Insights into the metabolism, signaling, and physiological effects of 2’,3’-cyclic nucleotide monophosphates in bacteria

References

• Abel S, Nürnberger T, Ahnert V, Krauss GJ, Glund K. 2000. Induction of an extracellular cyclic nucleotide phosphodiesterase as an accessory ribonucleolytic activity during phosphate starvation of cultured tomato cells. Plant Physiol. 122(2):543–552. doi:10.1104/pp.122.2.543.
   PubMed Web of Science ®Google Scholar
• Akanuma G, Yamazaki K, Yagishi Y, Iizuka Y, Ishizuka M, Kawamura F, Kato-Yamada Y. 2018. Magnesium suppresses defects in the formation of 70S ribosomes as well as in sporulation caused by lack of several individual ribosomal proteins. J Bacteriol. 200(18):e00212–18. doi:10.1128/JB.00212-18.
   PubMed Web of Science ®Google Scholar
• Anderson BW, Fung DK, Wang JD. 2021. Regulatory themes and variations by the stress-signaling nucleotide alarmones (p)ppGpp in bacteria. Annu Rev Genet. 55(1):115–133. doi:10.1146/annurev-genet-021821-025827.
   PubMedGoogle Scholar
• Anraku Y, Mizuno D. 1967. Ribonuclease-cyclic phosphodiesterase system in Escherichia coli. J Biochem. 61(1):81–88. doi:10.1093/oxfordjournals.jbchem.a128523.
   PubMed Web of Science ®Google Scholar
• Apura P, Gonçalves LG, Viegas SC, Arraiano CM. 2021. The world of ribonucleases from pseudomonads: a short trip through the main features and singularities. Microb Biotechnol. 14(6):2316–2333. doi:10.1111/1751-7915.13890.
   PubMed Web of Science ®Google Scholar
• Arn EA, Abelson JN. 1996. The 2’-5’ RNA ligase of escherichia coli. Purification, cloning, and genomic disruption. J Biol Chem. 271(49):31145–31153. doi:10.1074/jbc.271.49.31145.
   PubMed Web of Science ®Google Scholar
• Azarashvili T, Krestinina O, Galvita A, Grachev D, Baburina Y, Stricker R, Evtodienko Y, Reiser G. 2009. Ca 2+ -dependent permeability transition regulation in rat brain mitochondria by 2′,3′-cyclic nucleotides and 2′,3′-cyclic nucleotide 3′-phosphodiesterase. Am J Physiol Cell Physiol. 296(6):C1428–C1439. doi:10.1152/ajpcell.00006.2009.
   PubMed Web of Science ®Google Scholar
• Bähre H, Kaever V. 2014. Measurement of 2’,3’-cyclic nucleotides by liquid chromatography-tandem mass spectrometry in cells. J Chromatogr B Analyt Technol Biomed Life Sci. 964:208–211. doi:10.1016/j.jchromb.2014.02.046.
   PubMed Web of Science ®Google Scholar
• Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin AF. 2011. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. Embo J. 30(22):4616–4627. doi:10.1038/EMBOJ.2011.377.
   PubMed Web of Science ®Google Scholar
• Beppu T, Arima K. 1969. Induction by mercuric ion of extensive degradation of cellular ribonucleic acid in Escherichia coli. J Bacteriol. 98(3):888–897. doi:10.1128/jb.98.3.888-897.1969.
   PubMed Web of Science ®Google Scholar
• Bhatti AR, DeVoe IW, Ingram JM. 1976. The release and characterization of some periplasm located enzymes of Pseudomonas aeruginosa. Can J Microbiol. 22(10):1425–1429. doi:10.1139/m76-211.
   PubMed Web of Science ®Google Scholar
• Bordeleau E, Oberc C, Ameen E, da Silva AM, Yan H. 2014. Identification of cytidine 2′,3′-cyclic monophosphate and uridine 2′,3′-cyclic monophosphate in Pseudomonas fluorescens pfo-1 culture. Bioorg Med Chem Lett. 24(18):4520–4522. doi:10.1016/j.bmcl.2014.07.080.
   PubMed Web of Science ®Google Scholar
• Boutte CC, Crosson S. 2013. Bacterial lifestyle shapes stringent response activation. Trends Microbiol. 21(4):174–180. doi:10.1016/j.tim.2013.01.002.
   PubMed Web of Science ®Google Scholar
• Braun F, Recalde A, Bähre H, Seifert R, Albers S-V. 2021. Putative nucleotide-based second messengers in the archaeal model organisms haloferax volcanii and sulfolobus acidocaldarius. Front Microbiol. 12:779012. doi:10.3389/fmicb.2021.779012.
