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Arvizu Hernández I, Hernández Flores JL, Caballero Pérez J, Gutiérrez Sánchez H, Ramos López MÁ, Romero Gómez S, Cruz Hernández A, Saldaña Gutierrez C, Álvarez Hidalgo E, Jones GH, Campos Guillén J. Analysis of tRNA Cys processing under salt stress in Bacillus subtilis spore outgrowth using RNA sequencing data. F1000Res 2020; 9:501. [PMID: 33976872 PMCID: PMC8097732 DOI: 10.12688/f1000research.23780.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 11/20/2022] Open
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 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.
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Affiliation(s)
- Iván Arvizu Hernández
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - José Luis Hernández Flores
- Laboratorio de Bioseguridad y Análisis de Riesgo, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, 36824, Mexico
| | | | - Héctor Gutiérrez Sánchez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Miguel Ángel Ramos López
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Sergio Romero Gómez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Andrés Cruz Hernández
- Escuela de Agronomía, Universidad De La Salle Bajío, Campus Campestre, León, Guanajuato, 37150, Mexico
| | - Carlos Saldaña Gutierrez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - Erika Álvarez Hidalgo
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
| | - George H Jones
- Department of Biology, Emory University, Atlanta, Georgia, 30322, USA
| | - Juan Campos Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro, Qro., 76010, Mexico
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Campos Guillén J, Arvizu Gómez JL, Jones GH, Hernández Flores JL, Ramos López MA, Cruz Hernández A, Romero Gómez S. Analysis of tRNA Cys processing in the absence of CCAase in Bacillus subtilis. Braz J Microbiol 2019; 50:613-618. [PMID: 31041723 DOI: 10.1007/s42770-019-00075-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/08/2019] [Indexed: 11/30/2022] Open
Abstract
In Bacillus subtilis, the tRNACys lacks an encoded CCA 3' end. To gain insight into the role of CCAase and RNases in tRNACys processing, several mutant strains were generated. Northern blot and RT-PCR results suggest that enzymes other than CCAase can participate in CCA addition at the 3' end of the immature tRNACys.
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MESH Headings
- Bacillus subtilis/chemistry
- Bacillus subtilis/enzymology
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Nucleic Acid Conformation
- RNA Nucleotidyltransferases/deficiency
- RNA Nucleotidyltransferases/genetics
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Cys/chemistry
- RNA, Transfer, Cys/genetics
- RNA, Transfer, Cys/metabolism
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Affiliation(s)
- Juan Campos Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, 76010, Querétaro, QRO, Mexico.
| | - Jackeline Lizzeta Arvizu Gómez
- Secretaria de Investigación y Posgrado, Centro de Innovación y Transferencia de Tecnología (CENIT2), Universidad Autónoma de Nayarit, Tepic, Mexico
| | - George H Jones
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - José Luis Hernández Flores
- Laboratorio de Bioseguridad y Análisis de Riesgo, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, 36824, Irapuato, GTO, Mexico
| | - Miguel Angel Ramos López
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, 76010, Querétaro, QRO, Mexico
| | - Andrés Cruz Hernández
- Escuela de Agronomia, Universidad De La Salle Bajío Campus Campestre, León, GTO, Mexico
| | - Sergio Romero Gómez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, 76010, Querétaro, QRO, Mexico
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Critical Minireview: The Fate of tRNA Cys during Oxidative Stress in Bacillus subtilis. Biomolecules 2017; 7:biom7010006. [PMID: 28117687 PMCID: PMC5372718 DOI: 10.3390/biom7010006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 12/15/2022] Open
Abstract
Oxidative stress occurs when cells are exposed to elevated levels of reactive oxygen species that can damage biological molecules. One bacterial response to oxidative stress involves disulfide bond formation either between protein thiols or between protein thiols and low-molecular-weight (LMW) thiols. Bacillithiol was recently identified as a major low-molecular-weight thiol in Bacillus subtilis and related Firmicutes. Four genes (bshA, bshB1, bshB2, and bshC) are involved in bacillithiol biosynthesis. The bshA and bshB1 genes are part of a seven-gene operon (ypjD), which includes the essential gene cca, encoding CCA-tRNA nucleotidyltransferase. The inclusion of cca in the operon containing bacillithiol biosynthetic genes suggests that the integrity of the 3′ terminus of tRNAs may also be important in oxidative stress. The addition of the 3′ terminal CCA sequence by CCA-tRNA nucleotidyltransferase to give rise to a mature tRNA and functional molecules ready for aminoacylation plays an essential role during translation and expression of the genetic code. Any defects in these processes, such as the accumulation of shorter and defective tRNAs under oxidative stress, might exert a deleterious effect on cells. This review summarizes the physiological link between tRNACys regulation and oxidative stress in Bacillus.
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Abstract
tRNAs are fundamental components of translation and emerging evidence places them more centrally in various other cellular processes. However, rather than being uniformly conserved, tRNA abundance is instead highly variable and adaptable. The amount of tRNA genes greatly differs among species. Moreover, even within the same genome, tRNA abundance shapes the proteome in a tissue- and cell-specific manner and is dynamically regulated in response to stress. Here, we review approaches for identification and quantification of tRNAs and their functional integrity. We discuss the resolution of each method and highlight new approaches with cell-wide resolution based on deep-sequencing technologies.
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