SpringerLink
Log in

An Overview of Ribonuclease Repertoire and RNA Processing Pathways in Archaea

  • Chapter
  • First Online:
RNA Metabolism and Gene Expression in Archaea

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 32))

Abstract

RNA processing plays a crucial role in post-transcriptional regulation of gene expression. Work conducted in Bacteria and Eukarya has defined the predominant mRNA maturation and decay pathways, as well as enzymes and cofactors responsible for these processes. In contrast, our knowledge of the mechanisms controlling RNA quality and processing in Archaea is more fragmentary. In essence, the major actors of RNA processing are ribonucleases acting in cleaving or trimming RNA molecules according to their nature and fate, making these enzymes fascinating and important players to study. More than 30 families of ribonucleases have been described in Bacteria and Eukarya, while only few have been identified in Archaea. This chapter is focused on the major ribonucleases in Archaea. After an overview of archaeal cellular RNA biotypes, we present synthetic up-to-date repertoire of the archaeal ribonuclease families as well as our state of knowledge on their roles in dedicated RNA processing pathways. In addition to this general description of archaeal RNA processing actors, specific pathways involved in processing of rRNAs, tRNAs, crRNAs and C/D sRNAs are detailed in other chapters.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
EUR 29.95
Price includes VAT (Germany)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
EUR 117.69
Price includes VAT (Germany)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
EUR 149.79
Price includes VAT (Germany)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
EUR 149.79
Price includes VAT (Germany)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Aravind L (1999) An evolutionary classification of the metallo-beta-lactamase fold proteins. In Silico Biol 1:69–91

    CAS  PubMed  Google Scholar 

  • Aravind L, Koonin EV (2001) A natural classification of Ribonucleases. Methods Enzymol 341:1–28

    Google Scholar 

  • Arkhipova V, Stolboushkina E, Kravchenko O, Kljashtorny V, Gabdulkhakov A, Garber M, Nikonov S, Martens B, Blasi U, Nikonov O (2015) Binding of the 5′-triphosphate end of mRNA to the gamma-subunit of translation initiation factor 2 of the crenarchaeon Sulfolobus solfataricus. J Mol Biol 427:3086–3095

    Article  CAS  PubMed  Google Scholar 

  • Arraiano CM, Mauxion F, Viegas SC, Matos RG, Seraphin B (2013) Intracellular ribonucleases involved in transcript processing and decay: precision tools for RNA. Biochim Biophys Acta 1829:491–513

    Article  CAS  PubMed  Google Scholar 

  • Bandyra KJ, Bouvier M, Carpousis AJ, Luisi BF (2013) The social fabric of the RNA degradosome. Biochim Biophys Acta 1829:514–522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barrangou R, Coute-Monvoisin AC, Stahl B, Chavichvily I, Damange F, Romero DA, Boyaval P, Fremaux C, Horvath P (2013) Genomic impact of CRISPR immunization against bacteriophages. Biochem Soc Trans 41:1383–1391

    Article  CAS  PubMed  Google Scholar 

  • Bini E, Dikshit V, Dirksen K, Drozda M, Blum P (2002) Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus. RNA 8:1129–1136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Current Opin Microbiol 14:274–281

    Article  Google Scholar 

  • Brooks SA (2010) Functional interactions between mRNA turnover and surveillance and the ubiquitin proteasome system. Wiley Interdiscip Rev RNA 1:240–252

    Article  CAS  PubMed  Google Scholar 

  • Bubeck D, Reijns MA, Graham SC, Astell KR, Jones EY, Jackson AP (2011) PCNA directs type 2 RNase H activity on DNA replication and repair substrates. Nucleic Acids Res 39:3652–3666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carpousis AJ (2007) The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61:71–87

    Article  CAS  PubMed  Google Scholar 

  • Carte J, Wang R, Li H, Terns RM, Terns MP (2008) Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 22:3489–3496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charpentier B, Muller S, Branlant C (2005) Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation. Nucleic Acids Res 33:3133–3144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chavarria NE, Hwang S, Cao S, Fu X, Holman M, Elbanna D, Rodriguez S, Arrington D, Englert M, Uthandi S, Soll D, Maupin-Furlow JA (2014) Archaeal Tuc1/Ncs6 homolog required for wobble uridine tRNA thiolation is associated with ubiquitin-proteasome, translation, and RNA processing system homologs. PLoS One 9:e99104