   PubMed Web of Science ®Google Scholar
• Burhenne H, Tschirner S, Seifert R, Kaever V. 2013. Identification and quantitation of 2’,3’-cGMP in murine tissues. BMC Pharmacol Toxicol. 14(S1):P12. doi:10.1186/2050-6511-14-S1-P12.
   PubMedGoogle Scholar
• Cabezas A, Costas MJ, Canales J, Pinto RM, Rodrigues JR, Ribeiro JM, Cameselle JC. 2022. Enzyme characterization of pro-virulent SntA, a cell wall-anchored protein of streptococcus suis, with phosphodiesterase activity on cyclic-di-amp at a level suited to limit the innate immune system. Front Microbiol. 13(March):843068. doi:10.3389/fmicb.2022.843068.
   PubMedGoogle Scholar
• Cammack KA, Wade HE. 1965. The sedimentation behaviour of ribonuclease-active and -inactive ribosomes from bacteria. Biochem J. 96(3):671–680. doi:10.1042/BJ0960671.
   PubMed Web of Science ®Google Scholar
• Cannistraro VJ, Kennell D. 1991. RNase I*, a form of RNase I, and mRNA degradation in Escherichia coli. J Bacteriol. 173(15):4653–4659. doi:10.1128/jb.173.15.4653-4659.1991.
   PubMed Web of Science ®Google Scholar
• Chauhan SS, Marotta NJ, Karls AC, Weinert EE. 2022. Binding of 2′,3′-Cyclic Nucleotide Monophosphates to Bacterial Ribosomes Inhibits Translation. ACS Cent Sci. 8(11):1518–1526. doi:10.1021/acscentsci.2c00681.
   PubMed Web of Science ®Google Scholar
• Chauhan SS, Weinert EE. 2023. Generation of nucleotide-linked resins for identification of novel binding proteins. Methods Enzymol. 679:323–330. doi:10.1016/bs.mie.2022.08.052.
   PubMedGoogle Scholar
• Chodasiewicz M, Kerber O, Gorka M, Moreno JC, Maruri-Lopez I, Minen RI, Sampathkumar A, Nelson ADL, Skirycz A. 2022. 2′,3′-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana. Plant Physiol. 188(4):1966–1978. doi:10.1093/plphys/kiac013.
   PubMed Web of Science ®Google Scholar
• Clouet-d’Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier L-K. 2018. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev. 42(5):579–613. doi:10.1093/femsre/fuy016.
   PubMed Web of Science ®Google Scholar
• Van Damme T, Blancquaert D, Couturon P, Van Der Straeten D, Sandra P, Lynen F. 2014. Wounding stress causes rapid increase in concentration of the naturally occurring 2′,3′-isomers of cyclic guanosine- and cyclic adenosine monophosphate (cGMP and cAMP) in plant tissues. Phytochemistry. 103:59–66. doi:10.1016/j.phytochem.2014.03.013.
   PubMed Web of Science ®Google Scholar
• Van Damme T, Zhang Y, Lynen F, Sandra P. 2012. Determination of cyclic guanosine- and cyclic adenosine monophosphate (cGMP and cAMP) in human plasma and animal tissues by solid phase extraction on silica and liquid chromatography–triple quadrupole mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 909:14–21. doi:10.1016/j.jchromb.2012.10.002.
   PubMed Web of Science ®Google Scholar
• Denninger JW, Marletta MA. 1999. Guanylate cyclase and the ⋅NO/cGMP signaling pathway. Biochim Biophys Acta. 1411(2-3):334–350. doi:10.1016/s0005-2728(99)00024-9.
   PubMed Web of Science ®Google Scholar
• Deshpande RA, Shankar V. 2002. Ribonucleases from T2 Family. Crit Rev Microbiol. 28(2):79–122. doi:10.1080/1040-840291046704.
   PubMed Web of Science ®Google Scholar
• Diez S, Ryu J, Caban K, Gonzalez RL, Jr., Dworkin J. 2020. The alarmones (p)ppGpp directly regulate translation initiation during entry into quiescence. Proc Natl Acad Sci U S A. 117(27):15565–15572. doi:10.1073/pnas.1920013117.
   PubMed Web of Science ®Google Scholar
• Duggal Y, Fontaine BM, Dailey DM, Ning G, Weinert EE. 2020. RNase I Modulates Escherichia coli Motility, Metabolism, and Resistance. ACS Chem Biol. 15(7):1996–2004. doi:10.1021/acschembio.0c00390.
