PXD044565-2

PXD044565 is an original dataset announced via ProteomeXchange.

Title	Multi-omics investigation of Rhodococcus sp. strain DN22
Description	Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a persistent nitramine explosive with long-lasting properties. Rhodococcus sp. strain DN22 has been discovered as one of the microorganisms capable of RDX degradation. Despite respectable studies on Rhodococcus sp. strain DN22, the proteins participating in RDX degradation (Oxidoreductase and Cytochrome P450) in the strain remain to be fragments. In this study, complete genome of Rhodococcus sp. strain DN22 was sequenced and analyzed, and the entire sequences of the two genes encoding Oxidoreductase and Cytochrome P450 in Rhodococcus sp. strain DN22 were predicted, which were validated through proteomic data. Besides, despite the identification of certain chemical substances as proposed characterized degradation intermediates of RDX, few studies have investigated the physiological changes and metabolic pathways occurring within Rhodococcus sp. cells when treated with RDX, particularly through the use of mass spectrometry-based omics. Hence, proteomics and metabolomics of Rhodococcus sp. strain DN22 were performed and analyzed with the presence or absence of RDX in the medium. A total of 3186 protein groups were identified and quantified between the two groups, with 117 proteins being significantly differentially expressed proteins. A total of 1056 metabolites were identified after merging positive and negative ion modes, among which 131 metabolites were significantly differential. Through the combined analysis of differential proteomics and metabolomics, several KEGG pathways, including two-component system, ABC transporters, alanine, aspartate and glutamate metabolism, arginine biosynthesis, purine metabolism, nitrogen metabolism, and phosphotransferase system (PTS) were found to be significantly enriched. We expect that our investigation will expand the acquaintance of Rhodococcus sp. strain DN22, and the knowledge of microbial degradation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:41:00.453.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhou Xiangzhe
SpeciesList	scientific name: Rhodococcus sp. DN22; NCBI TaxID: 357684;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-14 07:54:22	ID requested
1	2024-05-22 02:19:08	announced
⏵ 2	2024-10-22 06:41:01	announced	2024-10-22: Updated project metadata.

10.3390/microorganisms12010076;

Zhou X, Yao Q, Li N, Xia M, Deng Y, sp. Strain DN22. Microorganisms, 12(1):(2023) [pubmed]

submitter keyword: RDX biodegradation

Rhodococcus sp. strain DN22

Genome sequencing

Proteomics

Metabolomics

Yongqian Zhang
contact affiliation	Institute of Engineering Medicine, School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
contact email	zyq@bit.edu.cn
lab head
Zhou Xiangzhe
contact affiliation	Beijing Institute of Technology
contact email	3120211440@bit.edu.cn
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/2024/05/PXD044565

PRIDE project URI

• PRIDE
  1. PXD044565
     1. Label: PRIDE project
     2. Name: Multi-omics investigation of Rhodococcus sp. strain DN22