The role of the 5’ sensing function of ribonuclease E in cyanobacteria

References

• Laalami S, Zig L, Putzer H. Initiation of mRNA decay in bacteria. Cell Mol Life Sci. 2014;71(10):1799–1828. doi: 10.1007/s00018-013-1472-4
   PubMed Web of Science ®Google Scholar
• Hui MP, Foley PL, Belasco JG. Messenger RNA degradation in bacterial cells. Ann Rev Genet. 2014;48(1):537–559. doi: 10.1146/annurev-genet-120213-092340
   PubMedGoogle Scholar
• Tejada-Arranz A, de Crécy-Lagard V, de Reuse H. Bacterial RNA degradosomes: molecular machines under tight control. Trends Biochem Sci. 2020;45(1):42–57. doi: 10.1016/j.tibs.2019.10.002
   PubMed Web of Science ®Google Scholar
• Ono M, Kuwano M. A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of messenger RNA. J Mol Biol. 1979;129(3):343–357. doi: 10.1016/0022-2836(79)90500-X
   PubMed Web of Science ®Google Scholar
• Garrey SM, Mackie GA Roles of the 5’-phosphate sensor domain in RNase E. Mol Microbiol. 2011;80(6):1613–1624. doi: 10.1111/j.1365-2958.2011.07670.x
   PubMed Web of Science ®Google Scholar
• Garrey SM, Blech M, Riffell JL, et al. Substrate binding and active site residues in RNases E and G. J Biol Chem. 2009;284(46):31843–31850. doi: 10.1074/jbc.M109.063263
   PubMed Web of Science ®Google Scholar
• Kime L, Clarke JE, Romero AD, et al. Adjacent single-stranded regions mediate processing of tRNA precursors by RNase E direct entry. Nucleic Acids Res. 2014;42(7):4577–4589. doi: 10.1093/nar/gkt1403
   PubMed Web of Science ®Google Scholar
• Clarke JE, Kime L, Romero AD, et al. Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. Nucleic Acids Res. 2014;42(18):11733–11751. doi: 10.1093/nar/gku808
   PubMed Web of Science ®Google Scholar
• Mohanty BK, Kushner SR. Processing of the alaW alaX operon encoding the Ala2 tRNAs in Escherichia coli requires both RNase E and RNase P. Mol Microbiol. 2022;118(6):698–715. doi: 10.1111/mmi.14991
   PubMed Web of Science ®Google Scholar
• Gurevitz M, Jain SK, Apirion D. Identification of a precursor molecule for the RNA moiety of the processing enzyme RNase P. Proc Natl Acad Sci. 1983;80(14):4450. doi: 10.1073/pnas.80.14.4450
   PubMed Web of Science ®Google Scholar
• Lundberg U, Altman S Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli. RNA. 1995;1(3):327–334.
   PubMed Web of Science ®Google Scholar
• Lin-Chao S, Wei C-L, Lin Y-T. RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity. Proc Natl Acad Sci. 1999;96(22):12406–12411. doi: 10.1073/pnas.96.22.12406
   PubMed Web of Science ®Google Scholar
• Kim K-S, Lee Y Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Res. 2004;32(20):6057–6068. doi: 10.1093/nar/gkh939.
   PubMed Web of Science ®Google Scholar
• Miyakoshi M, Chao Y, Vogel J. Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J. 2015;34(11):1478–1492. doi: 10.15252/embj.201490546
   PubMed Web of Science ®Google Scholar
• Chao Y, Vogel J A 3’ UTR-Derived small RNA provides the regulatory noncoding arm of the inner membrane stress response. Mol Cell. 2016;61(3):352–363. doi: 10.1016/j.molcel.2015.12.023.
   PubMed Web of Science ®Google Scholar
• Chao Y, Li L, Girodat D, et al. In vivo cleavage map illuminates the central role of RNase E in coding and non-coding RNA pathways. Mol Cell. 2017;65(1):39–51. doi: 10.1016/j.molcel.2016.11.002
   PubMed Web of Science ®Google Scholar
• Bandyra KJ, Wandzik JM, Luisi BF Substrate recognition and autoinhibition in the central ribonuclease RNase E. Mol Cell. 2018;72(2):275–285.e4. doi: 10.1016/j.molcel.2018.08.039.
