Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of sulfur-respiring haloarchaea from hypersaline lakes

ABSTRACT: Dimitry Y. Sorokin et al., (2021, Russian Academy of Sciences, Russia and Delft University of Technology, The Netherlands) describe the isolation and physiological and genomic properties of a fifth functional group of sulfur-respiring haloarchaea enriched from hypersaline lake sediments with CO as the electron donor. Additional shotgun proteomic profiling of the described strains has been performed.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Archaea

SUBMITTER: Martin Pabst

LAB HEAD: Martin Pabst

PROVIDER: PXD028241 | Pride | 2022-12-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AArc_CO_merged_CooC.fasta	Fasta
	CT_19032021_Dmitrii_HCO2_3_ye_CO_DDA01.mzXML	Mzxml
	CT_19032021_Dmitrii_HCO2_3_ye_CO_DDA01.raw	Raw
	HSR_CO_merged.fasta	Fasta
	MP_CT16122019_Dmitri_3_AArC_CO_DDA01.mzXML	Mzxml

Items per page:

1 - 5 of 15

Similar Datasets

Xylan utilization by haloarchaea-nanohaloarchaea associations

Project description:In hypersaline brines, biodegradation of recalcitrant plant polymers can be inhibited by salt-induced microbial stress and/or caused by inadequate metabolic capabilities of extremely halophilic microbes. Therefore, woody materials can be well-preserved even in NaCl brines that are less biologically hostile than most other brines. Here, we considered whether the nanohaloarchaea, that live alongside (the related) haloarchaea, ever partake in the degradation of xylan, a major hemicellulose component of wood. Samples were taken from natural evaporitic brines and anthropogenic solar salterns located in various parts of Europe and Asia. We recently demonstrated that nanohaloarchaeon Ca. Nanohalobium constans lives as an ectosymbiont associated with the chitinolytic haloarchaeon Halomicrobium. Here, we describe an extremely halophilic xylan-degrading consortium with three members, where nanohaloarchaea act as ectosymbionts of Haloferax lucertensis, which in turn acts as a scavenger of xylan-degradation products, produced by a primary xylan hydrolytic Halorhabdus species. The two corresponding binary associations of nanohaloarchaea, Candidatus Nanohalococcus occultus SVXNc and Candidatus Nanohalovita haloferacivicina BNXNv and their hosts were obtained, stably cultivated and characterized. In contrast to the previously described association of chitinolytic haloarchaeon Halomicrobium and its amylolytic symbiont Ca. Nanohalobium, the host haloarchaea within the xylan-degrading consortium could metabolize α-glucans (glycogen and starch), and, thus, obtained no obvious trophic benefit from ectosymbionts. The current study has broadened the range of culturable ectosymbiontic nanohaloarchaea and demonstrates that they are an important ecophysiological component of polysaccharide-degrading halophilic microbial communities and can be readily isolated in binary co-cultures by using the appropriate enrichment strategy.

2023-10-24 | PXD036877 | Pride

Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes.

Project description:Anaerobic carboxydotrophy is a widespread catabolic trait in bacteria, with two dominant pathways: hydrogenogenic and acetogenic. The marginal mode by direct oxidation to CO2 using an external e-acceptor has only a few examples. Use of sulfidic sediments from two types of hypersaline lakes in anaerobic enrichments with CO as an e-donor and elemental sulfur as an e-acceptor led to isolation of two pure cultures of anaerobic carboxydotrophs belonging to two genera of sulfur-reducing haloarchaea: Halanaeroarchaeum sp. HSR-CO from salt lakes and Halalkaliarchaeum sp. AArc-CO from soda lakes. Anaerobic growth of extremely halophilic archaea with CO was obligatory depended on the presence of elemental sulfur as the electron acceptor and yeast extract as the carbon source. CO served as a direct electron donor and H2 was not generated from CO when cells were incubated with or without sulfur. The genomes of the isolates encode a catalytic Ni,Fe-CODH subunit CooS (distantly related to bacterial homologs) and its Ni-incorporating chaperone CooC (related to methanogenic homologs) within a single genomic locus. Similar loci were also present in a genome of the type species of Halalkaliarchaeum closely related to AArc-CO, and the ability for anaerobic sulfur-dependent carboxydotrophy was confirmed for three different strains of this genus. Moreover, similar proteins are encoded in three of the four genomes of recently described carbohydrate-utilizing sulfur-reducing haloarchaea belonging to the genus Halapricum and in two yet undescribed haloarchaeal species. Overall, this work demonstrated for the first time the potential for anaerobic sulfur-dependent carboxydotrophy in extremely halophilic archaea.

