in two strains of a single natronophilic species Dethiobacter alkaliphilus, the only cultured representative of “Dethiobacteria” class within Bacillota phylum. The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultatively chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered iron reducing ability of strain AHT1T, as well as the capability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This assumption was supported by meta-analysis of publicly available Dethiobacterial metagenomes, as well as by the enrichment of a novel phylotype from a deep subsurface non-serpentinizing slightly alkaline water after its amendment with an Fe(III) mineral. Genome analysis of D. alkaliphilus strains revealed that the most probable determinants of iron and sulfur redox transformations in the organism are multiheme c-type cytochromes. Their phylogeny reconstruction showed that sulfur and thiosulfate respiration is most probably provided by evolutionary early forms of unconventional octaheme tetrathionate and sulfite reductases sharing a root with structurally similar group of OmhA/OcwA Fe(III)-reductases. Large sets of other multihemes are likely to provide Fe(III) reduction in both strains. Also, several different, yet phylogenetically related, determinants of anaerobic Fe(II) oxidation were identified in Z-1002 genome, and the oxidation process was further experimentally proven. Considering these results and phylogenetic relatedness of D. alkaliphilus’s sulfur reductases with Fe(III) reducing cytochromes, but not with archetypal bacterial sulfur/thiosulfate reductases, we suggest that sustaining high variation of multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline anaerobic environments. We further propose that sulfur-enriched soda lakes are secondary habitats for D. alkaliphilus comparing to Fe-rich serpentinites, and discuss the evolutionary traits which might occur in prokaryotes on a crucial junction of the biosphere’s history, when intensification of the sulfur cycle outweighed the global significance of the iron cycle.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:08:29.514.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rustam Ziganshin
SpeciesList	scientific name: Dethiobacter alkaliphilus AHT 1; NCBI TaxID: 555088;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-17 01:57:45	ID requested
1	2023-10-24 12:10:14	announced
⏵ 2	2023-11-14 09:08:30	announced	2023-11-14: Updated project metadata.

Zavarzina DG, Merkel AY, Klyukina AA, Elizarov IM, Pikhtereva VA, Rusakov VS, Chistyakova NI, Ziganshin RH, Maslov AA, Gavrilov SN, in geochemically contrasting environments. Front Microbiol, 14():1108245(2023) [pubmed]

submitter keyword: LC-MSMS,Dethiobacter alkaliphilus, proteome

Sergey Gavrilov
contact affiliation	Extremophiles metabolism laboratory, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Russia
contact email	sngavrilov@gmail.com
lab head
Rustam Ziganshin
contact affiliation	Shemyakin-Ovchinnikov Institute of bioorganic chemistry Russian Academy of Sciences
contact email	rustam.ziganshin@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040929
     1. Label: PRIDE project
     2. Name: Iron and thiosulfate respiration in a natronophile Dethiobacter alkaliphilus