   PubMed Web of Science ®Google Scholar
• Bandyra KJ, Said N, Pfeiffer V, et al. The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell. 2012;47(6):943–953. doi: 10.1016/j.molcel.2012.07.015
   PubMed Web of Science ®Google Scholar
• Callaghan AJ, Marcaida MJ, Stead JA, et al. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature. 2005;437(7062):1187–1191. doi: 10.1038/nature04084.
   PubMed Web of Science ®Google Scholar
• Aït-Bara S, Carpousis AJ. RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs. Mol Microbiol. 2015;97(6):1021–1135. doi: 10.1111/mmi.13095
   PubMed Web of Science ®Google Scholar
• Clarke JE, Sabharwal K, Kime L, et al. The recognition of structured elements by a conserved groove distant from domains associated with catalysis is an essential determinant of RNase E. Nucleic Acids Res. 2023;51(1):365–379. doi: 10.1093/nar/gkac1228
   PubMed Web of Science ®Google Scholar
• Zhang J-Y, Deng X-M, Li F-P, et al. RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region. RNA. 2014;20(4):568–579. doi: 10.1261/rna.043513.113
   PubMed Web of Science ®Google Scholar
• Behler J, Sharma K, Reimann V, et al. The host-encoded RNase E endonuclease as the crRNA maturation enzyme in a CRISPR–cas subtype III-Bv system. Nat Microbiol. 2018;3(3):367–377. doi: 10.1038/s41564-017-0103-5
   PubMed Web of Science ®Google Scholar
• Yan H, Qin X, Wang L, et al. Both enolase and the DEAD-Box RNA helicase CrhB can form complexes with RNase E in Anabaena sp. Strain PCC 7120. Appl Environ Microbiol. 2020;86(13):e00425–20. doi: 10.1128/AEM.00425-20
   PubMed Web of Science ®Google Scholar
• Zhou C, Zhang J, Hu X, et al. RNase II binds to RNase E and modulates its endoribonucleolytic activity in the cyanobacterium Anabaena PCC 7120. Nucleic Acids Res. 2020;48(7):3922–3934. doi: 10.1093/nar/gkaa092
   PubMed Web of Science ®Google Scholar
• Jourdan SS, McDowall KJ Sensing of 5’ monophosphate by Escherichia coli RNase G can significantly enhance association with RNA and stimulate the decay of functional mRNA transcripts in vivo. Mol Microbiol. 2008;67(1):102–115. doi: 10.1111/j.1365-2958.2007.06028.x
   PubMed Web of Science ®Google Scholar
• Kime L, Jourdan SS, Stead JA, et al. Rapid cleavage of RNA by RNase E in the absence of 5’ monophosphate stimulation. Mol Microbiol. 2010;76(3):590–604. doi: 10.1111/j.1365-2958.2009.06935.x
   PubMed Web of Science ®Google Scholar
• Mackie GA Determinants in the rpsT mRNAs recognized by the 5’-sensor domain of RNase E. Mol Microbiol. 2013;89(2):388–402. doi: 10.1111/mmi.12283
   PubMed Web of Science ®Google Scholar
• Babitzke P, Kushner SR. The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. Proc Natl Acad Sci. 1991;88(1):1–5. doi: 10.1073/pnas.88.1.1
   PubMed Web of Science ®Google Scholar
• Kaberdin VR, Walsh AP, Jakobsen T, et al. Enhanced cleavage of RNA mediated by an interaction between substrates and the arginine-rich domain of E. coli ribonuclease E. J Mol Biol. 2000;301(2):257–264. doi: 10.1006/jmbi.2000.3962
   PubMed Web of Science ®Google Scholar
• Redko Y, Tock MR, Adams CJ, et al. Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates. J Biol Chem. 2003;278(45):44001–44008. doi: 10.1074/jbc.M306760200
   PubMed Web of Science ®Google Scholar
• Anupama K, Leela JK, Gowrishankar J. Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol Microbiol. 2011;82(6):1330–1348. doi: 10.1111/j.1365-2958.2011.07895.x
   PubMed Web of Science ®Google Scholar
