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Journal articles on the topic 'RNase J1'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

Redko, Yulia, and Ciarán Condon. "Maturation of 23S rRNA in Bacillus subtilis in the Absence of Mini-III." Journal of Bacteriology 192, no. 1 (2009): 356–59. http://dx.doi.org/10.1128/jb.01096-09.

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ABSTRACT 23S rRNA maturation in Bacillus subtilis is catalyzed by the recently characterized enzyme Mini-RNase-III. Mini-III is dispensable, however, and 23S rRNA is matured by other ribonucleases in strains lacking this enzyme. Here we show that these RNases are the 5′-to-3′ exoribonuclease RNase J1 and the 3′-to-5′ exoribonucleases, principally RNase PH and YhaM.

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2

Bonnin, Rémy A., and Philippe Bouloc. "RNA Degradation inStaphylococcus aureus: Diversity of Ribonucleases and Their Impact." International Journal of Genomics 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/395753.

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The regulation of RNA decay is now widely recognized as having a central role in bacterial adaption to environmental stress. Here we present an overview on the diversity of ribonucleases (RNases) and their impact at the posttranscriptional level in the human pathogenStaphylococcus aureus. RNases in prokaryotes have been mainly studied in the two model organismsEscherichia coliandBacillus subtilis. Based on identified RNases in these two models, putative orthologs have been identified inS. aureus. The main staphylococcal RNases involved in the processing and degradation of the bulk RNA are (i)

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3

Raj, Rishi, Savitha Nadig, Twinkal Patel, and Balasubramanian Gopal. "Structural and biochemical characteristics of two Staphylococcus epidermidis RNase J paralogs RNase J1 and RNase J2." Journal of Biological Chemistry 295, no. 49 (2020): 16863–76. http://dx.doi.org/10.1074/jbc.ra120.014876.

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RNase J enzymes are metallohydrolases that are involved in RNA maturation and RNA recycling, govern gene expression in bacteria, and catalyze both exonuclease and endonuclease activity. The catalytic activity of RNase J is regulated by multiple mechanisms which include oligomerization, conformational changes to aid substrate recognition, and the metal cofactor at the active site. However, little is known of how RNase J paralogs differ in expression and activity. Here we describe structural and biochemical features of two Staphylococcus epidermidis RNase J paralogs, RNase J1 and RNase J2. RNase

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4

Ul Haq, Inam, and Sabine Brantl. "Moonlighting in Bacillus Subtilis: The Small Proteins SR1P and SR7P Regulate the Moonlighting Activity of Glyceraldehyde 3-Phosphate Dehydrogenase A (GapA) and Enolase in RNA Degradation." Microorganisms 9, no. 5 (2021): 1046. http://dx.doi.org/10.3390/microorganisms9051046.

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Moonlighting proteins are proteins with more than one function. During the past 25 years, they have been found to be rather widespread in bacteria. In Bacillus subtilis, moonlighting has been disclosed to occur via DNA, protein or RNA binding or protein phosphorylation. In addition, two metabolic enzymes, enolase and phosphofructokinase, were localized in the degradosome-like network (DLN) where they were thought to be scaffolding components. The DLN comprises the major endoribonuclease RNase Y, 3′-5′ exoribonuclease PnpA, endo/5′-3′ exoribonucleases J1/J2 and helicase CshA. We have ascertaine

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5

Yao, Shiyi, Jamie Richards, Joel G. Belasco, and David H. Bechhofer. "Decay of a Model mRNA in Bacillus subtilis by a Combination of RNase J1 5′ Exonuclease and RNase Y Endonuclease Activities." Journal of Bacteriology 193, no. 22 (2011): 6384–86. http://dx.doi.org/10.1128/jb.05939-11.

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The involvement of the recently characterized 5′ exonuclease activity of RNase J1 and endonuclease activity of RNase Y in the turnover of ΔermCmRNA inBacillus subtiliswas investigated. Evidence is presented that both of these activities determine the half-life of ΔermCmRNA.

