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Journal articles on the topic 'RNase J1'

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Author: Grafiati

Published: 6 September 2023

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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 (October 30, 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

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 (September 29, 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 J1 is a homodimer with exonuclease activity aided by two metal cofactors at the active site. RNase J2, on the other hand, has endonuclease activity and one metal ion at the active site and is predominantly a monomer. We note that the expression levels of these enzymes vary across Staphylococcal strains. Together, these observations suggest that multiple interacting RNase J paralogs could provide a strategy for functional improvisation utilizing differences in intracellular concentration, quaternary structure, and distinct active site architecture despite overall structural similarity.

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3

Korobeinikova, Anna, Soumaya Laalami, Clément Berthy, and Harald Putzer. "RNase Y Autoregulates Its Synthesis in Bacillus subtilis." Microorganisms 11, no. 6 (May 24, 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′ exonuclease J1 whose progression is blocked around position −15 of the rny mRNA, potentially by initiating ribosomes. This links the functional inactivation of the transcript by RNase J1 to translation efficiency, depending on the ribosome occupancy at the translation initiation site. By these mechanisms, RNase Y can initiate degradation of its own mRNA when the enzyme is not occupied with degradation of other RNAs and thus prevent its overexpression beyond the needs of RNA metabolism.

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4

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) endonucleases RNase III and RNase Y and (ii) exonucleases RNase J1/J2 and PNPase, having 5′ to 3′ and 3′ to 5′ activities, respectively. The diversity and potential roles of each RNase and of Hfq and RppH are discussed in the context of recent studies, some of which are based on next-generation sequencing technology.

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5

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 (May 12, 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 ascertained that the metabolic enzyme GapA is an additional component of the DLN. In addition, we identified two small proteins that bind scaffolding components of the degradosome: SR1P encoded by the dual-function sRNA SR1 binds GapA, promotes the GapA-RNase J1 interaction and increases the RNase J1 activity. SR7P encoded by the dual-function antisense RNA SR7 binds to enolase thereby enhancing the enzymatic activity of enolase bound RNase Y. We discuss the role of small proteins in modulating the activity of two moonlighting proteins.

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6

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 (September 9, 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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7

Yao, Shiyi, and David H. Bechhofer. "Initiation of Decay of Bacillus subtilis rpsO mRNA by Endoribonuclease RNase Y." Journal of Bacteriology 192, no. 13 (April 23, 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 cleavage, the upstream products were degraded by polynucleotide phosphorylase (PNPase), and the downstream products were degraded by the 5′ exonuclease activity of RNase J1. The rpsO mRNA half-life was unchanged in a strain that had decreased RNase J1 activity and no RNase J2 activity, but it was 2.3-fold higher in a strain with decreased activity of RNase Y, a recently discovered RNase of B. subtilis encoded by the ymdA gene. Accumulation of full-length rpsO mRNA and its decay intermediates was analyzed using a construct in which the rpsO transcription unit was under control of a bacitracin-inducible promoter. The results were consistent with RNase Y-mediated initiation of decay. This is the first report of a specific mRNA whose stability is determined by RNase Y.

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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 (August 23, 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 (January 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 (May 20, 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 (September 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 (October 22, 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 (March 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 (April 11, 2005): 2141–52. http://dx.doi.org/10.1093/nar/gki505.

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15

Yao, Shiyi, and David H. Bechhofer. "Processing and Stability of Inducibly Expressed rpsO mRNA Derivatives in Bacillus subtilis." Journal of Bacteriology 191, no. 18 (July 24, 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 to result in an RNA that was 24 nucleotides shorter than full length. Such processing was dependent on the presence of an accessible 5′ terminus; a lac-rpsO RNA that contained a strong stem-loop at the 5′ end was not processed and was extremely stable. Interestingly, this stability depended also on ribosome binding to a nearby Shine-Dalgarno sequence but was independent of downstream translation. Either RNase J1 or RNase J2 was capable of processing lac-rpsO RNA, demonstrating for the first time a particular in vivo processing event that could be catalyzed by both enzymes. Decay intermediates were detected in the pnpA strain only for a lac-rpsO RNA that was untranslated. Analysis of processing of an untranslated lac-rpsO RNA in the pnpA strain shortly after induction of transcription suggested that endonuclease cleavage at 3′-proximal sites was an early step in turnover of mRNA.

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16

Britton, Robert A., Tingyi Wen, Laura Schaefer, Olivier Pellegrini, William C. Uicker, Nathalie Mathy, Crystal Tobin, Roula Daou, Jacek Szyk, and Ciarán Condon. "Maturation of the 5' end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1." Molecular Microbiology 63, no. 1 (January 2007): 127–38. http://dx.doi.org/10.1111/j.1365-2958.2006.05499.x.