• Schilder A, Görke B. Role of the 5′ end phosphorylation state for small RNA stability and target RNA regulation in bacteria. Nucleic Acids Res. 2023;51(10):5125–5143. doi: 10.1093/nar/gkad226
   PubMed Web of Science ®Google Scholar
• Zhang J-Y, Hess WR, Zhang C-C. “Life is short, and art is long”: RNA degradation in cyanobacteria and model bacteria. mLife. 2022;1(1):21–39. doi: 10.1002/mlf2.12015
   Google Scholar
• Horie Y, Ito Y, Ono M, et al. Dark-induced mRNA instability involves RNase E/G-type endoribonuclease cleavage at the AU-box and SD sequences in cyanobacteria. Mol Genet Genomics. 2007;278(3):331–346. doi: 10.1007/s00438-007-0254-9
   PubMed Web of Science ®Google Scholar
• Sakurai I, Stazic D, Eisenhut M, et al. Positive regulation of psbA gene expression by cis-encoded antisense RNAs in Synechocystis sp. PCC 6803. Plant Physiol. 2012;160(2):1000–1010. doi: 10.1104/pp.112.202127
   PubMed Web of Science ®Google Scholar
• Georg J, Dienst D, Schürgers N, et al. The small regulatory RNA SyR1/PsrR1 controls photosynthetic functions in cyanobacteria. Plant Cell. 2014;26(9):3661–3679. doi: 10.1105/tpc.114.129767
   PubMed Web of Science ®Google Scholar
• Schein A, Sheffy-Levin S, Glaser F, et al. The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme. RNA. 2008;14(6):1057–1068. doi: 10.1261/rna.907608
   PubMed Web of Science ®Google Scholar
• Kaberdin VR, Miczak A, Jakobsen JS, et al. The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Proc Natl Acad Sci. 1998;95(20):11637–11642. doi: 10.1073/pnas.95.20.11637
   PubMed Web of Science ®Google Scholar
• Cavaiuolo M, Chagneau C, Laalami S, et al. Impact of RNase E and RNase J on global mRNA metabolism in the cyanobacterium Synechocystis PCC6803. Front Microbiol. 2020;11:1055. doi: 10.3389/fmicb.2020.01055
   PubMed Web of Science ®Google Scholar
• Hoffmann UA, Heyl F, Rogh SN, et al. Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition. Nucleic Acids Res. 2021;49(22):13075–13091. doi: 10.1093/nar/gkab1161
   PubMed Web of Science ®Google Scholar
• Stazic D, Lindell D, Steglich C. Antisense RNA protects mRNA from RNase E degradation by RNA–RNA duplex formation during phage infection. Nucleic Acids Res. 2011;39(11):4890–4899. doi: 10.1093/nar/gkr037
   PubMed Web of Science ®Google Scholar
• Trautmann D, Voss B, Wilde A, et al. Microevolution in Cyanobacteria: Re-sequencing a motile substrain of Synechocystis sp. PCC 6803. DNA Res. 2012;19(6):435–448. doi: 10.1093/dnares/dss024
   PubMed Web of Science ®Google Scholar
• Rippka R, Deruelles J, Waterbury JB, et al. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology. 1979;111(1):1–61. doi: 10.1099/00221287-111-1-1
   Web of Science ®Google Scholar
• Köbler C, Schultz S-J, Kopp D, et al. The role of the Synechocystis sp. PCC 6803 homolog of the circadian clock output regulator RpaA in day–night transitions. Mol Microbiol. 2018;110(5):847–861. doi: 10.1111/mmi.14129
   PubMed Web of Science ®Google Scholar
• Schindelin J, Arganda-Carreras I, Frise E, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676–682. doi: 10.1038/nmeth.2019
   PubMed Web of Science ®Google Scholar
• Innocenti N, Golumbeanu M, Fouquier d’Hérouël A, et al. Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis. RNA. 2015;21(5):1018–1030. doi: 10.1261/rna.048470.114
   PubMed Web of Science ®Google Scholar
• Afgan E, Baker D, Batut B, et al. The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018;46(W1):W537–W544. doi: 10.1093/nar/gky379