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chlebowski A, Lubas M, Jensen TH, Dziembowski A (2013) RNA decay machines: the exosome. Biochim Biophys Acta 1829:552–560

    Article  CAS  PubMed  Google Scholar 

  • Cho HD, Verlinde CL, Weiner AM (2005) Archaeal CCA-adding enzymes: central role of a highly conserved beta-turn motif in RNA polymerization without translocation. J Biol Chem 280:9555–9566

    Article  CAS  PubMed  Google Scholar 

  • Cho IM, Lai LB, Susanti D, Mukhopadhyay B, Gopalan V (2010) Ribosomal protein L7Ae is a subunit of archaeal RNase P. Proc Natl Acad Sci U S A 107:14573–14578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clouet-d’Orval B, Rinaldi D, Quentin Y, Carpousis AJ (2010) Euryarchaeal beta-CASP proteins with homology to bacterial RNase J Have 5′- to 3′-exoribonuclease activity. J Biol Chem 285:17574–17583

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Clouet-d’Orval B, Phung DK, Langendijk-Genevaux PS, Quentin Y (2015) Universal RNA-degrading enzymes in Archaea: prevalence, activities and functions of beta-CASP ribonucleases. Biochimie 118:278–285

    Article  PubMed  CAS  Google Scholar 

  • Condon C, Putzer H (2002) The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res 30:5339–5346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daiyasu H, Osaka K, Ishino Y, Toh H (2001) Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold. FEBS Lett 503:1–6

    Article  CAS  PubMed  Google Scholar 

  • Dar D, Prasse D, Schmitz RA, Sorek R (2016) Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea. Nat Microbiol 1:16143

    Article  CAS  PubMed  Google Scholar 

  • Dennis PP, Omer A (2005) Small non-coding RNAs in Archaea. Curr Opin Microbiol 8:685–694

    Article  CAS  PubMed  Google Scholar 

  • Dennis PP, Omer A, Lowe T (2001) A guided tour: small RNA function in Archaea. Mol Microbiol 40:509–519

    Article  CAS  PubMed  Google Scholar 

  • Deutscher MP (2009) Maturation and degradation of ribosomal RNA in bacteria. Prog Mol Biol Transl Sci 85:369–391

    Article  CAS  PubMed  Google Scholar 

  • Dominski Z (2007) Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism. Crit Rev Biochem Mol Biol 42:67–93

    Article  CAS  PubMed  Google Scholar 

  • Dominski Z, Carpousis AJ, Clouet-d’Orval B (2013) Emergence of the beta-CASP ribonucleases: highly conserved and ubiquitous metallo-enzymes involved in messenger RNA maturation and degradation. Biochim Biophys Acta 1829:532–551

    Article  CAS  PubMed  Google Scholar 

  • Dziembowski A, Lorentzen E, Conti E, Seraphin B (2007) A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol 14:15–22

    Article  CAS  PubMed  Google Scholar 

  • Evguenieva-Hackenberg E, Klug G (2009) RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli. Prog Mol Biol Transl Sci 85:275–317

    Article  CAS  PubMed  Google Scholar 

  • Evguenieva-Hackenberg E, Walter P, Hochleitner E, Lottspeich F, Klug G (2003) An exosome-like complex in Sulfolobus solfataricus. EMBO Rep 4:889–893

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Evguenieva-Hackenberg E, Hou L, Glaeser S, Klug G (2014) Structure and function of the archaeal exosome. Wiley Interdiscip Rev RNA 5:623–635

    CAS  PubMed  Google Scholar 

  • Farhoud MH, Wessels HJ, Steenbakkers PJ, Mattijssen S, Wevers RA, van Engelen BG, Jetten MS, Smeitink JA, van den Heuvel LP, Keltjens JT (2005) Protein complexes in the archaeon Methanothermobacter thermautotrophicus analyzed by blue native/SDS-PAGE and mass spectrometry. Mol Cell Proteomics 4:1653–1663