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17

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 (September 2011): 1241–51. http://dx.doi.org/10.1016/j.str.2011.06.017.

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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 (March 15, 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 (March 8, 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 (May 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 (April 7, 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 (April 1, 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 (November 1, 2013): 318–24. http://dx.doi.org/10.1128/jb.01053-13.

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24

Li, Chaoqun, Xiaojia Zhao, Xiaomin Zhu, Pengtao Xie, and Guangju Chen. "Structural Studies of the 3′,3′-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation." International Journal of Molecular Sciences 19, no. 11 (November 9, 2018): 3527. http://dx.doi.org/10.3390/ijms19113527.

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Riboswtich RNAs can control gene expression through the structural change induced by the corresponding small-molecule ligands. Molecular dynamics simulations and free energy calculations on the aptamer domain of the 3′,3′-cGAMP riboswitch in the ligand-free, cognate-bound and noncognate-bound states were performed to investigate the structural features of the 3′,3′-cGAMP riboswitch induced by the 3′,3′-cGAMP ligand and the specificity of ligand recognition. The results revealed that the aptamer of the 3′,3′-cGAMP riboswitch in the ligand-free state has a smaller binding pocket and a relatively compact structure versus that in the 3′,3′-cGAMP-bound state. The binding of the 3′,3′-cGAMP molecule to the 3′,3′-cGAMP riboswitch induces the rotation of P1 helix through the allosteric communication from the binding sites pocket containing the J1/2, J1/3 and J2/3 junction to the P1 helix. Simultaneously, these simulations also revealed that the preferential binding of the 3′,3′-cGAMP riboswitch to its cognate ligand, 3′,3′-cGAMP, over its noncognate ligand, c-di-GMP and c-di-AMP. The J1/2 junction in the 3′,3′-cGAMP riboswitch contributing to the specificity of ligand recognition have also been found.

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25

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 (August 18, 2008): 183–96. http://dx.doi.org/10.1111/j.1365-2958.2008.06400.x.

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26

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 (March 1, 2016): 590–99. http://dx.doi.org/10.1099/mic.0.000247.

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27

Ando, Tsuyoshi, Takeshi Nabeshima, Shingo Inoue, Mya Myat Ngwe Tun, Miho Obata, Weiyin Hu, Hiroshi Shimoda, et al. "Severe Fever with Thrombocytopenia Syndrome in Cats and Its Prevalence among Veterinarian Staff Members in Nagasaki, Japan." Viruses 13, no. 6 (June 14, 2021): 1142. http://dx.doi.org/10.3390/v13061142.

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In this study, we investigated severe fever with thrombocytopenia syndrome (SFTS) virus (SFTSV) infection in cats in Nagasaki, Japan. In total, 44 of 133 (33.1%) cats with suspected SFTS were confirmed to be infected with SFTSV. Phylogenetic analyses of SFTSV isolates from cats indicated that the main genotype in Nagasaki was J1 and that unique reassortant strains with J2 (S segment) and unclassified genotypes (M and L segments) were also present. There were no significant differences in virus growth in cell cultures or fatality in SFTSV-infected mice between the SFTSV strains that were isolated from recovered and fatal cat cases. Remarkably, SFTSV RNAs were detected in the swabs from cats, indicating that the body fluids contain SFTSV. To evaluate the risk of SFTSV infection when providing animal care, we further examined the seroprevalence of SFTSV infection in veterinarian staff members; 3 of 71 (4.2%) were seropositive for SFTSV-specific antibodies. Our results provide useful information on the possibility of using cats as sentinel animals and raised concerns of the zoonotic risk of catching SFTSV from animals.

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28

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 (April 29, 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 Ptetconstruct [Ptet(O)3] had low uninduced expression, its induction level was low, while the two-operator construct [Ptet(O)2] was inducible to a high level but showed significant constitutive expression. Use of Ptet(O)3in the chromosome allowed us to demonstrate previously that RNases J1 and J2 are required for growth of GAS. Here we report that the uninduced level from the chromosomally inserted Ptet(O)2construct was too high for us to observe differential growth. For the highly expressed histone-like protein (Hlp) of GAS, neither chromosomal insertion of Ptet(O)2or Ptet(O)3nor their use on a high-copy-number plasmid to produce antisense RNA specific tohlpresulted in adequate differential expression. However, by replacing the ribosome binding site ofhlpwith an engineered riboswitch to control translation of Hlp, we demonstrated for the first time that this protein is essential for GAS growth.