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6

Yao, Shiyi, and David H. Bechhofer. "Initiation of Decay of Bacillus subtilis rpsO mRNA by Endoribonuclease RNase Y." Journal of Bacteriology 192, no. 13 (2010): 3279–86. http://dx.doi.org/10.1128/jb.00230-10.

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ABSTRACT rpsO mRNA, a small monocistronic mRNA that encodes ribosomal protein S15, was used to study aspects of mRNA decay initiation in Bacillus subtilis. Decay of rpsO mRNA in a panel of 3′-to-5′ exoribonuclease mutants was analyzed using a 5′-proximal oligonucleotide probe and a series of oligonucleotide probes that were complementary to overlapping sequences starting at the 3′ end. The results provided strong evidence that endonuclease cleavage in the body of the message, rather than degradation from the native 3′ end, is the rate-determining step for mRNA decay. Subsequent to endonuclease

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7

Korobeinikova, Anna, Soumaya Laalami, Clément Berthy, and Harald Putzer. "RNase Y Autoregulates Its Synthesis in Bacillus subtilis." Microorganisms 11, no. 6 (2023): 1374. http://dx.doi.org/10.3390/microorganisms11061374.

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The instability of messenger RNA is crucial to the control of gene expression. In Bacillus subtilis, RNase Y is the major decay-initiating endoribonuclease. Here, we show how this key enzyme regulates its own synthesis by modulating the longevity of its mRNA. Autoregulation is achieved through cleavages in two regions of the rny (RNase Y) transcript: (i) within the first ~100 nucleotides of the open reading frame, immediately inactivating the mRNA for further rounds of translation; (ii) cleavages in the rny 5′ UTR, primarily within the 5′-terminal 50 nucleotides, creating entry sites for the 5

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8

Deikus, Gintaras, and David H. Bechhofer. "5′ End-independent RNase J1 Endonuclease Cleavage ofBacillus subtilisModel RNA." Journal of Biological Chemistry 286, no. 40 (2011): 34932–40. http://dx.doi.org/10.1074/jbc.m111.287409.

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9

Raj, Rishi, Sharmistha Mitra, and Balasubramanian Gopal. "Characterization of Staphylococcus epidermidis Polynucleotide phosphorylase and its interactions with ribonucleases RNase J1 and RNase J2." Biochemical and Biophysical Research Communications 495, no. 2 (2018): 2078–84. http://dx.doi.org/10.1016/j.bbrc.2017.12.056.

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10

Daou-Chabo, R., and C. Condon. "RNase J1 endonuclease activity as a probe of RNA secondary structure." RNA 15, no. 7 (2009): 1417–25. http://dx.doi.org/10.1261/rna.1574309.

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11

Yao, Shiyi, Joshua B. Blaustein, and David H. Bechhofer. "Erythromycin-induced ribosome stalling and RNase J1-mediated mRNA processing inBacillus subtilis." Molecular Microbiology 69, no. 6 (2008): 1439–49. http://dx.doi.org/10.1111/j.1365-2958.2008.06370.x.

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12

Yao, S., J. S. Sharp, and D. H. Bechhofer. "Bacillus subtilis RNase J1 endonuclease and 5' exonuclease activities in the turnover of ermC mRNA." RNA 15, no. 12 (2009): 2331–39. http://dx.doi.org/10.1261/rna.1749109.

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13

Daou-Chabo, Roula, Nathalie Mathy, Lionel Bénard, and Ciarán Condon. "Ribosomes initiating translation of thehbsmRNA protect it from 5′-to-3′ exoribonucleolytic degradation by RNase J1." Molecular Microbiology 71, no. 6 (2009): 1538–50. http://dx.doi.org/10.1111/j.1365-2958.2009.06620.x.

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14

Even, S. "Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E." Nucleic Acids Research 33, no. 7 (2005): 2141–52. http://dx.doi.org/10.1093/nar/gki505.

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15

Britton, Robert A., Tingyi Wen, Laura Schaefer, et al. "Maturation of the 5' end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1." Molecular Microbiology 63, no. 1 (2007): 127–38. http://dx.doi.org/10.1111/j.1365-2958.2006.05499.x.