   PubMed Web of Science ®Google Scholar
• Duggal Y, Kurasz JE, Fontaine BM, Marotta NJ, Chauhan SS, Karls AC, Weinert EE. 2022. Cellular effects of 2′,3′-cyclic nucleotide monophosphates in gram-negative bacteria.O’Toole G, editor. J Bacteriol. 204(1):e0020821. doi:10.1128/JB.00208-21.
   PubMed Web of Science ®Google Scholar
• Fontaine BM, Martin KS, Garcia-Rodriguez JM, Jung C, Briggs L, Southwell JE, Jia X, Weinert EE. 2018. RNase I regulates Escherichia coli 2′,3′-cyclic nucleotide monophosphate levels and biofilm formation. Biochem J. 475(8):1491–1506. doi:10.1042/BCJ20170906.
   PubMedGoogle Scholar
• Genschik P, Drabikowski K, Filipowicz W. 1998. Characterization of the Escherichia coli RNA 3’-terminal phosphate cyclase and its σ54-regulated operon. J Biol Chem. 273(39):25516–25526. doi:10.1074/jbc.273.39.25516.
   PubMed Web of Science ®Google Scholar
• Girard ME, Gopalkrishnan S, Grace ED, Halliday JA, Gourse RL, Herman C. 2018. DksA and ppGpp regulate the sigma(S) stress response by activating promoters for the small RNA DsrA and the anti-adapter protein IraP. J Bacteriol. 200(2):e00463–17. doi:10.1128/JB.00463-17.
   PubMed Web of Science ®Google Scholar
• Goodman HL, Kroon JTM, Tom DFA, Hamilton JMU, Alqarni AO, Chivasa S. 2022. Extracellular ATP targets Arabidopsis RIBONUCLEASE 1 to suppress mycotoxin stress-induced cell death. New Phytol. 235(4):1531–1542. doi:10.1111/nph.18211.
   PubMed Web of Science ®Google Scholar
• Greulich W, Wagner M, Gaidt MM, Stafford C, Cheng Y, Linder A, Carell T, Hornung V. 2019. TLR8 is a sensor of RNase T2 degradation products. Cell. 179(6):1264–1275.e13. doi:10.1016/j.cell.2019.11.001.
   PubMed Web of Science ®Google Scholar
• Grünberg S, Coxam B, Chen TH, Dai N, Saleh L, Corrêa IR, Nichols NM, Yigit E. 2021. E. coli RNase I exhibits a strong Ca2+-dependent inherent double-stranded RNase activity. Nucleic Acids Res. 49(9):5265–5277. doi:10.1093/NAR/GKAB284.
   PubMed Web of Science ®Google Scholar
• Hammann C, Luptak A, Perreault J, De La Peña M. 2012. The ubiquitous hammerhead ribozyme. RNA. 18(5):871–885. doi:10.1261/rna.031401.111.
   PubMed Web of Science ®Google Scholar
• Harms A, Brodersen DE, Mitarai N, Gerdes K. 2018. Toxins, targets, and triggers: an overview of toxin-antitoxin biology. Mol Cell. 70(5):768–784. doi:10.1016/j.molcel.2018.01.003.
   PubMed Web of Science ®Google Scholar
• Hengge R. 2009. Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol. 7(4):263–273. doi:10.1038/nrmicro2109.
   PubMed Web of Science ®Google Scholar
• Hengge R. 2021. High-specificity local and global c-di-GMP signaling. Trends Microbiol. 29(11):993–1003. doi:10.1016/j.tim.2021.02.003.
   PubMed Web of Science ®Google Scholar
• Hiniker A, Bardwell JCA. 2004. In vivo substrate specificity of periplasmic disulfide oxidoreductases. J Biol Chem. 279(13):12967–12973. doi:10.1074/jbc.M311391200.
   PubMed Web of Science ®Google Scholar
• Hughes KJ, Chen X, Burroughs AM, Aravind L, Wolin SL. 2020. An RNA repair operon regulated by damaged tRNAs. Cell Rep. 33(12):108527. doi:10.1016/j.celrep.2020.108527.
   PubMed Web of Science ®Google Scholar
• Hulscher RM. 2017. Structural changes in the E. coli ribosome during assembly and cellular stress Johns Hopkins University. http://jhir.library.jhu.edu/handle/1774.2/60234
   Google Scholar
• Irving SE, Choudhury NR, Corrigan RM. 2021. The stringent response and physiological roles of (pp)pGpp in bacteria. Nat Rev Microbiol. 19(4):256–271. doi:10.1038/s41579-020-00470-y.