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29

Wiegard, Jana Christin, Katrin Damm, Marcus Lechner, Clemens Thölken, Saravuth Ngo, Harald Putzer, and Roland K. Hartmann. "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-1 RNA function, but rather regulates its decay: the generated 5’-monophosphate on matured 6S-1 RNA propels endonucleolytic cleavage in its apical loop region. The major 6S-2 RNA degradation pathway is initiated by endonucleolytic cleavage in the 5'-central bubble to trigger 5’-to-3’-exoribonucleolytic degradation of the downstream fragment by RNase J1. The four 3'-exonucleases of B. subtilis – RNase R, PNPase, YhaM and particularly RNase PH – are involved in 3'-end trimming of both 6S RNAs, degradation of 6S-1 RNA fragments, and decay of abortive transcripts (so-called product RNAs, ~14 nt in length) synthesized on 6S-1 RNA during outgrowth from stationary phase. In the case of the growth-retarded RNase Y deletion strain, we were unable to infer a specific role of RNase Y in 6S RNA decay. Yet, a participation of RNase Y in 6S RNA decay still remains possible, as evidence for such a function may have been obscured by overlapping substrate specificities of RNase Y, RNase J1 and RNase J2.

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30

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 consists of a highly dynamic complex of RNase Y and binding partners. We found similar changes in molecule dynamics for RNase Y, CshA, PNPase and enolase, but not for phosphofructokinase, RNase J1 and J2, to inhibition of transcription. However, the absence of PfkA or of RNase J2 affected molecule dynamics of RNase Y-mVenus, indicating that these two proteins are indeed part of the degradosome. Molecule counting suggests that RNase Y is present as a dimer in cells, at an average copy number of about 500, of which 46% are present in a slow-diffusive state and thus likely engaged within degradosomes. Thus, RNase Y, CshA, PNPase and enolase likely play central roles, and RNase J1, J2 and PfkA more peripheral roles, in degradosome architecture.

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31

Guimarães, Vanessa Andrade, Alexandre Le Scornet, Vanessa Khemici, Stéphane Hausmann, Joshua Armitano, Julien Prados, Ambre Jousselin, Caroline Manzano, Patrick Linder, and Peter Redder. "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. We show here that pSA564 from the RepA_N-family is regulated by a small antisense RNA (RNA1), which, when over-expressed in trans, blocks plasmid replication and cures the bacterial host. The 5′ untranslated region (5′UTR) of the plasmid replication initiation gene (repA) potentially forms two mutually exclusive secondary structures, ON and OFF, where the latter both sequesters the repA ribosome binding site and acts as a rho-independent transcriptional terminator. Duplex formation between RNA1 and the 5′UTR shifts the equilibrium to favor the putative OFF-structure, enabling a single small RNA to down-regulate repA expression at both transcriptional and translational levels. We further examine which sequence elements on the antisense RNA and on its 5′UTR target are needed for this regulation. Finally, we identify the host-encoded exoribonucleases RNase J1 and J2 as the enzymes responsible for rapidly degrading the replication-inhibiting section of RNA1. This region accumulates and blocks RepA expression in the absence of either RNase J1 or J2, which are therefore essential host factors for pSA564 replication in Staphylococcus aureus.

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32

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 and kinA mRNA share 7 complementary regions. Base-pairing between SR1 and kinA mRNA decreases kinA translation without affecting kinA mRNA stability and represses transcription of the KinA/Spo0A downstream targets spoIIE, spoIIGA and cotA. The initial interaction between SR1 and kinA mRNA occurs 10 nt downstream of the kinA start codon and is decisive for inhibition. The sr1 encoded peptide SR1P is dispensable for kinA regulation. Deletion of sr1 accelerates sporulation resulting in low quality spores with reduced stress resistance and altered coat protein composition which can be compensated by sr1 overexpression. Neither CsrA nor Hfq influence sporulation or spore properties.

