PXD017801

PXD017801 is an original dataset announced via ProteomeXchange.

Title	Exploiting Dynamics of Genomic Islands to Edit the Genome of Vibrio cholerae and Identify Novel Interactions Between Core and Acquired Genome
Description	Horizontally acquired genetic elements (HGEs) plays a major for determination of virulence, antimicrobial resistance, adaptation and evolution in pathogenic bacteria. Conserved integrative mobile genetic elements (MGEs) of Vibrio cholerae contribute in the disease development, antimicrobial resistance and metabolic functions. To understand the dynamics of integrative MGEs and cross talk between MGEs and core genome, engineered genome of V. cholerae was monitored in the presence and absence of horizontally acquired genetic elements. Deletion of more than 250 revealed that CTX contributes to the essentiality of SOS response master regulator LexA in V. cholerae. Also, he core genome encoded RecA helps CTX to bypass the host immunity and replicate in the host cell in the presence of similar prophage in the host chromosome. Finally, our multiomics data reveal importance of MGEs in modulating the level of cellular proteome and metabolome in V. cholerae. This study for the first time engineered the genome of V. cholerae strains to eliminate all the GIs, ICE and prophages from their genome and revealed new interactions between core and acquired genomes. The engineered strain could be a potential candidate for understanding evolution of cholera pathogen and development of therapeutics.
HostingRepository	PRIDE
AnnounceDate	2020-09-28
AnnouncementXML	Submission_2020-09-27_23:21:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bhoj Kumar
SpeciesList	scientific name: Vibrio cholerae O1 biovar El Tor str. N16961; NCBI TaxID: 243277;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetic acid derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-01 23:43:45	ID requested
⏵ 1	2020-09-27 23:21:20	announced

Pant A, Bag S, Saha B, Verma J, Kumar P, Banerjee S, Kumar B, Kumar Y, Desigamani A, Maiti S, Maiti TK, Banerjee SK, Bhadra RK, Koley H, Dutta S, Nair GB, Ramamurthy T, Das B, . Proc Natl Acad Sci U S A, 117(38):23762-23773(2020) [pubmed]

submitter keyword: Vibrio cholerae, DIA, SWATH-MS

Tushar Kanti Maiti
contact affiliation	Regional Centre for Biotechnology, Faridabad, India
contact email	tkmaiti@rcb.res.in
lab head
Bhoj Kumar
contact affiliation	Regional Centre for Biotechnology NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway P.O. Box No. 3, Faridabad - 121 001 Haryana (NCR Delhi), India
contact email	bhoj.kumar@rcb.res.in
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/09/PXD017801

PRIDE project URI

• PRIDE
  1. PXD017801
     1. Label: PRIDE project
     2. Name: Exploiting Dynamics of Genomic Islands to Edit the Genome of Vibrio cholerae and Identify Novel Interactions Between Core and Acquired Genome