   PubMed Web of Science ®Google Scholar
• Jackson EK. 2011. The 2’,3’-cAMP-adenosine pathway. Am J Physiol Renal Physiol. 301(6):F1160–1167. doi:10.1152/ajprenal.00450.2011.
   PubMed Web of Science ®Google Scholar
• Jackson EK. 2015. Discovery and Roles of 2′,3′-cAMP in Biological Systems. In: Seifert R, editor. Non-canonical cyclic nucleotides. Vol. 238. New York: Springer New York LLC. p. 229–252. doi:10.1007/164_2015_40.
   Google Scholar
• Jackson EK, Menshikova EV, Mi Z, Verrier JD, Bansal R, Janesko-Feldman K, Jackson TC, Kochanek PM. 2016. Renal 2 ‘,3 ‘-Cyclic Nucleotide 3 ‘-phosphodiesterase is an important determinant of AKI severity after ischemia-reperfusion. J Am Soc Nephrol. 27(7):2069–2081. doi:10.1681/ASN.2015040397.
   PubMed Web of Science ®Google Scholar
• Jackson EK, Mi Z, Janesko-Feldman K, Jackson TC, Kochanek PM. 2019. 2′,3′-cGMP exists in vivo and comprises a 2′,3′-cGMP-guanosine pathway. Am J Physiol Regul Integr Comp Physiol. 316(6):R783–R790. doi:10.1152/ajpregu.00401.2018.
   PubMed Web of Science ®Google Scholar
• Jackson EK, Ren J, Mi ZC. 2009. Extracellular 2 ‘,3 ‘-cAMP is a source of adenosine. J Biol Chem. 284(48):33097–33106. doi:10.1074/jbc.M109.053876.
   PubMed Web of Science ®Google Scholar
• Jenal U, Reinders A, Lori C. 2017. Cyclic di-GMP: second messenger extraordinaire. Nat Rev Microbiol. 15(5):271–284. doi:10.1038/nrmicro.2016.190.
   PubMed Web of Science ®Google Scholar
• Jia X, Fontaine B, Strobel F, Weinert E. 2014. A facile and sensitive method for quantification of cyclic nucleotide monophosphates in mammalian organs: basal levels of eight cNMPs and identification of 2’,3’-cIMP. Biomolecules. 4(4):1070–1092. doi:10.3390/biom4041070.
   PubMedGoogle Scholar
• Jung S, von Thülen T, Yang I, Laukemper V, Rupf B, Janga H, Panagiotidis G-D, Schoen A, Nicolai M, Schulte LN, et al. 2020. A ribosomal RNA fragment with 2’,3’-cyclic phosphate and GTP-binding activity acts as RIG-I ligand. Nucleic Acids Res. 48(18):10397–10412. doi:10.1093/nar/gkaa739.
   PubMed Web of Science ®Google Scholar
• Kalia D, Merey G, Nakayama S, Zheng Y, Zhou J, Luo YL, Guo M, Roembke BT, Sintim HO. 2013. Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis. Chem Soc Rev. 42(1):305–341. doi:10.1039/c2cs35206k.
   PubMed Web of Science ®Google Scholar
• Keppetipola N, Shuman S. 2008. A Phosphate-binding histidine of binuclear metallophosphodiesterase enzymes is a determinant of 2,3-Cyclic nucleotide phosphodiesterase activity. *J Biol Chem. 283(45):30942–30949. doi:10.1074/jbc.M805064200.
   PubMedGoogle Scholar
• Kosmacz M, Luzarowski M, Kerber O, Leniak E, Gutiérrez-Beltrán E, Moreno JC, Gorka M, Szlachetko J, Veyel D, Graf A, et al. 2018. Interaction of 2’,3’-cAMP with Rbp47b Plays a Role in Stress Granule Formation. Plant Physiol. 177(1):411–421. doi:10.1104/pp.18.00285.
   PubMed Web of Science ®Google Scholar
• Kurylo CM, Alexander N, Dass RA, Parks MM, Altman RA, Vincent CT, Mason CE, Blanchard SC. 2016. Genome sequence and analysis of escherichia coli mre600, a colicinogenic, nonmotile strain that lacks RNase I and the type I methyltransferase, EcoKI. Genome Biol Evol. 8(3):742–752. accessed 2021 Nov 7. doi:10.1093/GBE/EVW008.
   PubMed Web of Science ®Google Scholar
• Lee J, Lee M, Lee K. 2021. Trans-acting regulators of ribonuclease activity. J Microbiol. 59(4):341–359. doi:10.1007/s12275-021-0650-6.