   PubMed Web of Science ®Google Scholar
• Kaneko T, Sato S, Kotani H, et al. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 1996;3(3):109–136. doi: 10.1093/dnares/3.3.109
   PubMedGoogle Scholar
• Kopf M, Klähn S, Scholz I, et al. Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803. DNA Res. 2014;21(5):527–539. doi: 10.1093/dnares/dsu018.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi: 10.1186/s13059-014-0550-8
   PubMed Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102(43):15545–15550. doi: 10.1073/pnas.0506580102
   PubMed Web of Science ®Google Scholar
• Yu G, Wang L-G, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics J Integr Biol. 2012;16(5):284–287. doi: 10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Crooks GE, Hon G, Chandonia J-M, et al. WebLogo: A Sequence Logo Generator. Genome Res. 2004;14(6):1188–1190. doi: 10.1101/gr.849004
   PubMed Web of Science ®Google Scholar
• Lorenz R, Bernhart SH, Höner Zu Siederdissen C, et al. ViennaRNA package 2.0. Algorithms Mol Biol. 2011;6(1):26. doi: 10.1186/1748-7188-6-26
   PubMed Web of Science ®Google Scholar
• Carver T, Harris SR, Berriman M, et al. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinf. 2012;28(4):464–469. doi: 10.1093/bioinformatics/btr703
   PubMed Web of Science ®Google Scholar
• Madeira F, Park YM, Lee J, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 2019;47(W1):W636–W641. doi: 10.1093/nar/gkz268
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinf. 2004;5(1):Article 113. doi: 10.1186/1471-2105-5-113
   PubMedGoogle Scholar
• Waterhouse AM, Procter JB, Martin DMA, et al. Jalview version 2 - a multiple sequence alignment editor and analysis workbench. Bioinf. 2009;25(9):1189–1191. doi: 10.1093/bioinformatics/btp033.
   PubMed Web of Science ®Google Scholar
• Watanabe S, Stazic D, Georg J, et al. Regulation of RNase E during the UV-stress response in the cyanobacterium Synechocystis sp. PCC 6803. mLife. 2023;2(1) :43–57. doi: 10.1002/mlf2.12056
   Google Scholar
• Ali N, Gowrishankar J. Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E. Nucleic Acids Res. 2020;48(2):847–861. doi: 10.1093/nar/gkz1152
   PubMed Web of Science ®Google Scholar
• Tsunekawa K, Shijuku T, Hayashimoto M, et al. Identification and characterization of the Na+/H+ antiporter NhaS3 from the thylakoid membrane of Synechocystis sp. PCC 6803. J Biol Chem. 2009;284(24):16513–16521. doi: 10.1074/jbc.M109.001875
   PubMed Web of Science ®Google Scholar
• Nagy C, Thiel K, Mulaku E, et al. Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number. Microb Cell Factories. 2021;20(1):130. doi: 10.1186/s12934-021-01622-2
   PubMed Web of Science ®Google Scholar
• Mitschke J, Georg J, Scholz I, et al. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci. 2011;108(5):2124–2129. doi: 10.1073/pnas.1015154108
   PubMed Web of Science ®Google Scholar
• Baumgartner D, Kopf M, Klähn S, et al. Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome. BMC Microbiol. 2016;16(1):Article 285. doi: 10.1186/s12866-016-0896-z
   PubMedGoogle Scholar
• Huang D-D, Wang W-Y, Gough SP, et al. δ-aminolevulinic acid-synthesizing enzymes need an RNA moiety for activity. Sci. 1984;225(4669):1482–1484. doi: 10.1126/science.6206568
   PubMed Web of Science ®Google Scholar
• Schön A, Krupp G, Gough S, et al. The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nat. 1986;322(6076):281–284. doi: 10.1038/322281a0
   Google Scholar