    Article  CAS  PubMed  Google Scholar 

  • Fernandez-Pevida A, Kressler D, de la Cruz J (2015) Processing of preribosomal RNA in Saccharomyces cerevisiae. Wiley Interdiscip Rev RNA 6:191–209

    Article  CAS  PubMed  Google Scholar 

  • Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9:102–114

    Article  CAS  PubMed  Google Scholar 

  • Frank DN, Pace NR (1998) Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67:153–180

    Article  CAS  PubMed  Google Scholar 

  • Franzetti B, Sohlberg B, Zaccai G, von Gabain A (1997) Biochemical and serological evidence for an RNase E-like activity in halophilic Archaea. J Bacteriol 179:1180–1185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garrett RA (2016) Archaeal physiology: The secrets of termination. Nat Microbiol 1:16159

    Article  CAS  PubMed  Google Scholar 

  • Gopalan V (2007) Uniformity amid diversity in RNase P. Proc Natl Acad Sci U S A 104:2031–2032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hasenohrl D, Lombo T, Kaberdin V, Londei P, Blasi U (2008) Translation initiation factor a/eIF2(-gamma) counteracts 5′ to 3′ mRNA decay in the archaeon Sulfolobus solfataricus. Proc Natl Acad Sci U S A 105:2146–2150

    Article  PubMed  PubMed Central  Google Scholar 

  • Hasenohrl D, Konrat R, Blasi U (2011) Identification of an RNase J ortholog in Sulfolobus solfataricus: implications for 5′-to-3′ directional decay and 5′-end protection of mRNA in Crenarchaeota. RNA 17:99–107

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hellmich UA, Weis BL, Lioutikov A, Wurm JP, Kaiser M, Christ NA, Hantke K, Kotter P, Entian KD, Schleiff E, Wohnert J (2013) Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA-protein interactions during small ribosomal subunit biogenesis. Proc Natl Acad Sci U S A 110:15253–15258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hennigan AN, Reeve JN (1994) mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing. Mol Microbiol 11:655–670

    Article  CAS  PubMed  Google Scholar 

  • Henras AK, Plisson-Chastang C, O'Donohue MF, Chakraborty A, Gleizes PE (2015) An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdiscip Rev RNA 6:225–242

    Article  CAS  PubMed  Google Scholar 

  • Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H (2012) X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res 40:10554–10566

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hochstrasser ML, Doudna JA (2015) Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem Sci 40:58–66

    Article  CAS  PubMed  Google Scholar 

  • Holzle A, Fischer S, Heyer R, Schutz S, Zacharias M, Walther P, Allers T, Marchfelder A (2008) Maturation of the 5S rRNA 5′ end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii. RNA 14:928–937

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huang HY, Hopper AK (2016) Multiple layers of stress-induced regulation in tRNA biology. Life (Basel) 6(2). pii: E16. doi:10.3390/life6020016

  • Hui MP, Foley PL, Belasco JG (2014) Messenger RNA degradation in bacterial cells. Annu Rev Genet 48:537–559

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jager A, Samorski R, Pfeifer F, Klug G (2002) Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase. Nucleic Acids Res 30:5436–5443

    Article  PubMed  PubMed Central  Google Scholar 

  • Jarrous N, Gopalan V (2010) Archaeal/eukaryal RNase P: subunits, functions and RNA diversification. Nucleic Acids Res 38:7885–7894

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanai A, Oida H, Matsuura N, Doi H (2003) Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus. Biochem J 372:253–261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kitamura S, Fujishima K, Sato A, Tsuchiya D, Tomita M, Kanai A (2010) Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus. Biochem J 426:337–344

    Article  CAS  PubMed  Google Scholar 

  • Kjems J, Garrett RA (1988) Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium Desulfurococcus mobilis. Cell 54:693–703

    Article  CAS  PubMed  Google Scholar 

  • Klemm BP, Wu N, Chen Y, Liu X, Kaitany KJ, Howard MJ, Fierke CA (2016) The diversity of ribonuclease P: protein and RNA catalysts with analogous biological functions. Biomolecules 6(2). pii: E27. doi:10.3390/biom6020027

  • Klug G, Evguenieva-Hackenberg E, Omer A, Dennis PP, Marchfelder A (2007) RNA processing. In: Cavicchioli R (ed) Archaea: molecular and cellular biology. ASM Press, Washington, DC, pp 158–174