   PubMed Web of Science ®Google Scholar
• Litt M. 1962. The pH-rate profile of the ribonuclease-catalysed hydrolysis of cytidine 2′,3′-cyclic phosphate. Biochim Biophys Acta. 60(3):644–645. doi:10.1016/0006-3002(62)90884-3.
   PubMedGoogle Scholar
• Liu A, Yu Y, Sheng Q, Zheng X-Y, Yang J-Y, Li P-Y, Shi M, Zhou B-C, Zhang Y-Z, Chen X-L. 2016. Identification of four kinds of 2′,3′-cNMPs in Escherichia coli and a method for their preparation. ACS Chem Biol. 11(9):2414–2419. doi:10.1021/acschembio.6b00426.
   PubMed Web of Science ®Google Scholar
• Liu X, Cao B, Yang L, Gu JD. 2022. Biofilm control by interfering with c-di-GMP metabolism and signaling. Biotechnol Adv. 56:107915. doi:10.1016/j.biotechadv.2022.107915.
   PubMed Web of Science ®Google Scholar
• López-Villamizar I, Cabezas A, Pinto RM, Canales J, Ribeiro JM, Cameselle JC, Costas MJ. 2016. The characterization of escherichia coli CpdB as a Recombinant protein reveals that, besides having the expected 3’-Nucleotidase and 2’,3’-cyclic mononucleotide phosphodiesterase activities, it is also active as cyclic dinucleotide phosphodiesterase. Stevenson B, editor. PLoS One. 11(6):e0157308. doi:10.1371/journal.pone.0157308.
   PubMed Web of Science ®Google Scholar
• López-Villamizar I, Cabezas A, Pinto RM, Canales J, Ribeiro JM, Rodrigues JR, Costas MJ, Cameselle JC. 2021. Molecular dissection of escherichia coli cpdb: roles of the n domain in catalysis and phosphate inhibition, and of the c domain in substrate specificity and adenosine inhibition. Int J Mol Sci. 22(4):1977. doi:10.3390/ijms22041977.
   PubMed Web of Science ®Google Scholar
• Lucas KA, Pitari GM, Kazerounian S, Ruiz-Stewart I, Park J, Schulz S, Chepenik KP, Waldman SA. 2000. Guanylyl cyclases and signaling by cyclic GMP. Pharmacol Rev. 52(3):375–414. http://www.ncbi.nlm.nih.gov/pubmed/10977868.
   PubMed Web of Science ®Google Scholar
• Mathieu-Demazière C, Poinsot V, Masson-Boivin C, Garnerone A-M, Batut J. 2013. Biochemical and functional characterization of SpdA, a 2’, 3’ cyclic nucleotide phosphodiesterase from Sinorhizobium meliloti. BMC Microbiol. 13(1):268. doi:10.1186/1471-2180-13-268.
   PubMedGoogle Scholar
• McDowell JR, Bai G, Lasek‐Nesselquist E, Eisele LE, Wu Y, Hurteau G, Johnson R, Bai Y, Chen Y, Chan J, et al. 2023. Mycobacterial phosphodiesterase Rv0805 is a virulence determinant and its cyclic nucleotide hydrolytic activity is required for propionate detoxification. Mol Microbiol. 119(4):401–422. doi:10.1111/mmi.15030.
   PubMed Web of Science ®Google Scholar
• Meador J, Cannon B, Cannistraro VJ, Kennell D. 1990. Purification and characterization of Escherichia coli RNase I. Comparisons with RNase M. Eur J Biochem. 187(3):549–553. doi:10.1111/j.1432-1033.1990.tb15336.x.
   PubMedGoogle Scholar
• Megel C, Hummel G, Lalande S, Ubrig E, Cognat V, Morelle G, Salinas-Giegé T, Duchêne A-M, Maréchal-Drouard L. 2019. Plant RNases T2, but not Dicer-like proteins, are major players of tRNA-derived fragments biogenesis. Nucleic Acids Res. 47(2):941–952. doi:10.1093/nar/gky1156.
   PubMed Web of Science ®Google Scholar
• Meier K. 2017. Cyclic nucleotide signaling in Arabidopsis thaliana and the identification of cGMP binding proteins. Technische Universität München. https://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:91-diss-20170308-1327135-1-5
   Google Scholar
• Messens J, Collet JF, Van Belle K, Brosens E, Loris R, Wyns L. 2007. The oxidase DsbA folds a protein with a nonconsecutive disulfide. J Biol Chem. 282(43):31302–31307. doi:10.1074/jbc.M705236200.
