PXD025403

PXD025403 is an original dataset announced via ProteomeXchange.

Title	Molecular basis for coordinating secondary metabolite production by bacterial and plant signaling molecules
Description	The production of secondary metabolites is one of the major mechanisms for beneficial rhizobacteria to antagonize plant pathogens. However, simultaneously producing large quantities of different secondary metabolites can pose great metabolic burdens and exerts a significant fitness cost on the producers. Here, we showed that PhlH from the rhizobacterium Pseudomonas fluorescens is a TetR-family regulator that plays a central role in coordinating biosynthesis of several secondary metabolites including 2,4-diacetylphloroglucinol (2,4-DAPG), mupirocin, and pyoverdine. Structures of PhlH in both its apo-form and 2,4-DAPG-bound were also presented, elucidating its ligand-recognizing and allosteric switching mechanisms. The ligand 2,4-DAPG was fully buried in a long hydrophobic interior tunnel and subsequent docking and mutagenesis analysis confirmed that this tunnel could also be occupied by the plant flavonoid phloretin, providing a structural basis for the ligand-binding promiscuity in PhlH. Moreover, dissociation of 2,4-DAPG from the ligand-binding domain (LBD) alone was sufficient to allosterically trigger a pendulum-like movement of the DNA-binding domains (DBD) within the PhlH dimer, leading to a closed to open conformational transition. Molecular dynamics simulation further confirmed that these two distinct conformational states were stabilized by specific hydrogen bonding interactions and disruption of these hydrogen bonds had profound effects on signal transmission from LBD to DBD. These findings revealed a potential route of allosteric signal transduction, which is well-conserved in numerous PhlH-like regulators and provides novel insights into ligand-triggered conformational switching of TetR-family regulators.
HostingRepository	iProX
AnnounceDate	2021-04-15
AnnouncementXML	Submission_2023-02-20_19:18:35.670.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yongxing He
SpeciesList	scientific name: Pseudomonas fluorescens F113; NCBI TaxID: 1114970;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-14 19:35:14	ID requested
1	2021-04-14 19:36:09	announced
⏵ 2	2023-02-20 19:18:36	announced	2023-02-21: Update information.

Zhang N, Wu J, Zhang S, Yuan M, Xu H, Li J, Zhang P, Wang M, Kempher ML, Tao X, Zhang LQ, Ge H, He YX, Molecular basis for coordinating secondary metabolite production by bacterial and plant signaling molecules. J Biol Chem, 298(6):102027(2022) [pubmed]

submitter keyword: Pseudomonas fluorescens, secondary metabolite, 2,4-DAPG

Yongxing He
contact affiliation	Lanzhou University
contact email	heyx@lzu.edu.cn
lab head
Yongxing He
contact affiliation	Lanzhou University
contact email	heyx@lzu.edu.cn
dataset submitter

iProX dataset URI