    Chapter  Google Scholar 

  • Kochiwa H, Tomita M, Kanai A (2007) Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evol Biol 7:128

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Koonin EV, Wolf YI, Aravind L (2001) Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res 11:240–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lai LB, Vioque A, Kirsebom LA, Gopalan V (2010) Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett 584:287–296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lapinaite A, Simon B, Skjaerven L, Rakwalska-Bange M, Gabel F, Carlomagno T (2013) The structure of the box C/D enzyme reveals regulation of RNA methylation. Nature 502:519–523

    Article  CAS  PubMed  Google Scholar 

  • Levy S, Portnoy V, Admon J, Schuster G (2011) Distinct activities of several RNase J proteins in methanogenic archaea. RNA Biol 8:1073–1083

    Article  CAS  PubMed  Google Scholar 

  • Li H (2015) Structural principles of CRISPR RNA processing. Structure 23:13–20

    Article  CAS  PubMed  Google Scholar 

  • Li de la Sierra-Gallay I, Zig L, Jamalli A, Putzer H (2008) Structural insights into the dual activity of RNase J. Nat Struct Mol Biol 15:206–212

    Article  PubMed  CAS  Google Scholar 

  • Li L, Ye K (2006) Crystal structure of an H/ACA box ribonucleoprotein particle. Nature 443:302–307

    Article  CAS  PubMed  Google Scholar 

  • Li H, Trotta CR, Abelson J (1998) Crystal structure and evolution of a transfer RNA splicing enzyme. Science 280:279–284

    Article  CAS  PubMed  Google Scholar 

  • Liu Q, Greimann JC, Lima CD (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127:1223–1237

    Article  CAS  PubMed  Google Scholar 

  • Lopes RR, Kessler AC, Polycarpo C, Alfonzo JD (2015) Cutting, dicing, healing and sealing: the molecular surgery of tRNA. Wiley Interdiscip Rev RNA 6:337–349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lykke-Andersen J, Garrett RA (1997) RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history. EMBO J 16:6290–6300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T, Patel DJ (2005) Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434:666–670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mackie GA (2013) RNase E: at the interface of bacterial RNA processing and decay. Nat Rev Microbiol 11:45–57

    Article  CAS  PubMed  Google Scholar 

  • Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV (2015) An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 13:722–736

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marck C, Grosjean H (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8:1189–1232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marck C, Grosjean H (2003) Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA 9:1516–1531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martens B, Amman F, Manoharadas S, Zeichen L, Orell A, Albers SV, Hofacker I, Blasi U (2013) Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2. PLoS One 8:e76569

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Martens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Blasi U (2017) The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts. Nucleic Acids Res 45(13):7938–7949. doi:10.1093/nar/gkx437

  • Mathy N, Benard L, Pellegrini O, Daou R, Wen T, Condon C (2007) 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129:681–692

    Article  CAS  PubMed  Google Scholar 

  • Matos RG, Lopez-Vinas E, Gomez-Puertas P, Arraiano CM (2012) The only exoribonuclease present in Haloferax volcanii has an unique response to temperature changes. Biochim Biophys Acta 1820:1543–1552

    Article  CAS  PubMed  Google Scholar 

  • Mir-Montazeri B, Ammelburg M, Forouzan D, Lupas AN, Hartmann MD (2011) Crystal structure of a dimeric archaeal cleavage and polyadenylation specificity factor. J Struct Biol 173:191–195

    Article  CAS  PubMed  Google Scholar 

  • Nagarajan VK, Jones CI, Newbury SF, Green PJ (2013) XRN 5′-->3′ exoribonucleases: structure, mechanisms and functions. Biochim Biophys Acta 1829:590–603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Newman JA, Hewitt L, Rodrigues C, Solovyova A, Harwood CR, Lewis RJ (2011) Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1. Structure 19:1241–1251

    Article  CAS  PubMed  Google Scholar 

  • Nishida Y, Ishikawa H, Baba S, Nakagawa N, Kuramitsu S, Masui R (2010) Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii. Proteins 78:2395–2398

    Article  CAS  PubMed  Google Scholar 

  • Nolivos S, Carpousis AJ, Clouet-d’Orval B (2005) The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn. Nucleic Acids Res 33:6507–6514