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16

Newman, Joseph A., Lorraine Hewitt, Cecilia Rodrigues, Alexandra Solovyova, Colin R. Harwood, and Richard J. Lewis. "Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained by Crystal Structure Analysis of RNase J1." Structure 19, no. 9 (2011): 1241–51. http://dx.doi.org/10.1016/j.str.2011.06.017.

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17

Yao, Shiyi, and David H. Bechhofer. "Processing and Stability of Inducibly Expressed rpsO mRNA Derivatives in Bacillus subtilis." Journal of Bacteriology 191, no. 18 (2009): 5680–89. http://dx.doi.org/10.1128/jb.00740-09.

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ABSTRACT The Bacillus subtilis rpsO gene specifies a small (388-nucleotide), monocistronic mRNA that encodes ribosomal protein S15. We showed earlier that rpsO mRNA decay intermediates accumulated to a high level in a strain lacking polynucleotide phosphorylase. Here, we used inducibly expressed derivatives of rpsO, encoding smaller RNAs that had the complex 5′ region deleted, to study aspects of mRNA processing in B. subtilis. An IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible rpsO transcript that contained lac sequences at the 5′ end, called lac-rpsO RNA, was shown to undergo processing

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18

Figaro, S., S. Durand, L. Gilet, N. Cayet, M. Sachse, and C. Condon. "Bacillus subtilis Mutants with Knockouts of the Genes Encoding Ribonucleases RNase Y and RNase J1 Are Viable, with Major Defects in Cell Morphology, Sporulation, and Competence." Journal of Bacteriology 195, no. 10 (2013): 2340–48. http://dx.doi.org/10.1128/jb.00164-13.

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19

Durand, Sylvain, Laetitia Gilet, Philippe Bessières, Pierre Nicolas, and Ciarán Condon. "Three Essential Ribonucleases—RNase Y, J1, and III—Control the Abundance of a Majority of Bacillus subtilis mRNAs." PLoS Genetics 8, no. 3 (2012): e1002520. http://dx.doi.org/10.1371/journal.pgen.1002520.

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20

Mathy, Nathalie, Lionel Bénard, Olivier Pellegrini, Roula Daou, Tingyi Wen, and Ciarán Condon. "5′-to-3′ Exoribonuclease Activity in Bacteria: Role of RNase J1 in rRNA Maturation and 5′ Stability of mRNA." Cell 129, no. 4 (2007): 681–92. http://dx.doi.org/10.1016/j.cell.2007.02.051.

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21

Hausmann, Stéphane, Vanessa Andrade Guimarães, Dominique Garcin, Natalia Baumann, Patrick Linder, and Peter Redder. "Both exo- and endo-nucleolytic activities of RNase J1 from Staphylococcus aureus are manganese dependent and active on triphosphorylated 5′-ends." RNA Biology 14, no. 10 (2017): 1431–43. http://dx.doi.org/10.1080/15476286.2017.1300223.

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22

Chen, Xi, Justin Merritt, Fengxia Qi, Sharukh Khajotia, and Nan Liu. "RNases J1 and J2 are critical pleiotropic regulators in Streptococcus mutans." Microbiology 161, no. 4 (2015): 797–806. http://dx.doi.org/10.1099/mic.0.000039.

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23

Jamalli, A., A. Hebert, L. Zig, and H. Putzer. "Control of Expression of the RNases J1 and J2 in Bacillus subtilis." Journal of Bacteriology 196, no. 2 (2013): 318–24. http://dx.doi.org/10.1128/jb.01053-13.

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24

Mäder, Ulrike, Léna Zig, Julia Kretschmer, Georg Homuth, and Harald Putzer. "mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale." Molecular Microbiology 70, no. 1 (2008): 183–96. http://dx.doi.org/10.1111/j.1365-2958.2008.06400.x.

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25

Jahn, Natalie, and Sabine Brantl. "Heat-shock-induced refolding entails rapid degradation of bsrG toxin mRNA by RNases Y and J1." Microbiology 162, no. 3 (2016): 590–99. http://dx.doi.org/10.1099/mic.0.000247.

