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bioRxiv · 10.1101/2025.10.13.681863

tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations

Tsui, H.-C. T.·Chan, C.-K.·Yuan, Y.·Elias, R.·Sun, J.·Marchand, V.·Jaroch, M.·Sun, G.·Manzoor, I.·Kutchuashvili, A.·Leszczynska, G.·Seaton, K.·Motorin, Y.·Rice, K. C.·Swairjo, M.·Dedon, P. C.·Winkler, M. E.·de Crecy-Lagard, V.
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Abstract

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 preQ 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 NLJ-threonylcarbamoyladenosine (tLJA) 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 {Delta}tsaE mutants, albeit with reduced growth. Our finding highlights the functional importance of modifications in the recognition of tRNAs by aminoacyl-tRNA synthetases.

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Tsui, H.-C. T., Chan, C.-K., Yuan, Y., Elias, R., Sun, J., Marchand, V., Jaroch, M., Sun, G., Manzoor, I., Kutchuashvili, A., Leszczynska, G., Seaton, K., Motorin, Y., Rice, K. C., Swairjo, M., Dedon, P. C., Winkler, M. E., de Crecy-Lagard, V.. 2025-10-13. tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations. https://doi.org/10.1101/2025.10.13.681863

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