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M (2004) Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29. RNA 10:1423–1432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ohtani N, Yanagawa H, Tomita M, Itaya M (2004a) Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucleic Acids Res 32:5809–5819

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ohtani N, Yanagawa H, Tomita M, Itaya M (2004b) Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction. Biochem J 381:795–802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW (1999) RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci U S A 96:7803–7808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peeters E, Peixeiro N, Sezonov G (2013) Cis-regulatory logic in archaeal transcription. Biochem Soc Trans 41:326–331

    Article  CAS  PubMed  Google Scholar 

  • Peeters E, Driessen RP, Werner F, Dame RT (2015) The interplay between nucleoid organization and transcription in archaeal genomes. Nat Rev Microbiol 13:333–341

    Article  CAS  PubMed  Google Scholar 

  • Phung DK, Rinaldi D, Langendijk-Genevaux PS, Quentin Y, Carpousis AJ, Clouet-d’Orval B (2013) Archaeal beta-CASP ribonucleases of the aCPSF1 family are orthologs of the eukaryal CPSF-73 factor. Nucleic Acids Res 41:1091–1103

    Article  CAS  PubMed  Google Scholar 

  • Portnoy V, Schuster G (2006) RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Res 34:5923–5931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Portnoy V, Evguenieva-Hackenberg E, Klein F, Walter P, Lorentzen E, Klug G, Schuster G (2005) RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus. EMBO Rep 6:1188–1193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Proudfoot NJ (2011) Ending the message: poly(A) signals then and now. Genes Dev 25:1770–1782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ramos CR, Oliveira CL, Torriani IL, Oliveira CC (2006) The Pyrococcus exosome complex: structural and functional characterization. J Biol Chem 281:6751–6759

    Article  CAS  PubMed  Google Scholar 

  • Randau L, Schroder I, Soll D (2008) Life without RNase P. Nature 453:120–123

    Article  CAS  PubMed  Google Scholar 

  • Redko Y, Li de Lasierra-Gallay I, Condon C (2007) When all’s zed and done: the structure and function of RNase Z in prokaryotes. Nat Rev Microbiol 5:278–286

    Article  CAS  PubMed  Google Scholar 

  • Samanta MP, Lai SM, Daniels CJ, Gopalan V (2016) Sequence analysis and comparative study of the protein subunits of archaeal RNase P. Biomolecules 6

    Google Scholar 

  • Santangelo TJ, Cubonova L, Skinner KM, Reeve JN (2009) Archaeal intrinsic transcription termination in vivo. J Bacteriol 191:7102–7108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schierling K, Rosch S, Rupprecht R, Schiffer S, Marchfelder A (2002) tRNA 3′ end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii. J Mol Biol 316:895–902

    Article  CAS  PubMed  Google Scholar 

  • Schiffer S, Rosch S, Marchfelder A (2002) Assigning a function to a conserved group of proteins: the tRNA 3′-processing enzymes. EMBO J 21:2769–2777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Silva AP, Chechik M, Byrne RT, Waterman DG, Ng CL, Dodson EJ, Koonin EV, Antson AA, Smits C (2011) Structure and activity of a novel archaeal beta-CASP protein with N-terminal KH domains. Structure 19:622–632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sinapah S, Wu S, Chen Y, Pettersson BM, Gopalan V, Kirsebom LA (2011) Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection. Nucleic Acids Res 39:1105–1116

    Article  CAS  PubMed  Google Scholar 

  • Sorek R, Lawrence CM, Wiedenheft B (2013) CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem 82:237–266

    Article  CAS  PubMed  Google Scholar 

  • Spang A, Saw JH, Jorgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spath B, Canino G, Marchfelder A (2007) tRNase Z: the end is not in sight. Cell Mol Life Sci 64:2404–2412

    Article  CAS  PubMed  Google Scholar 

  • Spath B, Schubert S, Lieberoth A, Settele F, Schutz S, Fischer S, Marchfelder A (2008) Two archaeal tRNase Z enzymes: similar but different. Arch Microbiol 190:301–308