• O’Neill GP, Peterson DM, Schön A, et al. Formation of the chlorophyll precursor delta-aminolevulinic acid in cyanobacteria requires aminoacylation of a tRNAGlu species. J Bacteriol. 1988;170(9):3810–3816. doi: 10.1128/jb.170.9.3810-3816.1988
   PubMed Web of Science ®Google Scholar
• Ghora BK, Apirion D. Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rne mutant of E. coli. Cell. 1978;15(3):1055–1066. doi: 10.1016/0092-8674(78)90289-1
   PubMed Web of Science ®Google Scholar
• Cormack RS, Mackie GA. Structural requirements for the processing of Escherichia coli 5 S ribosomal RNA by RNase E in vitro. J Mol Biol. 1992;228(4):1078–1090. doi: 10.1016/0022-2836(92)90316-C
   PubMed Web of Science ®Google Scholar
• Stazic D, Pekarski I, Kopf M, et al. A novel strategy for exploitation of host RNase E activity by a marine cyanophage. Genetics. 2016;203(3):1149–1159. doi: 10.1534/genetics.115.183475
   PubMed Web of Science ®Google Scholar
• Jain C, Belasco JG. RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity. Genes Dev. 1995;9(1):84–96. doi: 10.1101/gad.9.1.84
   PubMed Web of Science ®Google Scholar
• Song K, Baumgartner D, Hagemann M, et al. Atpθ is an inhibitor of F0F1 ATP synthase to arrest ATP hydrolysis during low-energy conditions in cyanobacteria. Curr Biol. 2022;32(1):136–148.e5. doi: 10.1016/j.cub.2021.10.051
   PubMed Web of Science ®Google Scholar
• Song K, Hagemann M, Georg J, et al. Expression of the cyanobacterial F0F1 ATP synthase regulator AtpΘ depends on small DNA-binding proteins and differential mRNA stability. Microbiol Spectr. 2022;10(3):e02562–21. doi: 10.1128/spectrum.02562-21
   PubMed Web of Science ®Google Scholar
• de Porcellinis AJ, Klähn S, Rosgaard L, et al. The non-coding RNA Ncr0700/PmgR1 is required for photomixotrophic growth and the regulation of glycogen accumulation in the cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol. 2016;57(10):2091–2103. doi: 10.1093/pcp/pcw128
   PubMed Web of Science ®Google Scholar
• Klähn S, Bolay P, Wright PR, et al. A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria. Nucleic Acids Res. 2018;46(19):10082–10094. doi: 10.1093/nar/gky709
   PubMed Web of Science ®Google Scholar
• Bolay P, Rokhsareh R, Muro-Pastor MI, et al. The novel PII-interacting protein PirA controls flux into the cyanobacterial ornithine-ammonia cycle. MBio. 2021;12(2):e00229–21. doi: 10.1128/mBio.00229-21
   PubMed Web of Science ®Google Scholar
• García-Domínguez M, Reyes JC, Florencio FJ. NtcA represses transcription of gifA and gifB, genes that encode inhibitors of glutamine synthetase type I from Synechocystis sp. PCC 6803. Mol Microbiol. 2000;35(5):1192–1201. doi: 10.1046/j.1365-2958.2000.01789.x
   PubMed Web of Science ®Google Scholar
• Klähn S, Orf I, Schwarz D, et al. Integrated transcriptomic and metabolomic characterization of the low-carbon response using an ndhR mutant of Synechocystis sp. PCC 6803. Plant Physiol. 2015;169(3):1540–1556. doi: 10.1104/pp.114.254045
   PubMed Web of Science ®Google Scholar
• Song J-Y, Cho HS, Cho J-I, et al. Near-UV cyanobacteriochrome signaling system elicits negative phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. Proc Natl Acad Sci. 2011;108(26):10780. doi: 10.1073/pnas.1104242108
   PubMed Web of Science ®Google Scholar
• Lacey RF, Binder BM. Ethylene regulates the physiology of the cyanobacterium Synechocystis sp. PCC 6803 via an ethylene receptor. Plant Physiol. 2016;171(4):2798–2809. doi: 10.1104/pp.16.00602