   PubMed Web of Science ®Google Scholar
• Milon P, Tischenko E, Tomsic J, Caserta E, Folkers G, La Teana A, Rodnina MV, Pon CL, Boelens R, Gualerzi CO. 2006. The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proc Natl Acad Sci U S A. 103(38):13962–13967. doi:10.1073/pnas.0606384103.
   PubMed Web of Science ®Google Scholar
• Mitkevich VA, Ermakov A, Kulikova AA, Tankov S, Shyp V, Soosaar A, Tenson T, Makarov AA, Ehrenberg M, Hauryliuk V. 2010. Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP, GTP, or ppGpp. J Mol Biol. 402(5):838–846. doi:10.1016/j.jmb.2010.08.016.
   PubMed Web of Science ®Google Scholar
• Mitsutomi S, Akimitsu N, Sekimizu K, Kaito C. 2019. Identification of 2H phosphoesterase superfamily proteins with 2′-CPDase activity. Biochimie. 165:235–244. doi:10.1016/j.biochi.2019.08.008.
   PubMed Web of Science ®Google Scholar
• Neu HC. 1968. The 5′-Nucleotidases and Cyclic Phosphodiesterases (3′-Nucleotidases) of the Enterobacteriaceae. J Bacteriol. 95(5):1732–1737. doi:10.1128/jb.95.5.1732-1737.1968.
   PubMed Web of Science ®Google Scholar
• Neu HC, Heppel LA. 1964. The release of ribonuclease into the medium when escherichia coli cells are converted to spheroplasts. J Biol Chem. 239(11):3893–3900. doi:10.1016/s0021-9258(18)91220-2.
   PubMed Web of Science ®Google Scholar
• Nürnberger T, Abel S, Jost W, Glund K. 1990. Induction of an extracellular ribonuclease in cultured tomato cells upon phosphate starvation. Plant Physiol. 92(4):970–976. doi:10.1104/pp.92.4.970.
   PubMed Web of Science ®Google Scholar
• Ostendorf T, Zillinger T, Andryka K, Schlee-Guimaraes TM, Schmitz S, Marx S, Bayrak K, Linke R, Salgert S, Wegner J, et al. 2020. Immune sensing of synthetic, bacterial, and protozoan rna by toll-like receptor 8 requires coordinated processing by RNase T2 and RNase 2. Immunity. 52(4):591–605.e6. doi:10.1016/j.immuni.2020.03.009.
   PubMed Web of Science ®Google Scholar
• Pabst M, Grass J, Fischl R, Léonard R, Jin C, Hinterkörner G, Borth N, Altmann F. 2010. Nucleotide and nucleotide sugar analysis by liquid chromatography- electrospray ionization-mass spectrometry on surface-conditioned porous graphitic carbon. Anal Chem. 82(23):9782–9788. doi:10.1021/ac101975k.
   PubMed Web of Science ®Google Scholar
• Pesavento C, Hengge R. 2009. Bacterial nucleotide-based second messengers. Curr Opin Microbiol. 12(2):170–176. doi:10.1016/j.mib.2009.01.007
   PubMed Web of Science ®Google Scholar
• Qvortrup K, Hultqvist LD, Nilsson M, Jakobsen TH, Jansen CU, Uhd J, Andersen JB, Nielsen TE, Givskov M, Tolker-Nielsen T. 2019. Small molecule anti-biofilm agents developed on the basis of mechanistic understanding of biofilm formation. Front Chem. 7:742. doi:10.3389/fchem.2019.00742.
   PubMed Web of Science ®Google Scholar
• Rall TW, Sutherland EW. 1958. Formation of a cyclic adenine ribonucleotide by tissue particles. J Biol Chem. 232(2):1065–1076. https://www.ncbi.nlm.nih.gov/pubmed/13549487. doi:10.1016/S0021-9258(19)77422-5.
   PubMed Web of Science ®Google Scholar
• Rao F, Qi Y, Murugan E, Pasunooti S, Ji Q. 2010. 2′,3′-cAMP hydrolysis by metal-dependent phosphodiesterases containing DHH, EAL, and HD domains is non-specific: implications for PDE screening. Biochem Biophys Res Commun. 398(3):500–505. doi:10.1016/j.bbrc.2010.06.107.
   PubMed Web of Science ®Google Scholar
• Remus BS, Jacewicz A, Shuman S. 2014. Structure and mechanism of E. coli RNA 2’,3’-cyclic phosphodiesterase. RNA. 20(11):1697–1705. doi:10.1261/rna.046797.114.