| S-EPMC9123189 | biostudies-literature

Human peripheral blood mononuclear cells stimulated in vitro by BCG strains or PPD

Project description:This experiment explored the transcriptional response of human peripheral blood mononuclear cells (PBMC) isolated from BCG-vaccinated individuals following 6 days of in vitro stimulation with 2x10^5 cfu of different Bacillus Calmette-Guérin (BCG) strains or 100 ng/ml Mycobacterium tuberculosis-derived purified protein derivative (PPD). The BCG strains used were BCG Russia (Russian BCG-I sub-strain), BCG Japan (Tokyo 172 sub-strain), BCG Denmark (Danish 1331 sub-strain) & BCG Pasteur.

2022-01-26 | E-MTAB-11345 | biostudies-arrayexpress

Molecular study on Haloarchaea

Project description:Molecular study on haloarchaea producing industerially important enzymes

| PRJEB18746 | ENA

ustuyzhna

Project description:Genotypes of Russian people from Ustuyzhna (Vologda Oblast, Russia)

| EGAD00010001775 | EGA

Community of haloarchaea, enriched at low temperature

Project description:Community of haloarchaea, enriched at low temperature

| PRJEB15147 | ENA

Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis

Project description:Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin transcriptional activators, proteins harbouring a domain of unknown function (DUF2249), and a cyanoglobin. Additionally, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.

2024-04-22 | GSE245042 | GEO

Molecular study on Haloarchaea metagenomic assembly

Project description:EMG produced TPA metagenomics assembly of the Molecular study on haloarchaea producing industerially important enzymes (Molecular study on Haloarchaea) data set

| PRJEB22526 | ENA

Metaproteome, Deep Lake, Antarctica

Project description:Deep Lake is a hypersaline system in Antarctica (68°33’36.8S, 78°11’48.7E) that is so saline it remains liquid at –20°C (DeMaere et al 2013). The lake is dominated by haloarchaea, comprising a low-complexity community that differs greatly to warm-hot latitude hypersaline systems, is hierarchical structured, and supports a high level of intergenera gene exchange. Metaproteomics was performed on biomass that was collected in the austral summer of 2008 by sequential size fractionation (20 – 3 µm, 3 – 0.8 µm, 0.8 – 0.1 µm). The data were integrated to obtain a systems level view of the active host-virus interactions occurring in this novel aquatic Antarctic system. DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JA, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe SG, Cavicchioli R (2013) High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110: 16939-16944

2015-07-21 | PXD001436 | Pride

Quantitative proteomics of cold adaptation of the Antarctic archaeon Halohasta litchfieldiae and Halorubrum lacusprofundi

Project description:Halohasta litchfieldiae and Halorubrum lacusprofundi are important members of Deep Lake in Antarctica, representing ~44% (the most abundance) and ~10% (the 3rd most abundance) of the lake population. Deep Lake is in the Vestfold Hills, East Antarctica (68°33’36.8S, 78°11’48.7E) and is 36 m deep, monomictic, and perennially cold (down to -20C) (DeMaere et al., 2013; Williams et al., 2014; Tschitschko et al., 2015; Tschitschko et al., 2016). In this project, using quantitative proteomics (8-plex iTRAQ labeling), proteins, pathways and cellular processes important for cold adaptation were determined for both Hht. litchfieldiae and Hrr. lacusprofundi. The data provided a new level of understanding about molecular mechanisms and regulatory networks involved in adaptation of the Antarctic haloarchaea to cold environment. DeMaere, M. Z., Williams, T. J., Allen, M. A., Brown, M. V., Gibson, J. A., Rich, J., et al. (2013) High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110: 16939-16944. Tschitschko, B., Williams, T. J., Allen, M. A., Páez-Espino, D., Kyrpides, N., Zhong, L., et al. (2015) Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J 9: 2094-2107. Tschitschko, B., Williams, T. J., Allen, M. A., Zhong, L., Raftery, M. J., and Cavicchioli, R. (2016) Ecophysiological distinctions of haloarchaea from a hypersaline Antarctic lake determined using metaproteomics. Appl Environ Microbiol 82: 3165 – 3173. Williams, T. J., Allen, M. A., DeMaere, M. Z., Kyrpides, N. C., Tringe, S. G., Woyke, T., and Cavicchioli, R. (2014) Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J 8: 1645-1658.

2017-02-27 | PXD005076 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data