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33

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 (April 5, 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 thespoVG5′-untranslated region interacted with Rli31. In addition, we observed thatspoVG-deficient bacteria were nonmotile in soft agar and suppressor mutations that restored swarming motility were identified in the gene encoding a major RNase in Gram-positive bacteria, RNase J1. Collectively, these findings suggest that SpoVG is similar to global posttranscriptional regulators, a class of RNA-binding proteins that interact with noncoding RNA, regulate genes in concert with RNases, and control pleiotropic aspects of bacterial physiology.IMPORTANCEspoVGis widely conserved among bacteria; however, the function of this gene has remained unclear since its initial characterization in 1977. Mutation ofspoVGimpacts various phenotypes in Gram-positive bacteria, including methicillin resistance, capsule formation, and enzyme secretion inStaphylococcus aureusand also asymmetric cell division, hemolysin production, and sporulation inBacillus subtilis. Here, we demonstrate thatspoVGmutant strains ofListeria monocytogenesare hyper-lysozyme resistant, hypervirulent, nonmotile, and misregulate genes controlling carbon metabolism. Furthermore, we demonstrate that SpoVG is an RNA-binding protein. These findings suggest that SpoVG has a role inL. monocytogenes, and perhaps in other bacteria, as a global gene regulator. Posttranscriptional gene regulators help bacteria adapt to various environments and coordinate differing aspects of bacterial physiology. SpoVG may help the organism coordinate environmental growth and virulence to survive as a facultative pathogen.

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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 from repression by the NADH-sensitive transcription factor Rex and binds to the extreme 5’-end of yflS mRNA. This impairs the 5’-3’ exoribonuclease activity of RNase J1, increasing the half-life of the primary transcript and concomitantly enhancing ribosome binding to increase expression of the transporter. Globally, the different targets regulated by RoxS suggest that it helps readjust the cellular NAD+/NADH balance when perturbed by different stimuli.

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Wang, Hongzhou, Jennifer H. Simpson, Madison E. Kotra, Yuanting Zhu, Saumya Wickramasinghe, David A. Mills, and Norman H. L. Chiu. "Epitranscriptomic profile of Lactobacillus agilis and its adaptation to growth on inulin." BMC Research Notes 14, no. 1 (April 21, 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 rRNA modifications) consists of 17 different RNA modifications. By capturing the L. agilis cells during exponential growth, reproducible profiling was achieved. In a comparative study, the standard source of energy (glucose) in the medium was substituted by a prebiotic inulin, and a downward trend in the L. agilis epitranscriptome was detected. This marks the first report on a system-wide variation of a bacterial epitranscriptome that resulted from adapting to an alternative energy source. No correlation was found between the down-regulated RNA modifications and the expression level of corresponding writer genes. Whereas, the expression level of a specific exonuclease gene, RNase J1, was detected to be higher in cells grown on inulin.

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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 (May 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 be crucial for the integration of metabolic signals and the regulation of energy balance. Based on RNAseq studies, we recently identified an uncharacterized neuronal population of the ARC that robustly express the New arcuate transcript ( Nat). According to their localization and GABAergic phenotype, we hypothesize that Nat-expressing neurons are sensitive to various metabolic signals and that they play an important role in the control of energy homeostasis. Therefore, we aimed to characterize the molecular signature of Nat-expressing neurons in the ARC. We also aimed to determine whether leptin and GLP-1 can modulate the activity of these neurons.We first used the RNAscope® multiplex in situ hybridization technology on coronal brain slices from male mice. This allowed us to validate the GABAergic nature of Nat-expressing neurons, to confirm that they are distinct from POMC and AgRP neurons, and to determine whether they express the leptin and GLP-1 receptors ( Lepr and Glp1r respectively). We then administered leptin and the GLP1R agonist liraglutide to mice and evaluated C-FOS immunoreactivity in Nat-expressing neurons of the ARC.We found that Nat-expressing neurons represent a GABAergic population highly enriched in the ARC, and distinct from POMC and AgRP neurons. Subsets of Nat-expressing neurons co-express Lepr (18.3%), while others co-express Glp1r (35.3%). Finally, C-FOS immunoreactivity suggests that the activity of Nat-expressing neurons can be modulated in response to some metabolic signals. Together, our results suggest a potential role for Nat-expressing neurons in the integration of various metabolic cues. The recent development of a novel Nat-IRES-Cre mouse model will allow us to better characterize the metabolic functions of this new GABAergic neuronal population of the ARC. This work was supported by funding from the Canada Research Chairs Program (to A.C.), the Montreal Diabetes Research Center (to A.C.), the foundation of the Quebec Heart and Lung Institute (FIUCPQ, to A.C), and the Fonds d'enseignement et de recherche (FER) of the Faculty of Pharmacy of Université Laval (to N.J.M. and A.C.). N.J.M. was supported by a Sentinel North Partnered Research Chair in Sleep Pharmacometabolism (Canada First Research Excellence Fund) and a Fonds de Recherche du Québec – Santé (FRQS) Research Scholar J1 award. O.L. was supported by a Canada graduate scholarship (CIHR) and a Fonds de Recherche du Québec – Santé (FRQS) graduate scholarship. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

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