PXD035204

PXD035204 is an original dataset announced via ProteomeXchange.

Title	R. etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network
Description	Abstract A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30% and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of coexpression of transcriptional regulators (TF´s) in the profiles, by selection of genes whose matrices were clustered with matrices of TF´s, TRN´s were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF´s and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene–target relationships for bases to construct a TRN.
HostingRepository	PRIDE
AnnounceDate	2022-09-27
AnnouncementXML	Submission_2022-09-27_12:11:28.744.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD035204
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Hermenegildo Taboada
SpeciesList	scientific name: Rhizobium etli CFN 42; NCBI TaxID: 347834;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-09 09:18:08	ID requested
⏵ 1	2022-09-27 12:11:29	announced

Dataset with its publication pending

submitter keyword: LC-MS/MS, Transcriptional, regulation, network, Rhizobium

Sergio Manuel Encarnación Guevara
contact affiliation	Associated Researcher
contact email	encarnac@ccg.unam.mx
lab head
Hermenegildo Taboada
contact affiliation	Academic
contact email	htaboada@ccg.unam.mx
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD035204
     1. Label: PRIDE project
     2. Name: R. etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network