PXD063434

PXD063434 is an original dataset announced via ProteomeXchange.

Title	Diversity and distribution of the lanthanome in aerobic methane-oxidizing bacteria
Description	Lanthanides (Ln) play essential roles in the metabolism of certain bacteria, catalysing key reactions in methane oxidation. This study investigates the diversity and distribution of Ln-dependent proteins, collectively termed the lanthanome, in aerobic methane-oxidizing bacteria (MOB) using genome, plasmid, and metatranscriptome data from methane-rich lake sediments. A custom database of 180 MOB genomes revealed various methanol dehydrogenase (MDH) isoforms, including XoxF variants, distributed across Proteobacteria and Verrucomicrobia phyla. We conducted an experimental study with Methylosinus trichosporium OB3B exposed to CeCl₃ and an ore containing mixed lanthanides, measuring methane oxidation rates and using proteomics to assess shifts in protein expression. Despite differences in adaptation times, methane oxidation rates were consistent across treatments, indicating similar overall metabolic efficiencies after acclimatisation. The genomic analysis uncovered several Ln-binding proteins, including the TonB-dependent receptors LanA and lutH-like, as well as Lanmodulin and LanPepsy, with unique phylogenetic patterns. Metatranscriptomic data showed active lanthanome expression, particularly in Proteobacteria, with the XoxF5 MDH variant prevalent in MOB genomes. The discovery of Ln-binding proteins in plasmids suggests potential horizontal gene transfer, highlighting adaptive mechanisms of MOB to Ln availability and their ecological role in methane cycling. This work expands our understanding of Ln-utilising bacteria, particularly in the context of lanthanide-driven methane oxidation, and offers potential biotechnological applications for Ln-dependent processes.
HostingRepository	PRIDE
AnnounceDate	2025-04-29
AnnouncementXML	Submission_2025-04-29_02:30:05.750.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eleonora Silvano
SpeciesList	scientific name: Methylosinus trichosporium OB3b; NCBI TaxID: 595536;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-29 02:25:01	ID requested
⏵ 1	2025-04-29 02:30:06	announced

Dataset with its publication pending

submitter keyword: lanthanides, methane-oxidising bacteria,Methanotrophs, OB3b, Warwick_RTP, Methylosinus

Yin Chen
contact affiliation	School of Biosciences, University of Birmingham
contact email	y.chen.22@bham.ac.uk
lab head
Eleonora Silvano
contact affiliation	University of Warwick
contact email	eleonora.silvano@warwick.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063434
     1. Label: PRIDE project
     2. Name: Diversity and distribution of the lanthanome in aerobic methane-oxidizing bacteria