Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomes of Wenzhouxiangella isolate grown on three substrates

ABSTRACT: A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3 was isolated from a system of alkaline soda lakes in the Kulunda Steppe. Its complete, circular genome was assembled from combined nanopore and illumina sequencing and its proteome was determined for three different experimental conditions: growth on Staphylococcus cells, casein, or peptone. AB-CW3 is an aerobic bacterium feeding mainly on proteins and peptides.

INSTRUMENT(S):

ORGANISM(S): Wenzhouxiangellaceae Bacterium

SUBMITTER: Jackie Zorz

LAB HEAD: Marc Strous

PROVIDER: PXD021036 | Pride | 2020-11-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Run2_Case1_400ng.msf	Msf
	Run2_Case1_400ng.pep.xml	Pepxml
	Run2_Case1_400ng.raw	Raw
	Run2_Case2_400ng.msf	Msf
	Run2_Case2_400ng.pep.xml	Pepxml

Items per page:

1 - 5 of 28

Similar Datasets

Frequency of change determines effectiveness of microbial response strategies in sulfidic stream microbiomes

Project description:Chemostat incubations were established and inoculated with sediments collected from Canyon Creek, Calgary, Alberta, Canada. The chemostats experienced oxic-anoxic change of different frequency, High-frequency, Medium-frequency and Low-frequency. 18 samples were collected at the end of the final oxic phase and the final anoxic phase in the triplicated chemostats for metagenomic and metaproteomic analysis. 26 genomes were assembled from metagenomes. Proteomes were used to investigate translational regulation of each population associated with a genome.

2023-04-26 | PXD028583 | Pride

Metaproteomes of phototrophic mats from four soda lakes found in the Cariboo Plateau region of British Columbia, Canada

Project description:In this study we used metaproteomics to discern the metabolism and physiology of the microorganisms occurring in the phototrophic mats of four soda lakes in the interior of British Columbia, Canada. Binned and assembled metagenomes were used as the database for protein identification.

2019-07-29 | PXD011230 | Pride

Proteomics of groundwater microbiomes collected from five wells in Alberta, Canada

Project description:Groundwater samples were collected from five wells in Alberta, Canada. The sampling location and time are indicated in the table below. 13 to 29 genomes were assembled from each metagenome. Proteomic analyses were performed to investigate which genomes and genes were expressed in each well. Sample ID Location Latitude (NAD 83) Longitude (NAD 83) Sampling date 19GWC19026 218 Cluny 50.85 -112.84 30/07/2019 19GWC19028 114 Ross Creek 49.99 -110.46 31/07/2019 19GWC19045 265 Metiskow 52.42 -110.61 18/09/2019 19GWE00050 991 Cynthia 56.22 -117.81 04/09/2019 19GWE00515 33 Fort McMurray 56.98 -111.85 17/09/2019

2024-05-21 | PXD044305 | Pride

Metaproteomics of phototrophic biomats from two soda lakes in the Canadian Rocky Mountains

Project description:This data is a case study done in the context of developing methods for assessing the taxonomic composition of microbial communities using metaproteomics. For this study with analyzed phototrophic biomats from two Soda Lakes in the Canadian Rocky Mountains using metaproteomics. For protein identification we generated a metagenome from which we predicted and annotated the protein sequences used to analyze the metaproteomes. The database is available in this PRIDE submission. Lake1 refers to Goodenough Lake (GEM, 51°19'47.64"N 121°38'28.90"W) and Lake2 referes to Last Chance Lake (LCM, 51°19'39.3" N 121°37'59.3"W).

2017-05-12 | PXD006343 | Pride

Proteomics of Ca. Riegeria standrea – the chemosynthetic symbionts of the marine flatworm Paracatenula from the Bay of Sant´Andrea (Elba, Italy)

Project description:Paracatenula are marine catenulid flatworms occuring in shallow water sediments. Adult Paracatenula lack a mouth and a digestive system. Instead, a trophosome containing intracellular alphaproteobacterial symbionts, namely Ca. Riegeria fill most of the worm´s body (Gruber-Vodicka et al., 2011). Paracatenula sp. ‘standrea’ that harbor Ca. Riegeria sp. 812A (standrea) were sampled in Elba, Italy in April 2016. Based on the genome of Ca. Riegeria sp. 812A (standrea) we discovered a versatile combination of storage and biosynthesis and a convergence with unrelated intracellular thiotrophic symbionts. Proteomic analyses were performed to investigate which symbiont genes related to the host nutrition were expressed.

