Analysis of tRNA^Cys processing under salt stress in Bacillus subtilis spore outgrowth using RNA sequencing data

• Type of Material: Article
• Authors: Iván Arvizu Hernández, Universidad Autónoma de Querétaro; José Luis Hernández Flores, Centro de Investigacion y de Estudio Avanzados, Campus Guanajuato; Juan Caballero Pérez, Databiology Ltd; Héctor Gutiérrez Sánchez, Universidad Autónoma de Querétaro; Miguel Á Ramos López, Universidad Autónoma de Querétaro; Sergio Romero Gómez, Universidad Autónoma de Querétaro; Andrés Cruz Hernández, Universidad de la Salle Bajío; Carlos Saldaña Gutierrez, Universidad Autónoma de Querétaro; Erika Álvarez Hidalgo, Universidad Autónoma de Querétaro; George Jones, Emory University; Juan Campos Guillén, Universidad Autónoma de Querétaro
• Language: English
• Date: 2020-01-01
• Publisher: F1000 Research Ltd
• Publication Version: Final Published Version
• Copyright Statement: © 2020 Arvizu Hernández I et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.12688/f1000research.23780.1
• Title of Journal or Parent Work: F1000Research
• Volume: 9
• Start Page: 501
• End Page: 501
• Grant/Funding Information: This study was partially financed by the Universidad Autónoma de Querétaro (FONDEC-UAQ-2019-FCQ202001 and FONDO “QUÍMICA SOMOS TODOS” 2019-Folio 17).
• Keywords: tRNACys processing; B. subtilis spore germination; Bacillus subtilis; Spores, Bacterial; salt stress; RNA, Transfer; outgrowth; RNA; Salt Stress; RNA-Seq data; Sequence Analysis, RNA
• Research Categories: Biology, General

Abstract

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 3end. tRNA Cys with correct CCA addition at the 3end 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 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.