   PubMed Web of Science ®Google Scholar
• Ren J, Mi Z, Stewart NA, Jackson EK. 2009. Identification and Quantification of 2′,3′-cAMP Release by the Kidney. J Pharmacol Exp Ther. 328(3):855–865. doi:10.1124/jpet.108.146712.
   PubMed Web of Science ®Google Scholar
• Ribeiro JM, Canales J, Costas MJ, Cabezas A, Pinto RM, García-Díaz M, Martín-Cordero P, Cameselle JC. 2023. Genomic distribution of pro-virulent cpdb-like genes in eubacteria and comparison of the enzyme specificity of CpdB-like proteins from Salmonella enterica, Escherichia coli and Streptococcus suis. Int J Mol Sci. 24(4):4150. doi:10.3390/ijms24044150.
   PubMedGoogle Scholar
• Richards H, Das S, Smith CJ, Pereira L, Geisbrecht A, Devitt NJ, Games DE, Van Geyschem J, Gareth Brenton A, Newton RP. 2002. Cyclic nucleotide content of tobacco BY-2 cells. Phytochemistry. 61(5):531–537. doi:10.1016/S0031-9422(02)00266-2.
   PubMed Web of Science ®Google Scholar
• Rojas AM, Ehrenberg M, Andersson SG, Kurland CG. 1984. ppGpp inhibition of elongation factors Tu, G and Ts during polypeptide synthesis. Mol Gen Genet. 197(1):36–45. doi:10.1007/BF00327920.
   PubMedGoogle Scholar
• Römling U, Galperin MY, Gomelsky M. 2013. Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger. Microbiol Mol Biol Rev. 77(1):1–52. doi:10.1128/mmbr.00043-12.
   PubMed Web of Science ®Google Scholar
• Saitoh M, Green PJ, Lebrasseur ND, Macintosh GC, Pe MA. 2002. Local and systemic wound-induction of RNase and nuclease activities in Arabidopsis : RNS1 as a marker for a JA-independent systemic signaling pathway. 29. doi:10.1046/j.1365-313x.2002.01223.x.
   Google Scholar
• Sato S, Uchida T, Egami F. 1966. Action of ribonuclease T2 on 2′, 3′-cyclic nucleotides and related compounds. Arch Biochem Biophys. 115(1):48–52. doi:10.1016/S0003-9861(66)81036-6.
   PubMed Web of Science ®Google Scholar
• Shigematsu M, Morichika K, Kawamura T, Honda S, Kirino Y. 2019. Genome-wide identification of short 2’,3’-cyclic phosphate-containing RNAs and their regulation in aging. PLoS Genet. 15(11):e1008469. doi:10.1371/journal.pgen.1008469.
   PubMed Web of Science ®Google Scholar
• Sondermann H, Shikuma NJ, Yildiz FH. 2012. You’ve come a long way: c-di-GMP signaling. Curr Opin Microbiol. 15(2):140–146. doi:10.1016/j.mib.2011.12.008
   PubMed Web of Science ®Google Scholar
• Stone TW, Ceruti S, Abbracchio MP. 2009. Adenosine Receptors and Neurological Disease: neuroprotection and Neurodegeneration BT - Adenosine Receptors in Health and Disease. In: wilson CN, Mustafa SJ, editors. Berlin, Heidelberg: Springer Berlin Heidelberg. p. 535–587. doi:10.1007/978-3-540-89615-9_17.
   Google Scholar
• Sun S, He Z, Jiang P, Baral R, Pandelia M-E. 2022. Metal Dependence and functional diversity of type I Cas3 nucleases. Biochemistry. 61(5):327–338. doi:10.1021/acs.biochem.1c00779.
   PubMed Web of Science ®Google Scholar
• Sutherland EW, Rall TW. 1958. Fractionation and characterization of a cyclic adenine ribonucleotide formed by tissue particles. J Biol Chem. 232(2):1077–1091. https://www.ncbi.nlm.nih.gov/pubmed/13549488. doi:10.1016/S0021-9258(19)77423-7.
   PubMed Web of Science ®Google Scholar
• Tanaka N, Shuman S. 2011. RtcB is the RNA ligase component of an Escherichia coli RNA repair operon. J Biol Chem. 286(10):7727–7731. doi:10.1074/jbc.C111.219022.
