Analysis of tRNA Cys processing under salt stress in Bacillus subtilis spore outgrowth using RNA sequencing data [version 1; peer review: 2 approved, 2 approved with reservations]

• Published in: F1000 research Vol. 9; p. 501
• Main Authors: Arvizu Hernández, Iván, Hernández Flores, José Luis, Caballero Pérez, Juan, Gutiérrez Sánchez, Héctor, Ramos López, Miguel Ángel, Romero Gómez, Sergio, Cruz Hernández, Andrés, Saldaña Gutierrez, Carlos, Álvarez Hidalgo, Erika, Jones, George H, Campos Guillén, Juan
• Format: Journal Article
• Language: English
• Published: England Faculty of 1000 Ltd 2020; F1000 Research Limited
• Subjects: Abiotic stress; Bacillus subtilis; Bacillus subtilis - genetics; Enzymes; Gene expression; Genomes; Metabolism; Molecular modelling; Protein biosynthesis; Protein synthesis; Proteins; Ribonucleic acid; RNA; RNA, Transfer - genetics; Salt Stress; Sequence Analysis, RNA; Sodium chloride; Software; Spore germination; Spore outgrowth; Spore-forming bacteria; Spores, Bacterial - genetics; Sporulation; Transfer RNA; tRNA Cys; salt stress; outgrowth; RNA-Seq data; tRNACys processing; B. subtilis spore germination
• ISSN: 2046-1402
• DOI: 10.12688/f1000research.23780.1

Background: In spore-forming bacteria, the molecular mechanisms of accumulation of transfer RNA (tRNA) during sporulation must be a priority as tRNAs play an essential role in protein synthesis during spore germination and outgrowth. However, tRNA processing has not been extensively studied in these conditions, and knowledge of these mechanisms is important to understand long-term stress survival.   
Methods:To gain further insight into tRNA processing during spore germination and outgrowth, the expression of the single copy tRNA
Cys gene was analyzed in the presence and absence of 1.2 M NaCl in
Bacillus subtilis using RNA-Seq data obtained from the Gene Expression Omnibus (GEO) database. The CLC Genomics work bench 12.0.2 (CLC Bio, Aarhus, Denmark, https://www.qiagenbioinformatics.com/) was used to analyze reads from the tRNA
Cys gene. 
Results:The results show that spores store different populations of tRNA
Cys-related molecules.  One such population, representing 60% of total tRNA
Cys, was composed of tRNA
Cys fragments.  Half of these fragments (3´-tRF) possessed CC, CCA or incorrect additions at the 3´end. tRNA
Cys with correct CCA addition at the 3´end represented 23% of total tRNA
Cys, while with CC addition represented 9% of the total and with incorrect addition represented 7%. While an accumulation of tRNA
Cys precursors was induced by upregulation of the
rrnD operon under the control of  σ
A -dependent promoters under both conditions investigated, salt stress produced only a modest effect on tRNA
Cys expression and the accumulation of tRNA
Cys related species.
Conclusions:The results demonstrate that tRNA
Cys molecules resident in spores undergo dynamic processing to produce functional molecules that may play an essential role during protein synthesis.