    Article  PubMed  CAS  Google Scholar 

  • Stoecklin G, Muhlemann O (2013) RNA decay mechanisms: specificity through diversity. Biochim Biophys Acta 1829:487–490

    Article  CAS  PubMed  Google Scholar 

  • Tadokoro T, Kanaya S (2009) Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes. FEBS J 276:1482–1493

    Article  CAS  PubMed  Google Scholar 

  • Tang TH, Rozhdestvensky TS, Clouet-d’Orval B, Bortolin ML, Huber H, Charpentier B, Branlant C, Bachellerie JP, Brosius J, Huttenhofer A (2002) RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res 30:921–930

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tannous E, Kanaya S (2014) Divalent metal ion-induced folding mechanism of RNase H1 from extreme halophilic archaeon Halobacterium sp. NRC-1. PLoS One 9:e109016

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Thompson LD, Daniels CJ (1988) A tRNA(Trp) intron endonuclease from Halobacterium volcanii. Unique substrate recognition properties. J Biol Chem 263:17951–17959

    CAS  PubMed  Google Scholar 

  • van der Oost J, Westra ER, Jackson RN, Wiedenheft B (2014) Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol 12:479–492

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Veith T, Martin R, Wurm JP, Weis BL, Duchardt-Ferner E, Safferthal C, Hennig R, Mirus O, Bohnsack MT, Wohnert J, Schleiff E (2012) Structural and functional analysis of the archaeal endonuclease Nob1. Nucleic Acids Res 40:3259–3274

    Article  CAS  PubMed  Google Scholar 

  • Vincent HA, Deutscher MP (2009) The roles of individual domains of RNase R in substrate binding and exoribonuclease activity. The nuclease domain is sufficient for digestion of structured RNA. J Biol Chem 284:486–494

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vogel A, Schilling O, Spath B, Marchfelder A (2005) The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties. Biol Chem 386:1253–1264

    CAS  PubMed  Google Scholar 

  • Weiner AM (2004) tRNA maturation: RNA polymerization without a nucleic acid template. Curr Biol 14:R883–R885

    Article  CAS  PubMed  Google Scholar 

  • Werner F (2007) Structure and function of archaeal RNA polymerases. Mol Microbiol 65:1395–1404

    Article  CAS  PubMed  Google Scholar 

  • Werner F, Grohmann D (2011) Evolution of multisubunit RNA polymerases in the three domains of life. Nat Rev Microbiol 9:85–98

    Article  CAS  PubMed  Google Scholar 

  • Westra ER, Swarts DC, Staals RH, Jore MM, Brouns SJ, van der Oost J (2012) The CRISPRs, they are a-changin’: how prokaryotes generate adaptive immunity. Annu Rev Genet 46:311–339

    Article  CAS  PubMed  Google Scholar 

  • Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331–338

    Article  CAS  PubMed  Google Scholar 

  • Yip WS, Shigematsu H, Taylor DW, Baserga SJ (2016) Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs. Nucleic Acids Res 44:8976–8989

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zago MA, Dennis PP, Omer AD (2005) The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 55:1812–1828

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

BCO and MB are supported by the Centre National de la Recherche Scientifique (CNRS) with additional funding from the Agence Nationale de la Recherche (ANR-16-CE12-0016-01) and from the Université de Toulouse (IDEX « Emergence » call 2014).

Author information

Authors and Affiliations

  1. Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, 31062, Toulouse, France

    Duy Khanh Phung, Marie Bouvier & Béatrice Clouet-d’Orval

Authors
  1. Duy Khanh Phung
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marie Bouvier
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Béatrice Clouet-d’Orval
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Béatrice Clouet-d’Orval .

Editor information

Editors and Affiliations

  1. Laboratoire de Microbiologie et de Génétique, Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France

    Béatrice Clouet-d'Orval

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Phung, D.K., Bouvier, M., Clouet-d’Orval, B. (2017). An Overview of Ribonuclease Repertoire and RNA Processing Pathways in Archaea. In: Clouet-d'Orval, B. (eds) RNA Metabolism and Gene Expression in Archaea. Nucleic Acids and Molecular Biology, vol 32. Springer, Cham. https://doi.org/10.1007/978-3-319-65795-0_4

Download citation

Publish with us

Policies and ethics

Search

Navigation