   PubMed Web of Science ®Google Scholar
• Kuchmina E, Klähn S, Jakob A, et al. Ethylene production in Synechocystis sp. PCC 6803 promotes phototactic movement. Microbiology. 2017;163(12):1937–1945. doi: 10.1099/mic.0.000564
   PubMed Web of Science ®Google Scholar
• Kaneko T, Nakamura Y, Sasamoto S, et al. Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803. DNA Res. 2003;10(5):221–228. do i:
   PubMed Web of Science ®Google Scholar
• Lin-Chao S, Cohen SN. The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo. Cell. 1991;65(7):1233–1242. doi: 10.1016/0092-8674(91)90018-T
   PubMed Web of Science ®Google Scholar
• Nishio S, Itoh T. Arginine-rich RNA binding domain and protein scaffold domain of RNase E are important for degradation of RNAI but not for that of the Rep mRNA of the ColE2 plasmid. Plasmid. 2009;62(2):83–87. doi: 10.1016/j.plasmid.2009.04.002
   PubMed Web of Science ®Google Scholar
• Tomcsányi T, Apirion D. Processing enzyme ribonuclease E specifically cleaves RNA I: An inhibitor of primer formation in plasmid DNA synthesis. J Mol Biol. 1985;185(4):713–720. doi: 10.1016/0022-2836(85)90056-7
   PubMed Web of Science ®Google Scholar
• Kaltenbrunner A, Reimann V, Hoffmann UA, et al. Regulation of pSYSA defense plasmid copy number in Synechocystis through RNase E and a highly transcribed asRNA. Front Microbiol. 2023;14. doi: 10.3389/fmicb.2023.1112307
   PubMed Web of Science ®Google Scholar
• Ghora BK, Apirion D. Identification of a novel RNA molecule in a new RNA processing mutant of Escherichia coli which contains 5 S rRNA sequences. J Biol Chem. 1979;254(6):1951–1956. doi: 10.1016/S0021-9258(17)37749-9
   PubMed Web of Science ®Google Scholar
• Régnier P, Hajnsdorf E Decay of mRNA encoding ribosomal protein S15 of Escherichia coli is initiated by an RNase E-dependent endonucleolytic cleavage that removes the 3’ stabilizing stem and loop structure. J Mol Biol. 1991;217(2):283–292. doi: 10.1016/0022-2836(91)90542-E
   PubMed Web of Science ®Google Scholar
• Walter M, Piepenburg K, Schöttler MA, et al. Knockout of the plastid RNase E leads to defective RNA processing and chloroplast ribosome deficiency. Plant J. 2010;64(5):851–863. doi: 10.1111/j.1365-313X.2010.04377.x
   PubMed Web of Science ®Google Scholar
• Riediger M, Spät P, Bilger R, et al. Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). Plant Cell. 2021;33(2):248–269. doi: 10.1093/plcell/koaa017
   PubMed Web of Science ®Google Scholar
• Hoyos M, Huber M, Förstner KU, et al. Gene autoregulation by 3’ UTR-derived bacterial small RNAs. Elife. 2020;9:e58836. doi: 10.7554/eLife.58836
   PubMed Web of Science ®Google Scholar
• Zhan J, Steglich C, Scholz I, et al. Inverse regulation of light harvesting and photoprotection is mediated by a 3’-end-derived sRNA in cyanobacteria. Plant Cell. 2021;33(2):358–380. doi: 10.1093/plcell/koaa030
   PubMed Web of Science ®Google Scholar
• Börner J, Friedrich T, Bartkuhn M, et al. Ribonuclease E strongly impacts bacterial adaptation to different growth conditions. RNA Biol. 2023;20(1):120–135. doi: 10.1080/15476286.2023.2195733
   PubMed Web of Science ®Google Scholar
• Rajib S, Deng L, Allison H-O, et al. Diurnal regulation of cellular processes in the cyanobacterium Synechocystis sp. strain PCC 6803: Insights from transcriptomic, fluxomic, and physiological analyses. MBio. 2016;7(3). doi: 10.1128/mbio.00464-16
   Web of Science ®Google Scholar