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26

Bugrysheva, Julia V., Barbara J. Froehlich, Jeffrey A. Freiberg, and June R. Scott. "The Histone-Like Protein Hlp Is Essential for Growth of Streptococcus pyogenes: Comparison of Genetic Approaches To Study Essential Genes." Applied and Environmental Microbiology 77, no. 13 (2011): 4422–28. http://dx.doi.org/10.1128/aem.00554-11.

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ABSTRACTSelection of possible targets for vaccine and drug development requires an understanding of the physiology of bacterial pathogens, for which the ability to manipulate expression of essential genes is critical. ForStreptococcus pyogenes(the group A streptococcus [GAS]), an important human pathogen, the lack of genetic tools for such studies has seriously hampered research. To address this problem, we characterized variants of the inducible Ptetcassette, in both sense and antisense contexts, as tools to regulate transcription from GAS genes. We found that although the three-operator Ptet

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27

Wiegard, Jana Christin, Katrin Damm, Marcus Lechner, et al. "Processing and decay of 6S-1 and 6S-2 RNAs in Bacillus subtilis." RNA, June 27, 2023, rna.079666.123. http://dx.doi.org/10.1261/rna.079666.123.

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Non-coding 6S RNAs regulate transcription by binding to the active site of bacterial RNA polymerase holoenzymes. Processing and decay of 6S-1 and 6S-2 RNA were investigated in Bacillus subtilis by northern blot and RNA-seq analyses using different RNase knockout strains, as well as by in vitro processing assays. For both 6S RNA paralogs, we identified a key – but mechanistically different – role of RNase J1. RNase J1 catalyzes 5'-end maturation of 6S-1 RNA, yet relatively inefficient and possibly via the enzyme's 'sliding endonuclease' activity. 5'-end maturation has no detectable effect on 6S

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28

Oviedo-Bocanegra, Luis M., Rebecca Hinrichs, Daniel Andreas Orlando Rotter, Simon Dersch, and Peter L. Graumann. "Single molecule/particle tracking analysis program SMTracker 2.0 reveals different dynamics of proteins within the RNA degradosome complex in Bacillus subtilis." Nucleic Acids Research, August 20, 2021. http://dx.doi.org/10.1093/nar/gkab696.

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Abstract Single-molecule (particle) tracking is a powerful method to study dynamic processes in cells at highest possible spatial and temporal resolution. We have developed SMTracker, a graphical user interface for automatic quantifying, visualizing and managing of data. Version 2.0 determines distributions of positional displacements in x- and y-direction using multi-state diffusion models, discriminates between Brownian, sub- or superdiffusive behaviour, and locates slow or fast diffusing populations in a standardized cell. Using SMTracker, we show that the Bacillus subtilis RNA degradosome

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29

Guimarães, Vanessa Andrade, Alexandre Le Scornet, Vanessa Khemici, et al. "RNase J1 and J2 Are Host-Encoded Factors for Plasmid Replication." Frontiers in Microbiology 12 (May 4, 2021). http://dx.doi.org/10.3389/fmicb.2021.586886.

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Plasmids need to ensure their transmission to both daughter-cells when their host divides, but should at the same time avoid overtaxing their hosts by directing excessive host-resources toward production of plasmid factors. Naturally occurring plasmids have therefore evolved regulatory mechanisms to restrict their copy-number in response to the volume of the cytoplasm. In many plasmid families, copy-number control is mediated by a small plasmid-specified RNA, which is continuously produced and rapidly degraded, to ensure that its concentration is proportional to the current plasmid copy-number

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30

Ul Haq, Inam, Sabine Brantl, and Peter Müller. "A new role for SR1 from Bacillus subtilis: regulation of sporulation by inhibition of kinA translation." Nucleic Acids Research, September 3, 2021. http://dx.doi.org/10.1093/nar/gkab747.

