PXD048805-1

PXD048805 is an original dataset announced via ProteomeXchange.

Title	Mapping the tRNA Modification Landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse
Description	Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens—Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana. Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. B. quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
HostingRepository	PRIDE
AnnounceDate	2024-01-23
AnnouncementXML	Submission_2024-01-23_15:21:32.427.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Dedon
SpeciesList	scientific name: Bartonella quintana str. Toulouse; NCBI TaxID: 283165; scientific name: Bartonella henselae (strain ATCC 49882 / Houston 1) (Rochalimaea henselae); NCBI TaxID: 283166;
ModificationList	No PTMs are included in the dataset
Instrument	6495C Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-23 07:35:23	ID requested
⏵ 1	2024-01-23 15:21:32	announced

Dataset with its publication pending

submitter keyword: tRNA modification,Intracellular pathogens, mass spectrometry, next-generation sequencing.

Peter C. Dedonb
contact affiliation	Dr Peter C Dedon, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore (lab head)
contact email	pcdedon@mit.edu
lab head
Peter Dedon
contact affiliation	Massachusetts Institute of Technology
contact email	pcdedon@mit.edu
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/2024/01/PXD048805

PRIDE project URI

• PRIDE
  1. PXD048805
     1. Label: PRIDE project
     2. Name: Mapping the tRNA Modification Landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse