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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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Evaluation of the presence of Paenibacillus larvae in commercial bee pollen using PCR amplification of the gene for tRNA Cys. Braz J Microbiol 2019; 50:471-480. [PMID: 30666531 DOI: 10.1007/s42770-019-00039-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/21/2018] [Indexed: 01/20/2023] Open
Abstract
American foulbrood (AFB) caused by Paenibacillus larvae is the most destructive honeybee bacterial disease and its dissemination via commercial bee pollen is an important mechanism for the spread of this bacterium. Because Mexico imports bee pollen from several countries, we developed a tRNACys-PCR strategy and complemented that strategy with MALDI-TOF MS and amplicon-16S rRNA gene analysis to evaluate the presence of P. larvae in pollen samples. P. larvae was not detected when the tRNACys-PCR approach was applied to spore-forming bacterial colonies obtained from three different locations and this result was validated by bacterial identification via MALDI-TOF MS. The genera identified in the latter analysis were Bacillus (fourteen species) and Paenibacillus (six) species. However, amplicon-16S rRNA gene analysis for taxonomic composition revealed a low presence of Paenibacillaceae with 0.3 to 16.2% of relative abundance in the commercial pollen samples analyzed. Within this family, P. larvae accounted for 0.01% of the bacterial species present in one sample. Our results indicate that the tRNACys-PCR, combined with other molecular tools, will be a useful approach for identifying P. larvae in pollen samples and will assist in controlling the spread of the pathogen.
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Dos Santos RF, Quendera AP, Boavida S, Seixas AF, Arraiano CM, Andrade JM. Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:101-155. [PMID: 30340785 DOI: 10.1016/bs.pmbts.2018.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Boavida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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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: 1.0] [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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Cruz Hernández A, Millan ES, de Jesús Romero Gómez S, Antonio Cervantes Chávez J, Garcia Martínez R, Pastrana Martínez X, Gómez JLA, Jones GH, Guillén JC. Exposure of Bacillus subtilis to mercury induces accumulation of shorter tRNA Cys species. Metallomics 2013; 5:398-403. [PMID: 23529473 DOI: 10.1039/c3mt20203h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA processing is an essential pathway in the regulation of genetic expression in the cell. In this work, Bacillus subtilis was used to understand the effects of mercury on the mechanism of tRNA metabolism. The CVAAS (cold vapor atomic absorption spectroscopy) method revealed that from the addition of HgCl2 (0.75 μg ml(-1)) during the bacterial exponential phase, ca. 48% of the added mercury was taken up by the cells. This led to an immediate reduction in the rate of cell division. During this response, we observed accumulation of species shorter than mature tRNA(Cys) over a 10 h period. We did not observe this accumulation for another five tRNAs analyzed. tRNA processing is largely dependent on RNase R and PNPase in B. subtilis. Thus, when the exonuclease PNPase was absent, we found that the shorter tRNA(Cys) species increased and mature tRNA(Cys) decreased after mercury addition, but this proportion changed during the time analyzed. However, in the absence of RNase R and PNPase the accumulation of the shorter tRNA(Cys) was more pronounced and the mature form was not recovered. In the single rnr mutant strain the shorter tRNA(Cys) was not observed. All together, we provide in vivo evidence that PNPase and RNase R are indispensable in controlling tRNA(Cys) quality in the presence of mercury.
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Moreira RN, Domingues S, Viegas SC, Amblar M, Arraiano CM. Synergies between RNA degradation and trans-translation in Streptococcus pneumoniae: cross regulation and co-transcription of RNase R and SmpB. BMC Microbiol 2012; 12:268. [PMID: 23167513 PMCID: PMC3534368 DOI: 10.1186/1471-2180-12-268] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ribonuclease R (RNase R) is an exoribonuclease that recognizes and degrades a wide range of RNA molecules. It is a stress-induced protein shown to be important for the establishment of virulence in several pathogenic bacteria. RNase R has also been implicated in the trans-translation process. Transfer-messenger RNA (tmRNA/SsrA RNA) and SmpB are the main effectors of trans-translation, an RNA and protein quality control system that resolves challenges associated with stalled ribosomes on non-stop mRNAs. Trans-translation has also been associated with deficiencies in stress-response mechanisms and pathogenicity. RESULTS In this work we study the expression of RNase R in the human pathogen Streptococcus pneumoniae and analyse the interplay of this enzyme with the main components of the trans-translation machinery (SmpB and tmRNA/SsrA). We show that RNase R is induced after a 37°C to 15°C temperature downshift and that its levels are dependent on SmpB. On the other hand, our results revealed a strong accumulation of the smpB transcript in the absence of RNase R at 15°C. Transcriptional analysis of the S. pneumoniae rnr gene demonstrated that it is co-transcribed with the flanking genes, secG and smpB. Transcription of these genes is driven from a promoter upstream of secG and the transcript is processed to yield mature independent mRNAs. This genetic organization seems to be a common feature of Gram positive bacteria, and the biological significance of this gene cluster is further discussed. CONCLUSIONS This study unravels an additional contribution of RNase R to the trans-translation system by demonstrating that smpB is regulated by this exoribonuclease. RNase R in turn, is shown to be under the control of SmpB. These proteins are therefore mutually dependent and cross-regulated. The data presented here shed light on the interactions between RNase R, trans-translation and cold-shock response in an important human pathogen.
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Affiliation(s)
- Ricardo N Moreira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
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Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, Silva IJ, Viegas SC. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 2010; 34:883-923. [PMID: 20659169 DOI: 10.1111/j.1574-6976.2010.00242.x] [Citation(s) in RCA: 263] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The continuous degradation and synthesis of prokaryotic mRNAs not only give rise to the metabolic changes that are required as cells grow and divide but also rapid adaptation to new environmental conditions. In bacteria, RNAs can be degraded by mechanisms that act independently, but in parallel, and that target different sites with different efficiencies. The accessibility of sites for degradation depends on several factors, including RNA higher-order structure, protection by translating ribosomes and polyadenylation status. Furthermore, RNA degradation mechanisms have shown to be determinant for the post-transcriptional control of gene expression. RNases mediate the processing, decay and quality control of RNA. RNases can be divided into endonucleases that cleave the RNA internally or exonucleases that cleave the RNA from one of the extremities. Just in Escherichia coli there are >20 different RNases. RNase E is a single-strand-specific endonuclease critical for mRNA decay in E. coli. The enzyme interacts with the exonuclease polynucleotide phosphorylase (PNPase), enolase and RNA helicase B (RhlB) to form the degradosome. However, in Bacillus subtilis, this enzyme is absent, but it has other main endonucleases such as RNase J1 and RNase III. RNase III cleaves double-stranded RNA and family members are involved in RNA interference in eukaryotes. RNase II family members are ubiquitous exonucleases, and in eukaryotes, they can act as the catalytic subunit of the exosome. RNases act in different pathways to execute the maturation of rRNAs and tRNAs, and intervene in the decay of many different mRNAs and small noncoding RNAs. In general, RNases act as a global regulatory network extremely important for the regulation of RNA levels.
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Affiliation(s)
- Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.
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