PXD016527

PXD016527 is an original dataset announced via ProteomeXchange.

Title	EmhR is an indole-sensing transcriptional regulator responsive for the indole-induced antibiotic tolerance in Pseudomonas fluorescens
Description	Indole is ubiquitously synthesized by plants and bacteria and functions as an inter species signaling molecule to modulate a wide variety of cellular activities. However, it is not clear how the indole signal is perceived and responded by plant growth promoting rhizobacteria (PGPR) at the rhizosphere. Here, we demonstrated that indole enhanced antibiotic tolerance of Pseudomonas fluorescens 2P24, a PGPR well known for its biocontrol capacity. By conducting quantitative proteomic analysis, we showed that indole influences the expression of multiple genes including the emhABC operon encoding the major multidrug efflux pump in P. fluorescens 2P24. The indole-induced antibiotic tolerance was not related to bacterial dormancy or slow growth, but depended on the emhABC operon and the divergently transcribed TetR-like regulator emhR. By binding to the semi-palindromic operator sequence, EmhR repressed the expression of emhABC. It was further revealed that indole bound to EmhR and weakened the interaction between EmhR and the operator. This is consistent with our finding that indole-induced expression of the EmhABC efflux pump is dependent on EmhR. Using homology modeling and molecular dynamics simulation, we found that indole binding resulted in significantly decreased distance between the two DNA-recognizing α3 helices within the EmhR dimer, which would possibly account for its compromised DNA binding capacity. EmhR was further shown to globally influence protein expressions, especially transporters and proteins involved in the denitrification pathway. This EmhR-dependent, indole-induced antibiotic tolerance is likely to be prevalent in the Pseudomonas species, as the EmhR homologue in Pseudomonas syringae was also shown to be responsible for the indole-induced antibiotic tolerance. Taken together, our results revealed an indole-sensing transcription factor EmhR responsible for indole-induced antibiotic tolerance in Pseudomonas species and have important implications on the general mechanism for the indole sensing and responses in rhizobacteria.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:28.534.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jianting Han
SpeciesList	scientific name: Pseudomonas fluorescens F113; NCBI TaxID: 1114970;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-29 03:02:22	ID requested
1	2023-05-03 23:26:44	announced
⏵ 2	2023-11-14 08:45:36	announced	2023-11-14: Updated project metadata.

Han JT, Li DY, Zhang MY, Yu XQ, Jia XX, Xu H, Yan X, Jia WJ, Niu S, Kempher ML, Tao X, He YX, EmhR is an indole-sensing transcriptional regulator responsible for the indole-induced antibiotic tolerance in Pseudomonas fluorescens. Environ Microbiol, 23(4):2054-2069(2021) [pubmed]

submitter keyword: efflux pump,antibiotic tolerance, indole

Yong-Xing He
contact affiliation	Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University
contact email	heyx@lzu.edu.cn
lab head
Jianting Han
contact affiliation	Lanzhou University
contact email	hanjt11@lzu.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016527
     1. Label: PRIDE project
     2. Name: EmhR is an indole-sensing transcriptional regulator responsive for the indole-induced antibiotic tolerance in Pseudomonas fluorescens