PXD011842

PXD011842 is an original dataset announced via ProteomeXchange.

Title	Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1
Description	Until recently, rare-earth elements (REEs) had been thought to be biologically inactive. This view changed with the discovery of the methanol dehydrogenase (Mdh) XoxF that strictly relies on REEs for its activity. Some methylotrophs only contain xoxF, while others, including the model phyllosphere colonizer Methylobacterium extorquens PA1, harbor this gene in addition to mxaFI encoding a Ca2+-dependent enzyme. Here we found that REEs induce the expression of xoxF in M. extorquens PA1, while repressing mxaFI, suggesting that XoxF is the preferred Mdh. Using reporter assays and a suppressor screen, we found that La3+ is sensed both in a XoxF-dependent and independent manner. Furthermore, we investigated the role of REEs during Arabidopsis thaliana colonization. Element analysis of the phyllosphere revealed the presence of several REEs at concentrations up to 10 μg per g dry weight. Complementary proteome analyses of M. extorquens PA1 revealed XoxF as a top induced protein in planta and resulted in the identification of a core set of La3+-regulated proteins under defined artificial media conditions. Among these, we identified a potential REE-binding protein that is encoded next to a gene for a TonB-dependent transporter. The latter was essential for REE-dependent growth on methanol indicating chelator-assisted uptake of REEs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:51:02.861.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lucas Hemmerle
SpeciesList	scientific name: Methylobacterium extorquens PA1; NCBI TaxID: 419610;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-27 02:24:33	ID requested
1	2019-01-21 03:51:26	announced
⏵ 2	2024-10-22 04:51:10	announced	2024-10-22: Updated project metadata.

Ochsner AM, Hemmerle L, Vonderach T, N, ü, ssli R, Bortfeld-Miller M, Hattendorf B, Vorholt JA, Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1. Mol Microbiol, 111(5):1152-1166(2019) [pubmed]

10.1111/mmi.14208;

curator keyword: Biological

submitter keyword: Rare earth metals, Arabidopsis, Methanol, Ion transport, Proteomics, Methylobacterium extorquens

Julia A. Vorholt
contact affiliation	Department of Biology, Institute of Microbiology, ETH Zürich, Switzerland
contact email	jvorholt@ethz.ch
lab head
Lucas Hemmerle
contact affiliation	ETH Zürich
contact email	helucas@ethz.ch
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/2019/01/PXD011842

PRIDE project URI

• PRIDE
  1. PXD011842
     1. Label: PRIDE project
     2. Name: Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1