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Abstract SR1 is a dual-function sRNA from Bacillus subtilis. It inhibits translation initiation of ahrC mRNA encoding the transcription activator of the arginine catabolic operons. Base-pairing is promoted by the RNA chaperone CsrA, which induces a slight structural change in the ahrC mRNA to facilitate SR1 binding. Additionally, SR1 encodes the small protein SR1P that interacts with glyceraldehyde-3P dehydrogenase A to promote binding to RNase J1 and enhancing J1 activity. Here, we describe a new target of SR1, kinA mRNA encoding the major histidine kinase of the sporulation phosphorelay. SR1

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31

Burke, Thomas P., and Daniel A. Portnoy. "SpoVG Is a Conserved RNA-Binding Protein That RegulatesListeria monocytogenesLysozyme Resistance, Virulence, and Swarming Motility." mBio 7, no. 2 (2016). http://dx.doi.org/10.1128/mbio.00240-16.

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ABSTRACTIn this study, we sought to characterize the targets of the abundantListeria monocytogenesnoncoding RNA Rli31, which is required forL. monocytogeneslysozyme resistance and pathogenesis. Whole-genome sequencing of lysozyme-resistant suppressor strains identified loss-of-expression mutations in the promoter ofspoVG, and deletion ofspoVGrescued lysozyme sensitivity and attenuationin vivoof therli31mutant. SpoVG was demonstrated to be an RNA-binding protein that interacted with Rli31in vitro.The relationship between Rli31 and SpoVG is multifaceted, as both thespoVG-encoded protein and thes

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32

Durand, Sylvain, Frédérique Braun, Anne-Catherine Helfer, Pascale Romby, and Ciarán Condon. "sRNA-mediated activation of gene expression by inhibition of 5'-3’ exonucleolytic mRNA degradation." eLife 6 (April 24, 2017). http://dx.doi.org/10.7554/elife.23602.

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Post-transcriptional control by small regulatory RNA (sRNA) is critical for rapid adaptive processes. sRNAs can directly modulate mRNA degradation in Proteobacteria without interfering with translation. However, Firmicutes have a fundamentally different set of ribonucleases for mRNA degradation and whether sRNAs can regulate the activity of these enzymes is an open question. We show that Bacillus subtilis RoxS, a major trans-acting sRNA shared with Staphylococus aureus, prevents degradation of the yflS mRNA, encoding a malate transporter. In the presence of malate, RoxS transiently escapes fro

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33

Wang, Hongzhou, Jennifer H. Simpson, Madison E. Kotra, et al. "Epitranscriptomic profile of Lactobacillus agilis and its adaptation to growth on inulin." BMC Research Notes 14, no. 1 (2021). http://dx.doi.org/10.1186/s13104-021-05563-2.

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Abstract Objective Ribonucleic acids (RNA) are involved in many cellular functions. In general, RNA is made up by only four different ribonucleotides. The modifications of RNA (epitranscriptome) can greatly enhance the structural diversity of RNA, which in turn support some of the RNA functions. To determine whether the epitranscriptome of a specific probiotic is associated with its adaptation to the source of energy, Lactobacillus agilis (YZ050) was selected as a model and its epitranscriptome was profiled and compared by using mass spectrometry. Results The L. agilis epitranscriptome (minus

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34

Lavoie, Olivier, William Desrosiers, Julie Plamondon, Natalie Michael, and Alexandre Caron. "Identification and characterization of a novel population of hypothalamic neurons sensitive to leptin and GLP-1." Physiology 38, S1 (2023). http://dx.doi.org/10.1152/physiol.2023.38.s1.5729686.

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The arcuate nucleus of the hypothalamus (ARC) is considered a major site for the integration of metabolic signals and the regulation of energy balance. In the ARC, ‘catabolic’ pro-opiomelanocortin (POMC) and ‘anabolic’ agouti-related peptide (AgRP)-expressing neurons are widely recognized for their role in the regulation of energy homeostasis. Leptin and glucagon-like peptide 1 (GLP-1) are two important hormonal signals of the energy state that can mediate some of their effects through POMC and AgRP neurons. However, recent work suggests that unidentified GABAergic neurons of the ARC may also

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