2019-03-26 | PXD009856 | Pride

The Trichoplax H2 holobiont: a simple animal and its two intracellular symbionts

Project description:The Placozoa are an enigmatic group of simple marine metazoans where all taxa harbor intracellular bacteria. Despite four decades of research, the bacterial identities, their location and their roles remain elusive. Here we show that the placozoan Trichoplax H2 is associated with two intracellular bacteria. We detected the symbionts and reconstructed their physiology using metagenomic and metatranscriptomic evidence from the same single-animal specimens. One symbiont forms a new genus in the Midichloriaceae (Rickettsiales) and correlative fluorescent labelling and 3-D electron microscopic tomography showed that it inhabits the rough ER in the fiber-cells. It has mutualistic traits and occurs worldwide as we could detect it in 10% of all aquatic tag sequencing datasets. The second symbiont is an intracellular bacterium from the Margulisbacteria, a phylum-level clade previously only identified from DNA sequencing and not known to form intracellular associations. It resides in the digestive ventral epithelial cells, uses lipids digested by the host and has the physiological capacity to supplement the placozoan nutrition. Our single-individual approach revealed that this cultivable placozoan host forms a tripartite symbiosis and provides experimental access to microbial dark matter – a rickettsiales that inhabits a novel niche within eukaryote cells and an intracellular margulisbacterial symbiont.

2019-04-18 | PXD012106 | Pride

Environmental viscosity modulates interbacterial killing during habitat transition

Project description:In this study we employed a proteomics method to determine how bacteria respond at the protein level to a transition from a low- to a high-viscosity liquid environment. We applied this method to explore how the symbiotic marine bacterium Vibrio fischeri responds to changes in environmental viscosity associated with the transition from free-living to host-associated states. For this project cultures of ES401 were initially grown in low-viscosity liquid media and then transferred to either fresh low- or high-viscosity liquid media, which was generated by supplementing liquid media with 5% polyvinylpyrrolidone (w/vol). Samples were then incubated for one, 12, or 24 hours, and then collected by centrifugation and cell pellets frozen at -80°C. For each treatment four biological replicates were generated and analyzed.

2020-01-07 | PXD015403 | Pride

A strain-specific genomic island encodes regulatory proteins to activate type VI secretion system expression in the squid symbiont Vibrio fischeri.

Project description:We used the bioluminescent squid symbiont, Vibrio fischeri, to identify essential regulatory factors that control expression and function of a strain-specific T6SS encoded within a genomic island. Random transposon mutagenesis revealed that three genes located on the T6SS2-encoding genomic island are necessary to activate expression of a T6SS reporter. We used a proteomics approach to identify proteins that were differentially abundant in mutant strains compared to the wild type when cells were grown in a high-viscosity media.

2021-08-24 | PXD017722 | Pride

Proteomics of phage VPE25 treated Enterococcus faecalis OG1RF relative to untreated controls

Project description:E. faecalis OG1RF cultures were infected with lytic phage VPE25 and proteomic profile of infected cells were compared to uninfected E. faecalis cells using 1D-LC-MS/MS analyses.

2024-07-27 | PXD026873 | Pride

13C or 15N labeled metaproteome of phototrophic microbial mats from Goodenough soda lake in the Cariboo Plateau region of British Columbia, Canada

Project description:In this study, we used 13C and 15N labeled substrates to assess the carbon (C) and nitrogen (N) assimilation by detecting 13C and 15N in proteins from microorganisms in the phototrophic microbial mats in a soda lake on the Cariboo Plateau, British Columbia, Canada. Metagenomic database used for protein identification and metagenome assembled genome membership had been previousl generated in Zorz et.al. (2019).

2025-10-22 | PXD059992 | 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