Skip to main content

5′-3′ Exoribonucleases

  • Chapter
  • First Online:

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

Abstract

The 5′-3′ exoribonucleases have important functions in RNA processing, RNA degradation, RNA interference, transcription, and other cellular processes. The Xrn1 and Xrn2/Rat1 family of enzymes are the best characterized 5′-3′ exoribonucleases, and there has been significant recent progress in the understanding of their structure and function. Especially, the first structural information on Rat1 just became available. Other 5′-3′ exoribonucleases have been identified recently, including yeast Rrp17 and B. subtilis RNase J1, the first enzyme with 5′-3′ exoribonuclease activity found in prokaryotes. This review will summarize our current understanding of these enzymes, focusing on their sequence conservation, molecular structure, biochemical and cellular functions.

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

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Aldrich TL, di Segni G, McConaughy BL, Keen NJ, Whelen S, Hall BD (1993) Structure of the yeast TAP1 protein: dependence of transcription activation on the DNA context of the target gene. Mol Cell Biol 13:3434–3444

    PubMed  CAS  Google Scholar 

  • Amberg DC, Goldstein AL, Cole CN (1992) Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA. Genes Dev 6:1173–1189

    Article  PubMed  CAS  Google Scholar 

  • Bashkirov VI, Scherthan H, Solinger JA, Buerstedde JM, Heyer W-D (1997) A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates. J Cell Biol 136:761–773

    Article  PubMed  CAS  Google Scholar 

  • Buratowski S (2005) Connections between mRNA 3′ end processing and transcription termination. Curr Opin Cell Biol 17:257–261

    Article  PubMed  CAS  Google Scholar 

  • Ceska TA, Sayers JR, Stier G, Suck D (1996) A helical arch allowing single-stranded DNA to thread through T5 5′-exonuclease. Nature 382:90–93

    Article  PubMed  CAS  Google Scholar 

  • Chable-Bessia C, Meziane O, Latreille D, Triboulet R, Zamborlini A, Wagschal A, Jacquet J-M, Reynes J, Levy Y, Saib A et al (2009) Suppression of HIV-1 replication by microRNA effectors. Retrovirology 6:26

    Article  PubMed  CAS  Google Scholar 

  • Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA (2004) Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116:39–50

    Article  PubMed  CAS  Google Scholar 

  • Chen Y, Pane A, Schupbach T (2007) Cutoff and aubergine mutations result in retrotransposon upregulation and checkpoint activation in Drosophila. Curr Biol 17:637–642

    Article  PubMed  CAS  Google Scholar 

  • Cheng C-P, Serviene E, Nagy PD (2006) Suppression of viral RNA recombination by a host exoribonuclease. J Virol 80:2631–2640

    Article  PubMed  CAS  Google Scholar 

  • Chernyakov I, Whipple JM, Kotelawala L, Grayhack EJ, Phizicky EM (2008) Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5′-3′ exonucleases Rat1 and Xrn1. Genes Dev 22:1369–1380

    Article  PubMed  CAS  Google Scholar 

  • Clissold PM, Ponting CP (2000) PIN domains in nonsense-mediated mRNA decay and RNAi. Curr Biol 10:R888–R890

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Coller J, Parker R (2004) Eukaryotic mRNA decapping. Annu Rev Biochem 73:861–890

    Article  PubMed  CAS  Google Scholar 

  • Condon C (2010) What is the role of RNase J in mRNA turnover? RNA Biol 7:316–321

    Article  PubMed  CAS  Google Scholar 

  • Connelly S, Manley JL (1988) A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev 2:440–452

    Article  PubMed  CAS  Google Scholar 

  • Conti E, Izaurralde E (2005) Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol 17:316–325

    Article  PubMed  CAS  Google Scholar 

  • Danin-Kreiselman M, Lee CY, Chanfreau G (2003) RNase III-mediated degradation of unspliced pre-mRNAs and lariat introns. Mol Cell 11:1279–1289