   PubMed Web of Science ®Google Scholar
• Trülzsch K, Roggenkamp A, Pelludat C, Rakin A, Jacobi CA, Heesemann J. 2001. Cloning and characterization of the gene encoding periplasmic 2′,3′-cyclic phosphodiesterase of Yersinia enterocolitica O:8. Microbiology. 147(Pt 1):203–213. doi:10.1099/00221287-147-1-203.
   PubMedGoogle Scholar
• Verrier JD, Jackson TC, Bansal R, Kochanek PM, Puccio AM, Okonkwo DO, Jackson EK. 2012. The brain in vivo expresses the 2’,3’-cAMP-adenosine pathway. J Neurochem. 122(1):115–125. doi:10.1111/j.1471-4159.2012.07705.x.
   PubMed Web of Science ®Google Scholar
• Veyel D, Kierszniowska S, Kosmacz M, Sokolowska EM, Michaelis A, Luzarowski M, Szlachetko J, Willmitzer L, Skirycz A. 2017. System-wide detection of protein-small molecule complexes suggests extensive metabolite regulation in plants. Sci Rep. 7(1):42387. doi:10.1038/srep42387.
   PubMedGoogle Scholar
• Wade HE. 1961. The autodegradation of ribonucleoprotein in Escherichia coli. Biochem J. 78(3):457–472. doi:10.1042/bj0780457.
   PubMed Web of Science ®Google Scholar
• Wade HE, Robinson HK. 1963. Absence of ribonuclease from the ribosomes of pseudomonas fluorescens. Nature. 200(4907):661–663. doi:10.1038/200661a0.
   PubMedGoogle Scholar
• Wall M, Linkletter B, Williams D, Anne-Marie Lebuis, Hynes RC, Chin J. 1999. Rapid hydrolysis of 2’,3’-cAMP with a Cu(II) complex: effect of intramolecular hydrogen bonding on the basicity and reactivity of a metal-bound hydroxide. J. Am. Chem. Soc. 121(19):4710–4711. doi:10.1021/ja981227l.
   Web of Science ®Google Scholar
• Wang D, Qi J, Han W, Gao J-M, Horsman GP. 2020. Kanamycin-induced production of 2’,3’-cyclic AMP in Escherichia coli. Biochem Biophys Res Commun. 527(4):854–860. doi:10.1016/j.bbrc.2020.04.144.
   PubMed Web of Science ®Google Scholar
• Yakunin AF, Proudfoot M, Kuznetsova E, Savchenko A, Brown G, Arrowsmith CH, Edwards AM. 2004. The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2′,3′-cyclic phosphodiesterase, 2′-nucleotidase, and phosphatase activities. J Biol Chem. 279(35):36819–36827. doi:10.1074/jbc.M405120200.
   PubMed Web of Science ®Google Scholar
• Yu D, Song W, Tan EYJ, Liu L, Cao Y, Jirschitzka J, Li E, Logemann E, Xu C, Huang S, et al. 2022. TIR domains of plant immune receptors are 2′,3′-cAMP/cGMP synthetases mediating cell death. Cell. 185(13):2370–2386.e18. doi:10.1016/j.cell.2022.04.032.
   PubMed Web of Science ®Google Scholar
• Zambon A, Righi V, Parenti F, Libertini E, Rossi MC, Mucci A. 2019. Nucleoside 2 ‘,3 ‘-Cyclic monophosphates in aphanizomenon flos-aquae detected through nuclear magnetic resonance and mass spectrometry. J Agric Food Chem. 67(46):12780–12785. doi:10.1021/acs.jafc.9b05991.
   PubMed Web of Science ®Google Scholar
• Zaver SA, Woodward JJ. 2020. Cyclic dinucleotides at the forefront of innate immunity. Curr Opin Cell Biol. 63:49–56. doi:10.1016/j.ceb.2019.12.004.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Agrebi R, Bellows LE, Collet J-F, Kaever V, Gründling A. 2017. Evolutionary Adaptation of the essential tRNA methyltransferase TrmD to the signaling molecule 3′,5′-cAMP in bacteria. J Biol Chem. 292(1):313–327. doi:10.1074/jbc.M116.758896.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang J, Hara H, Kato I, Inouye M. 2005. Insights into the mRNA cleavage mechanism by MazF, an mRNA interferase. J Biol Chem. 280(5):3143–3150. doi:10.1074/jbc.M411811200.
   PubMed Web of Science ®Google Scholar
• Zhu M, Pan Y, Dai X. 2019. (p)ppGpp: the magic governor of bacterial growth economy. Curr Genet. 65(5):1121–1125. doi:10.1007/s00294-019-00973-z.
   PubMed Web of Science ®Google Scholar