PXD010845

PXD010845 is an original dataset announced via ProteomeXchange.

Title	Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens
Description	Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
HostingRepository	PRIDE
AnnounceDate	2019-11-12
AnnouncementXML	Submission_2019-11-12_13:29:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	xiaonan fu
SpeciesList	scientific name: Pseudomonas fluorescens; NCBI TaxID: 294;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-23 06:51:51	ID requested
⏵ 1	2019-11-12 13:29:31	announced

Liu X, Xu J, Zhu J, Du P, Sun A, . Front Microbiol, 10():94(2019) [pubmed]

curator keyword: Biological

submitter keyword: transcriptome, proteome, RpoS, regulon, Pseudomonas fluorescens

Xiaoxiang Liu
contact affiliation	School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, P.R.China
contact email	liuxiaoxiang413@126.com
lab head
xiaonan fu
contact affiliation	zhejiang scientific technology universitiy
contact email	2016460649@qq.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD010845
     1. Label: PRIDE project
     2. Name: Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens