Russian version English version
About the Journal
Editorial Board
Instructions for Authors
Information for Readers and Authors
Current Issue
Archive
Contact Us
Search

Send manuscript
 


Volume 19   Issue 2   Year 2024
References

  1. Lybecker M., Bilusic I., Raghavan R. Pervasive transcription: detecting functional RNAs in bacteria. Transcription. 2014;5. Article No. e944039. doi: 10.4161/21541272.2014.944039
  2. Soltani-Fard E., Taghvimi S., Abedi Kichi Z., Weber C., Shabaninejad Z., Taheri-Anganeh M., Hossein Khatami S., Mousavi P., Movahedpour A., Natarelli L. Insights into the function of regulatory RNAs in bacteria and archaea. Int. J. Transl. Med. 2021;1:403–423. doi: 10.3390/ijtm1030024
  3. Lagunas-Rangel F.A. Role of circular RNAs in DNA repair. RNA Biol. 2024;21:149–161. doi: 10.1080/15476286.2024.2429945
  4. Dance A. Circular logic: understanding RNA's strangest form yet. Nature. 2024;635:511–513. doi: 10.1038/d41586-024-03683-w
  5. Mamuye A.L., Merelli E., Tesei L. A graph grammar for modelling RNA folding. arXiv preprint. 2016. Article No. arXiv:1612.01639. doi: Cite to nonCR doi: 10.48550/arXiv.1612.01639
  6. Wu H., Yu H., Zhang Y., Yang B., Sun W., Ren L., Li Y., Li Q., Liu B., Ding Y., Zhang H. Unveiling RNA structure-mediated regulations of RNA stability in wheat. Nat. Commun. 2024;15. Article No. 10042. doi: 10.1038/s41467-024-54172-7
  7. Harris S.E., Alexis M.S., Giri G., Cavazos Jr F.F., Hu Y., Murn J., Aleman M.M., Burge C.B., Dominguez D. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. Nat. Commun. 2024;15. Article No. 8400. doi: 10.1038/s41467-024-52231-7
  8. Nguyen T.C., Zaleta-Rivera K., Huang X., Dai X., Zhong S. RNA, Action through Interactions. Trends Genet. 2018;34:867–882. doi: 10.1016/j.tig.2018.08.001
  9. Zhou M., Xiao M.S., Li Z.G., Huang C. New progresses of circular RNA biology: from nuclear export to degradation. RNA Biol. 2021;18:1365–1373. doi: 10.1080/15476286.2020.1853977
  10. Innocenti N., Nguyen H.-S., d'Herouel A.F., Aurell E. An observation of circular RNAs in bacterial RNA-seq data. arXiv preprint. 2016. Article No. arXiv:1606.04576. doi: Cite to nonCR doi: 10.48550/arXiv.1606.04576
  11. Shavkunov K.S., Markelova N.Y., Glazunova O.A., Kolzhetsov N.P., Panyukov V.V., Ozoline O.N. The fate and functionality of alien tRNA fragments in culturing medium and cells of Escherichia coli. Int. J. Mol. Sci. 2023;24. Article No. 12960. doi: 10.3390/ijms241612960
  12. Carrier M.-C., Lalaouna D., Masse E. Broadening the definition of bacterial small RNAs: characteristics and mechanisms of action. Annu. Rev. Microbiol. 2018;72:141–161. doi: 10.1146/annurev-micro-090817-062607
  13. Wagner E.G.H., Romby P. Small RNAs in bacteria and archaea: who they are, what they do, and how they do it. Adv. Genet. 2015;90:133–208. doi: 10.1016/bs.adgen.2015.05.001
  14. Miyakoshi M., Chao Y., Vogel J. Regulatory small RNAs from the 3' regions of bacterial mRNAs. Curr. Opin. Microbiol. 2015;24:132–139. doi: 10.1016/j.mib.2015.01.013
  15. Chao Y., Vogel J. A 3' UTR-derived small RNA provides the regulatory noncoding arm of the inner membrane stress response. Mol. Cell. 2016;61:352–363. doi: 10.1016/j.molcel.2015.12.023
  16. Ren G.-X., Guo X.-P., Sun Y.C. Regulatory 3'-untranslated regions of bacterial mRNAs. Front. Microbiol. 2017;8. Article No. 1276. doi: 10.3389/fmicb.2017.01276
  17. Manna A.C., Kim S., Cengher L., Corvaglia A., Leo S., Francois P., Cheung A.L. Small RNA teg49 is derived from a sarA transcript and regulates virulence genes independent of SarA in Staphylococcus aureus. Infect. Immun. 2018;86. Article No. e00635-17. doi: 10.1128/IAI.00635-17
  18. Lalaouna D., Carrier M.C., Semsey S., Brouard J.S., Wang J., Wade J.T., Masse E. A 3' external transcribed spacer in a tRNA transcript acts as a sponge for small RNAs to prevent transcriptional noise. Mol. Cell. 2015;58:393–405. doi: 10.1016/j.molcel.2015.03.013
  19. Shepherd J., Ibba M. Bacterial transfer RNAs. FEMS Microbiol. Rev. 2015;39:280–300. doi: 10.1093/femsre/fuv004
  20. Diebel K.W., Zhou K., Clarke A.B., Bemis L.T. Beyond the ribosome: extra-translational functions of tRNA fragments. Biomark. Insights. 2016;11(1):1–8. doi: 10.4137/BMI.S35904
  21. Hou J., Li Q., Wang J., Lu W. tRFs and tRNA halves: novel cellular defenders in multiple biological processes. Curr. Issues Mol. Biol. 2022;44:5949–5962. doi: 10.3390/cimb44120405
  22. George S., Rafi M., Aldarmaki M., ElSiddig M., Al Nuaimi M., Amiri K.M.A. tRNA derived small RNAs - small players with big roles. Front. Genet. 2022;13. Article No. 997780. doi: 10.3389/fgene.2022.997780
  23. Li Z., Stanton B.A. Transfer RNA-derived fragments, the underappreciated regulatory small RNAs in microbial pathogenesis. Front. Microbiol. 2021;12. Article No. 687632. doi: 10.3389/fmicb.2021.687632
  24. Ren B., Wang X., Duan J., Ma J. Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation. Science. 2019;365:919–922. doi: 10.1126/science.aav8907
  25. Morad I., Chapman-Shimshoni D., Amitsur M., Kaufmann G. Functional expression and properties of the tRNA(Lys)-specific core anticodon nuclease encoded by Escherichia coli prrC. J. Biol. Chem. 1993;268:26842–26849. doi: 10.1016/S0021-9258(19)74188-X
  26. Tomita K., Ogawa T., Uozumi T., Watanabe K., Masaki H. A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. Proc. Natl. Acad. Sci. USA. 2000;97:8278–8283. doi: 10.1073/pnas.140213797
  27. Cao K.-Y., Pan Y., Yan T.-M., Tao P., Xiao Y., Jiang Z.-H. Antitumor activities of tRNA-derived fragments and tRNA halves from non-pathogenic Escherichia coli strains on colorectal cancer and their structure-activity relationship. mSystems. 2022;7. Article No. e00164-22. doi: 10.1128/msystems.00164-22
  28. Wagner E.G., Simons R.W. Antisense RNA control in bacteria, phages, and plasmids. Annu. Rev. Microbiol. 1994;48:713–742. doi: 10.1146/annurev.mi.48.100194.003433
  29. Zhang Y., Liu X.S., Liu Q.R., Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 2006;34:3465–3475. doi: 10.1093/nar/gkl473
  30. Tutukina M.N., Shavkunov K.S., Masulis I.S., Ozoline O.N. Antisense transcription within the hns locus of Escherichia coli. Mol. Biol. 2010;44:439–447. doi: 10.1134/S002689331003012X
  31. Tutukina M.N., Dakhnovets A.I., Kaznadzey A.D., Gelfand M.S., Ozoline O.N. Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein. Front. Mol. Biosci. 2023;10. Article No. 1121376. doi: 10.3389/fmolb.2023.1121376
  32. Schwenk S., Arnvig K.B. Regulatory RNA in Mycobacterium tuberculosis, back to basics. Pathog. Dis. 2018;76. Article No. fty035. doi: 10.1093/femspd/fty035
  33. Coban I., Lamping J.P., Hirsch A.G., Wasilewski S., Shomroni O., Giesbrecht O., Salinas G., Krebber H. dsRNA formation leads to preferential nuclear export and gene expression. Nature. 2024;631:432–438. doi: 10.1038/s41586-024-07576-w
  34. Hör J., Matera G., Vogel J., Gottesman S., Storz G. Trans-acting small RNAs and their effects on gene expression in Escherichia coli and Salmonella enterica. EcoSal Plus. 2020;9. Article No. ESP-0030-2019. doi: 10.1128/ecosalplus.esp-0030-2019
  35. Boudry P., Piattelli E., Drouineau E., Peltier J., Boutserin A., Lejars M., Hajnsdorf E., Monot M., Dupuy B., Martin-Verstraete I. et al. Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile. RNA Biol. 2021;18:1931–1952. doi: 10.1080/15476286.2021.1882180
  36. Mandin P., Gottesman S. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J. 2010;29:3094–3107. doi: 10.1038/emboj.2010.179
  37. Ghosal A., Upadhyaya B.B., Fritz J.V., Heintz-Buschart A., Desai M.S., Yusuf D., Huang D., Baumuratov A., Wang K., Galas D., Wilmes P. The extracellular RNA complement of Escherichia coli. Microbiologyopen. 2015;4:252–266. doi: 10.1002/mbo3.235
  38. Koeppen K., Hampton T.H., Jarek M., Scharfe M., Gerber S.A., Mielcarz D.W., Demers E.G., Dolben E.L., Hammond J.H., Hogan D.A., Stanton B.A. A novel mechanism of host-pathogen interaction through sRNA in bacterial outer membrane vesicles. PLoS Pathog. 2016;12. Article No. e1005672. doi: 10.1371/journal.ppat.1005672
  39. Blenkiron C., Simonov D., Muthukaruppan A., Tsai P., Dauros P., Green S., Hong J., Print C.G., Swift S., Phillips A.R. Uropathogenic Escherichia coli releases extracellular vesicles that are associated with RNA. PLoS One. 2016;11. Article No. e0160440. doi: 10.1371/journal.pone.0160440
  40. Alikina O.V., Glazunova O.A., Bykov A.A., Kiselev S.S., Tutukina M.N., Shavkunov K.S., Ozoline O.N. A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli. FEMS Microbiol. Lett. 2018;365. Article No. fny262. doi: 10.1093/femsle/fny262
  41. Pita T., Feliciano J.R., Leitao J.H. Extracellular RNAs in bacterial infections: from emerging key players on host-pathogen interactions to exploitable biomarkers and therapeutic targets. Int. J. Mol. Sci. 2020;21. Article No. 9634. doi: 10.3390/ijms21249634
  42. Obregón-Henao A., Duque-Correa M.A., Rojas M., Garcia L.F., Brennan P.J., Ortiz B.L., Belisle J.T. Stable extracellular RNA fragments of Mycobacterium tuberculosis induce early apoptosis in human monocytes via a caspase-8 dependent mechanism. PLoS One. 2012;7. Article No. e29970. doi: 10.1371/journal.pone.0029970
  43. Markelova N., Glazunova O., Alikina O., Panyukov V., Shavkunov K., Ozoline O. Suppression of Escherichia coli growth dynamics via RNAs secreted by competing bacteria. Front. Mol. Biosci. 2021;8. Article No. 609979. doi: 10.3389/fmolb.2021.609979
  44. Lee H.J., Hong S.H. Analysis of microRNA-size, small RNAs in Streptococcus mutans by deep sequencing. FEMS Microbiol. Lett. 2012;326:131–136. doi: 10.1111/j.1574-6968.2011.02441.x
  45. Diallo I., Ho J., Lalaouna D., Masse E., Provost P. RNA sequencing unveils very small RNAs with potential regulatory functions in bacteria. Front. Mol. Biosci. 2022;9. Article No. 914991. doi: 10.3389/fmolb.2022.914991
  46. Bykov A., Glazunova O., Alikina O., Sukharicheva N., Masulis I., Shavkunov K., Ozoline O. Excessive promoters as silencers of genes horizontally acquired by Escherichia coli. Front. Mol. Biosci. 2020;7. Article No. 28. doi: 10.3389/fmolb.2020.00028
  47. Afgan E., Baker D., Batut B., van den Beek M., Bouvier D., Cech M., Chilton J., Clements D., Coraor N., Gruning B.A. 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
  48. Panyukov V.V., Kiselev S.S., Shavkunov K.S., Masulis I.S., Ozoline O.N. Mixed promoter islands as genomic regions with specific structural and functional properties. Math. Biol. Bioinf. 2013;8:432–448 (in Russ.). doi: 10.17537/2013.8.432
  49. Panyukov V.V., Ozoline O.N. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS One. 2013;8. Article No. e62601. doi: 10.1371/journal.pone.0062601
  50. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340
  51. Reuter J.S., Mathews D.H. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 2010;11. Article No. 129. doi: 10.1186/1471-2105-11-129
  52. Wolf S.G., Frenkiel D., Arad T., Finkel S.E., Kolter R., Minsky A. DNA protection by stress-induced biocrystallization. Nature. 1999;400:83–85. doi: 10.1038/21918
  53. Bykov A.A., Shavkunov K.S., Panyukov V.V., Ozoline O.N. Bacterial nucleoid protein Dps binds structured RNA molecules. Math. Biol. Bioinf. 2017;12(Suppl.):t1–t11. doi: 10.17537/2017.12.t1
  54. Ghatak, P., Karmakar K., Kasetty S., Chatterji D. Unveiling the role of Dps in the organization of mycobacterial nucleoid. PLoS One. 2011;6. Article No. e16019. doi: 10.1371/journal.pone.0016019
  55. Janissen R., Arens M.M.A., Vtyurina N.N., Rivai Z., Sunday N.D., Eslami-Mossallam B., Gritsenko A.A., Laan L., de Ridder D., Artsimovitch I., Dekker N.H., Abbondanzieri E.A., Meyer A.S. Global DNA compaction in stationary-phase bacteria does not affect transcription. Cell. 2018;174:1188–1199. doi: 10.1016/j.cell.2018.06.049
  56. Park C., Jin Y., Kim Y.J., Jeong H., Seong B.L. RNA-binding as chaperones of DNA binding proteins from starved cells. Biochem. Biophys. Res. Commun. 2020;524:484–489. doi: 10.1016/j.bbrc.2020.01.121
  57. Lacqua A., Wanner O., Colangelo T., Martinotti M.G., Landini P. Emergence of biofilm-forming subpopulations upon exposure of Escherichia coli to environmental bacteriophages. Appl. Environ. Microbiol. 2006;72:956–959. doi: 10.1128/AEM.72.1.956-959.2006
  58. Theoret J.R., Cooper K.K., Zekarias B., Roland K.L., Law B.F., Curtiss 3rd R., Joens L.A. The Campylobacter jejuni Dps homologue is important for in vitro biofilm formation and cecal colonization of poultry and may serve as a protective antigen for vaccination. Clin. Vaccine Immunol. 2012;19:1426–1431. doi: 10.1128/CVI.00151-12
  59. Pang B., Hong W., Kock N.D., Swords W.E. Dps promotes survival of nontypeable Haemophilus influenzae in biofilm communities in vitro and resistance to clearance in vivo. Front. Cell Infect. Microbiol. 2012;2. Article No. 58. doi: 10.3389/fcimb.2012.00058
  60. Leroy S., Lebert I., Andant C., Micheau P., Talon R. Investigating extracellular DNA release in Staphylococcus xylosus biofilm in vitro. Microorganisms. 2021;9. Article No. 2192. doi: 10.3390/microorganisms9112192
  61. Kawano M., Reynolds A.A., Miranda-Rios J., Storz G. Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res. 2005;33:1040–1050. doi: 10.1093/nar/gki256
  62. Wassarman K.M., Storz G. 6S RNA regulates E. coli RNA polymerase activity. Cell. 2000;101:613–623. doi: 10.1016/S0092-8674(00)80873-9
  63. Perumal K., Reddy R. The 3' end formation in small RNAs. Gene Expr. 2002;10:59–78.
  64. Depaix A., Grudzien-Nogalska E., Fedorczyk B., Kiledjian M., Jemielity J., Kowalska J. Preparation of RNAs with non-canonical 5' ends using novel di- and trinucleotide reagents for co-transcriptional capping. Front. Mol. Biosci. 2022;9. Article No. 854170. doi: 10.3389/fmolb.2022.854170
  65. Vishwakarma R.K., Brodolin K. The σ subunit-remodeling factors: an emerging paradigms of transcription regulation. Front. Microbiol. 2020;11. Article No. 1798. doi: 10.3389/fmicb.2020.01798
  66. Pallesen L., Madsen O., Klemm P. Regulation of the phase switch controlling expression of type 1 fimbriae in Escherichia coli. Mol. Microbiol. 1989;3:925–931. doi: 10.1111/j.1365-2958.1989.tb00242.x
  67. Greenblatt J., Mah T.F., Legault P., Mogridge J., Li J., Kay L.E. Structure and mechanism in transcriptional antitermination by the bacteriophage λ N protein. Cold Spring Harb. Symp. Quant. Biol. 1998;63:327–336. doi: 10.1101/sqb.1998.63.327
  68. Huang Q., Cheng X., Cheung M.K., Kiselev S.S., Ozoline O.N., Kwan H.S. High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS One. 2012;7. Article No. e33759. doi: 10.1371/journal.pone.0033759
  69. Goldman S.R., Sharp J.S., Vvedenskaya I.O., Livny J., Dove S.L., Nickels B.E. NanoRNAs prime transcription initiation in vivo. Mol. Cell. 2011;42:817–825. doi: 10.1016/j.molcel.2011.06.005
Table of Contents
Original Article
Shavkunov K.S., Markelova N.Yu., Alikina O.V., Glazunova O.A., Panyukov V.V., Kolzhetsov N.P., Kiselev S.S., Ozoline O.N. Products of abortive transcription can prime synthesis of chimeric oligonucleotides. Ìàthematical biology and bioinformatics. 2024;19(2):453-471. doi: 10.17537/2024.19.453
(published in English)

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
References
Supplementary data

 
  Copyright IMPB RAS © 2005-2026