PXD069173

PXD069173 is an original dataset announced via ProteomeXchange.

Title	tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations
Description	tRNA modifications are central to bacterial translational control. Here, we integrated genetics, mass spectrometry, epitranscriptomics, and comparative genomics to map the tRNA modification genes of the Gram-positive pathogens Streptococcus mutans and Streptococcus pneumoniae. Both species show a marked loss of modifications dependent on Fe–S enzymes, consistent with a broader trend of Fe–S enzyme reduction in Streptococcus central metabolism. In addition, the D, m1A, m7G, t6A, and i6A modifications were mapped in S. pneumoniae tRNAs, and we confirmed that a unique DusB1 enzyme is responsible for the insertion of all the detectable D modifications. We uncovered differences in queuosine (Q) metabolism: while S. mutans synthesizes Q de novo, S. pneumoniae instead salvages preQ₁ and accumulates the epoxy-Q precursor, a strategy shared with multiple other Streptococci as revealed by analysis of Q pathways in 1,599 sequenced streptococcal genomes. Comparative essentiality profiling of modification genes revealed notable differences, including the essentiality of the N⁶-threonylcarbamoyladenosine (t⁶A) synthesis enzyme TsaE in S. pneumoniae but not in S. mutans, which was confirmed by genetic studies. We found that suppressor mutations in asnS encoding asparaginyl-tRNA synthetase (AsnRS) restored viability to ∆tsaE mutants, albeit with reduced growth. Our finding highlights the functional importance of the recognition of an aminoacyl-tRNA synthetase with a modified tRNA.
HostingRepository	PRIDE
AnnounceDate	2026-02-27
AnnouncementXML	Submission_2026-02-27_05:10:27.066.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chi Kong Chan
SpeciesList	scientific name: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466); NCBI TaxID: NEWT:373153; scientific name: Streptococcus mutans UA159; NCBI TaxID: NEWT:210007;
ModificationList	No PTMs are included in the dataset
Instrument	6495C Triple Quadrupole LC/MS; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-06 15:23:13	ID requested
⏵ 1	2026-02-27 05:10:27	announced

10.1101/2025.10.13.681863;

submitter keyword: Dihydrouridine,tRNA modification, Queuosine, pseudogene, TsaE, t6A

Peter C Dedon
contact affiliation	Underwood-Prescott Professor, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 56-731 Cambridge, MA 02139-4307
contact email	pcdedon@mit.edu
lab head
Chi Kong Chan
contact affiliation	Department of Biological Engineering, Massachusetts Institute of Technology
contact email	mckchan@mit.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD069173
     1. Label: PRIDE project
     2. Name: tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations