Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Responses of Acidobacteria Granulicella sp. WH15 to carbon stress revealed by integrated omics analyses

ABSTRACT: Responses of Acidobacteria Granulicella sp. WH15 to carbon stress revealed by integrated omics analyses

PROVIDER: PRJNA559284 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9925600.fastq.gz	Fastqsanger.gz
	SRR9925601.fastq.gz	Fastqsanger.gz
	SRR9925602.fastq.gz	Fastqsanger.gz
	SRR9925603.fastq.gz	Fastqsanger.gz
	SRR9925598.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Responses of Acidobacteria Granulicella sp. WH15 to carbon stress revealed by integrated omics analyses

Project description:We used transcriptome analysis to evaluate the responses of one strain of Acidobacteria group 1, Granulicella sp WH15, to high quantities of carbon (3%) in culture medium.

2020-03-30 | GSE135558 | GEO

Acidobacteria Granulicella sp. WH15 responses to carbon stress

Project description:Acidobacteria is a widely distributed phylum in soils, which possesses a relatively small number of cultured representatives. In general, Acidobacteria are considered to be oligothroph, able to succeed growth in poor nutrient environments and exhibiting slow growth under laboratory conditions. However, some isolates are able to grow in higher sugar concentrations, and several genes encoding glycosyl hydrolases were already found in acidobacterial genomes. The objective of this study was to sequence the genome of one acidobacterium species strain, i.e. Granulicella sp. (WH15), and determine the transcriptome and proteome responses in conditions with low and high sugar concentrations. Our study demonstrated the presence of 217 carbohydrate associated enzymes in the genome of the strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that, in higher sugar concentrations, a stress response was triggered. Cell wall stress-related transcripts, such as sigma factor σW and the toxin-antitoxin (TA) systems were upregulated, as well as several proteins involved in detoxification and repair, for instance MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of the carbon metabolism, especially the pentose phosphate pathway, demonstrating a decline of cell activity, with reduction of protein synthesis, carbohydrates metabolism and cell division. The present study demonstrated that the addition of a high sugar concentration in the culture medium triggered a stress response in Granulicella sp WH15, intensifying excretory functions to eliminate toxic compounds and reallocating resources towards maintenance instead of growth.

2020-05-27 | PXD015715 | Pride

Positive effect of Manganese on growth of two strains of Granulicella sp. revealed by proteomic and genomic analyses

Project description:Members of Acidobacteria phylum are difficult to isolate and grow. Nevertheless, for some isolated strains, trace elements solution is needed in culture media for Acidobacteria growth but the impact of these metals on their growth and metabolism is not known. Here we evaluated the effect of trace element solution SL-10 in on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to Granulicella sp. and studied the proteomic responses to the metal with the best growth results, complementing with genomic characterization. Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal ions. Variations in tolerance to metal ion concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. The proteomic profiles of both strains indicated that Mn was more important in enhance enzymatic activity than to protein expression regulation. We did not find the most common transcriptional regulation of Mn homeostasis and we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment where these two strains were isolated. Furthermore, strain 5B5 is likely more adapted to survive in an environment with higher concentration of several metal ions when compared to strain WH15.

2021-02-15 | PXD016551 | Pride

Granulicella

Project description:Granulicella sp. overview

| PRJNA503511 | ENA

Responses of AcidobacteriaGranulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses.

Project description:The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.

| S-EPMC7074687 | biostudies-literature

Granulicella tundricola

Project description:Granulicella tundricola overview

| PRJNA164265 | ENA

Acidobacteria

Project description:Acidobacteria Raw sequence reads

| PRJNA592443 | ENA

Granulicella tundricola MP5ACTX9

Project description:Granulicella tundricola MP5ACTX9

| PRJNA47621 | ENA

uncultured Granulicella sp.

Project description:uncultured Granulicella sp. overview

| PRJNA1047256 | ENA

A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria

Project description:Investigation of the phylogenetic diversity of Acidobacteria taxa using PCR amplicons from positive control 16S rRNA templates and total genomic DNA extracted from soil and a soil clay fraction A ten chip study using PCR amplicons from cloned 16S rRNA genes and from diverse soil 16S rRNAs, with PCR primers specific to the Division Acidobacteria. Each chip measures the signal from 42,194 probes (in triplicate) targeting Acidobacteria division, subdivision, and subclades as well as other bacterial phyla. All samples except one (GSM464591) include 2.5 M betaine in the hybridization buffer. Pair files lost due to a computer crash.

2010-06-24 | E-GEOD-18711 | biostudies-arrayexpress

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