Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment, in Medicago truncatula roots

ABSTRACT: The extend of chromatin accessibility changes and its consequent impact on the transcriptional control of rhizobial infection, colonization, and nodule development, remain unknown. This understanding requires that the dynamic behavior of gene expression and chromatin accessibility be quantified. Thus, we uncovered the gene regulatory network in response to LCOs in M. truncatula roots by quantifying temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment.

ORGANISM(S): Medicago truncatula

PROVIDER: GSE154845 | GEO | 2022/07/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Sinorhizobium meliloti root nodule bacterial transcriptomes for wild type and four mutant strains.

Project description:We characterized transcriptomes of Sinorhizobium meliloti root nodule bacteria with mutations in sigma factor genes.

2018-09-05 | GSE116664 | GEO

Sinorhizobium meliloti Ser/Thr/Tyr phosphoproteome

Project description:Sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. In this study, TiO2 enrichment and LC-MS/MS were used to uncover the site-specific Ser/Thr/Tyr phosphoproteome of S. meliloti in minimum medium at stationary phase. There are a total of 96 unique phosphorylated sites, with a Ser/Thr/Tyr distribution of 65:32:5, in 78 proteins. Phosphoproteins identified in S. meliloti showed a wide distribution pattern regarding to functional categories, such as replication, transcription, translation, posttranslational modification, transport and metabolism of amino acids, carbohydrate, inorganic ion, succinoglycan etc. Ser/Thr/Tyr phosphosites identified within the conserved motif in proteins of key cellular function indicate a crucial role of phosphorylation in modulating cellular physiology. Moreover, phosphorylation events potentially involved in rhizobial adaptation to diverse stresses were also discussed, such as those identified in SMa0114 and PhaP2 (polyhydroxybutyrate synthesis), ActR (pH stress and microaerobic adaption), SupA (potassium stress), chaperonin GroEL2 (viability and potentially symbiosis), and ExoP (succinoglycan synthesis and secretion). These Ser/Thr/Tyr phosphosites identified herein would be helpful for our further investigation and understanding of the role of phosphorylation in rhizobial physiology.

2015-10-05 | PXD002064 | Pride

Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis

2014-01-21 | GSE54244 | GEO

Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [CtrA]

Project description:We characterized transcriptomes of a Sinorhizobium meliloti wild type strain (CL150) expressing either Ca. Liberibacter asiaticus ctrA or Sinorhizobium meliloti ctrA

2019-08-01 | GSE124977 | GEO

Identifying the regulon of the Sinorhizobium meliloti JspA protease

Project description:Sinorhizobium meliloti establishes symbiotic relationship with compatible leguminous plants by inducing root nodule formation, colonizing such nodules, and fixing molecular nitrogen for the host in exchange for carbon compounds. This mutualistic process requires complex communication and tight regulation to allow yet constrain infection to specific tissues. Production of succinoglycan, or exopolysaccharide-I (EPS-I), enables S. meliloti to invade the root cortex via infection threads. A previous genetic screen identified jspA (SMc03872), encoding an extracytoplasmic protease, as a regulator of EPS-I production. To elucidate its molecular role, we performed transcriptome analyses of strains overexpressing wild-type or mutant alleles of jspA. We observed changes in gene expression suggesting that JspA contributes to symbiosis efficiency by modulating the critical ExoR-ExoS-ChvI signaling pathway.

2023-05-10 | GSE155833 | GEO

Sinorhizobium meliloti as a model system to study Ca. Liberibacter asiaticus regulators. [RpoH]

Project description:We characterized transcriptomes of a Sinorhizobium meliloti rpoH1rpoH2 deletion mutant (RFF231; Lang et al. 2018, mSphere 3:e00454-18) expressing either Ca. Liberibacter asiaticus rpoH or Sinorhizobium meliloti rpoH1

2019-08-01 | GSE124982 | GEO

Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis

Project description:We profiled gene expression in synchronized cultures of Sinorhizobium meliloti treated with or without the nodule-specific cysteine-rich peptide 247. We compared gene expression between the two conditions at 5 timepoints (15, 30, 60, 90, 120) following the addition of the peptide A population of synchronized Sinorhizobium meliloti was subjected to two treatments (no treatment and treated with sublethal levels of the NCR247 peptide). A series of timepoints was taken to profile the gene expression in both populations.

2014-01-21 | E-GEOD-54244 | biostudies-arrayexpress

Novel genes and regulators for cell surface of Sinorhizobium meliloti.

Project description:We characterized the transcriptome of a Sinorhizobium meliloti emmA insertion mutant strain.

2017-11-30 | GSE100707 | GEO

The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

Project description:The Alphaproteobacterium Sinorhizobium meliloti lives in soil and is capable of fixing molecular nitrogen in symbiosis with legume plants. In this work, the small proteome of S. meliloti strain 2011 was studied to uncover translation of both annotated and novel small open reading frame (sORF)-encoded proteins (SEPs).

2023-03-13 | PXD034931 | Pride

Expression analysis of Sinorhizobium meliloti 1021rpoH1 rpoH2 mutant during heat shock

Project description:Investigation of whole genome gene expression level changes in a Sinorhizobium meliloti 1021 rpoH1 rpoH2 double mutant, compared to the wild-type strain. The mutations engineered into this strain render it deficient in symbiotic nitrogen fixation. The mutants analyzed in this study are further described in Mitsui, H, T. Sato, Y. Sato, and K. Minamisawa. 2004. Sinorhizobium meliloti RpoH1 is required for effective nitrogen-fixing symbiosis with alfalfa. Mol Gen Genomics 271:416-425.

2014-11-01 | GSE62900 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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