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Open AccessArticle

Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168

1
Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
2
Genetics Institute, University of Florida, Gainesville, FL 32611, USA
3
Department of Cancer Biology, University of Cincinnati, OH 45221, USA
4
UMR7365 IMoPA CNRS-UL and UMS2008 CNRS-UL-INSERM, Université de Lorraine, Biopôle UL, 54000 Nancy, France
5
Department of Chemistry, University of Cincinnati, OH 45221, USA
6
IBPS, Biology of Aging and Adaptation, Sorbonne University, 7 quai Saint Bernard, CEDEX 05, F-75252 Paris, France
*
Author to whom correspondence should be addressed.
Biomolecules 2020, 10(7), 977; https://doi.org/10.3390/biom10070977
Received: 4 June 2020 / Revised: 26 June 2020 / Accepted: 27 June 2020 / Published: 30 June 2020
(This article belongs to the Section Biomacromolecules)
Extensive knowledge of both the nature and position of tRNA modifications in all cellular tRNAs has been limited to two bacteria, Escherichia coli and Mycoplasma capricolum. Bacillus subtilis sp subtilis strain 168 is the model Gram-positive bacteria and the list of the genes involved in tRNA modifications in this organism is far from complete. Mass spectrometry analysis of bulk tRNA extracted from B. subtilis, combined with next generation sequencing technologies and comparative genomic analyses, led to the identification of 41 tRNA modification genes with associated confidence scores. Many differences were found in this model Gram-positive bacteria when compared to E. coli. In general, B. subtilis tRNAs are less modified than those in E. coli, even if some modifications, such as m1A22 or ms2t6A, are only found in the model Gram-positive bacteria. Many examples of non-orthologous displacements and of variations in the most complex pathways are described. Paralog issues make uncertain direct annotation transfer from E. coli to B. subtilis based on homology only without further experimental validation. This difficulty was shown with the identification of the B. subtilis enzyme that introduces ψ at positions 31/32 of the tRNAs. This work presents the most up to date list of tRNA modification genes in B. subtilis, identifies the gaps in knowledge, and lays the foundation for further work to decipher the physiological role of tRNA modifications in this important model organism and other bacteria.
Keywords: tRNA modifications; model bacteria; Gram-positive; methylation; pseudouridine synthase; YhcT; YjbO tRNA modifications; model bacteria; Gram-positive; methylation; pseudouridine synthase; YhcT; YjbO
MDPI and ACS Style

de Crécy-Lagard, V.; Ross, R.L.; Jaroch, M.; Marchand, V.; Eisenhart, C.; Brégeon, D.; Motorin, Y.; Limbach, P.A. Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168. Biomolecules 2020, 10, 977.

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