• Scheurer NM, Rajarathinam Y, Timm S, et al. Homologs of circadian clock proteins impact the metabolic switch between light and dark growth in the cyanobacterium Synechocystis sp. PCC 6803. Front Plant Sci. 2021;12:12. doi: 10.3389/fpls.2021.675227
   Web of Science ®Google Scholar
• Summerfield Tina C, Sherman Louis A. Role of sigma factors in controlling global gene expression in light/dark transitions in the cyanobacterium Synechocystis sp. Strain PCC 6803. J Bacteriol. 2007;189(21):7829–7840. doi: 10.1128/jb.01036-07
   PubMed Web of Science ®Google Scholar
• Li Z, Deutscher MP. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA. 2002;8(1):97–109. doi: 10.1017/S1355838202014929
   PubMed Web of Science ®Google Scholar
• Mohanty BK, Petree JR, Kushner SR. Endonucleolytic cleavages by RNase E generate the mature 3′ termini of the three proline tRNAs in Escherichia coli. Nucleic Acids Res. 2016;44(13):6350–6362. doi: 10.1093/nar/gkw517
   PubMed Web of Science ®Google Scholar
• Mohanty BK, Maples V, Kushner SR The C nucleotide at the mature 5’ end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the 3’ terminus as well as functionality. Nucleic Acids Res. 2022;50(3):1639–1649. doi: 10.1093/nar/gkab1260
   PubMed Web of Science ®Google Scholar
• Kannangara CG, Gough SP, Oliver RP, et al. Biosynthesis of δ-aminolevulinate in greening barley leaves VI. Activation of glutamate by ligation to RNA. Carlsberg Res Commun. 1984;49(3):417. doi: 10.1007/BF02907783
   Google Scholar
• Wang W-Y, Gough SP, Kannangara CG Biosynthesis of δ-aminolevulinate in greening barley leaves IV. Isolation of three soluble enzymes required for the conversion of glutamate to δ-aminolevulinate. Carlsberg Res Commun. 1981;46(4):243. doi: 10.1007/BF02906501
   Google Scholar
• O’Neill GP, Söll D. Expression of the Synechocystis sp. strain PCC 6803 tRNA(Glu) gene provides tRNA for protein and chlorophyll biosynthesis. J Bacteriol. 1990;172(11):6363–6371. doi: 10.1128/jb.172.11.6363-6371.1990
   PubMed Web of Science ®Google Scholar
• Rieble S, Beale SI. Transformation of glutamate to delta-aminolevulinic acid by soluble extracts of Synechocystis sp. PCC 6803 and other oxygenic prokaryotes. J Biol Chem. 1988;263(18):8864–8871. doi: 10.1016/S0021-9258(18)68388-7
   PubMed Web of Science ®Google Scholar
• Hartmann RK, Gößringer M, Späth B, et al. The making of tRNAs and more – RNase P and tRNase Z. In: Condon C, editor. Progress in Molecular Biology and Translational Science. Cambridge, United States: Academic Press; 2009. p. 319–368.
   Google Scholar
• Kirsebom LA, Svärd SG. Base pairing between Escherichia coli RNase P RNA and its substrate. EMBO J. 1994;13(20):4870–4876. doi: 10.1002/j.1460-2075.1994.tb06814.x
   PubMed Web of Science ®Google Scholar
• LaGrandeur TE, Hüttenhofer A, Noller HF, et al. Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA. EMBO J. 1994;13(17):3945–3952. doi: 10.1002/j.1460-2075.1994.tb06710.x
   PubMed Web of Science ®Google Scholar
• Fingerhut C, Schön A Sequence and functional characterization of RNase P RNA from the chl a/b containing cyanobacterium Prochlorothrix hollandica. FEBS Lett. 1998;428(3):161–164. doi: 10.1016/s0014-5793(98)00519-5
   PubMed Web of Science ®Google Scholar
• Hess WR, Fingerhut C, Schön A. RNase P RNA from Prochlorococcus marinus: contribution of substrate domains to recognition by a cyanobacterial ribozyme. FEBS Lett. 1998;431(2):138–142. doi: 10.1016/s0014-5793(98)00729-7
   PubMed Web of Science ®Google Scholar