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Deana A, Celesnik H, Belasco JG (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451:355–358

    Article  PubMed  CAS  Google Scholar 

  • Dengl S, Cramer P (2009) Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro. J Biol Chem 284:21270–21279

    Article  PubMed  CAS  Google Scholar 

  • Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC (2007) Crystal structure of bacteriophage T4 5′ nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates. J Biol Chem 282:31713–31724

    Article  PubMed  CAS  Google Scholar 

  • di Segni G, McConaughy BL, Shapiro RA, Aldrich TL, Hall BD (1993) TAP1, a yeast gene that activates the expression of a tRNA gene with a defective internal promoter. Mol Cell Biol 13:3424–3433

    PubMed  Google Scholar 

  • Dichtl B, Stevens A, Tollervey D (1997) Lithium toxicity in yeast is due to the inhibition of RNA processing enzymes. EMBO J 16:7184–7195

    Article  PubMed  CAS  Google Scholar 

  • Doma MK, Parker R (2007) RNA quality control in eukaryotes. Cell 131:660–668

    Article  PubMed  CAS  Google Scholar 

  • Dominski Z, Marzluff WF (2007) Formation of the 3′ end of histone mRNA: getting closer to the end. Gene 396:373–390

    Article  PubMed  CAS  Google Scholar 

  • Dominski Z, Yang X-C, Marzluff WF (2005) The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing. Cell 123:37–48

    Article  PubMed  CAS  Google Scholar 

  • Dykstra CC, Kitada K, Clark AB, Hamatake RK, Sugino A (1991) Cloning and characterization of DST2, the gene for DNA strand transfer protein beta from Saccharomyces cerevisiae. Mol Cell Biol 11:2583–2592

    PubMed  CAS  Google Scholar 

  • El Hage A, Koper M, Kufel J, Tollervey D (2008) Efficient termination of transcription by RNA polymerase I requires the 5′ exonuclease Rat1 in yeast. Genes Dev 22:1069–1081

    Article  PubMed  CAS  Google Scholar 

  • Esteban R, Vega L, Fujimura T (2008) 20S RNA Narnavirus defies the antiviral activity of SKI1/XRN1 in Saccharomyces cerevisiae. J Biol Chem 283:25812–25820

    Article  PubMed  CAS  Google Scholar 

  • Fang F, Phillips S, Butler JS (2005) Rat1p and Rai1p function with the nuclear exosome in the processing and degradation of rRNA precursors. RNA 11:1571–1578

    Article  PubMed  CAS  Google Scholar 

  • Fatica A, Tollervey D (2002) Making ribosomes. Curr Opin Cell Biol 14:313–318

    Article  PubMed  CAS  Google Scholar 

  • Gazzani S, Lawrenson T, Woodward C, Headon D, Sablowski R (2004) A link between mRNA turnover and RNA interference in Arabidopsis. Science 306:1046–1048

    Article  PubMed  CAS  Google Scholar 

  • Geerlings TH, Vos JC, Raue HA (2000) The final step in the formation of 25 S rRNA in Saccharomyces cerevisiae is performed by 5′–>3′ exonucleases. RNA 6:1698–1703

    Article  PubMed  CAS  Google Scholar 

  • Ghazal G, Gagnon J, Jacques P-E, Landry J-R, Robert F, Elela SA (2009) Yeast RNase III triggers polyadenylation-independent transcription termination. Mol Cell 36:99–109

    Article  PubMed  CAS  Google Scholar 

  • Gilmour DS, Fan R (2008) Derailing the locomotive: transcription termination. J Biol Chem 283:661–664

    Article  PubMed  CAS  Google Scholar 

  • Glavan F, Behm-Ansmant I, Izaurralde E, Conti E (2006) Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J 25:5117–5125

    Article  PubMed  CAS  Google Scholar 

  • Gregory BD, O’Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 14:854–866

    Article  PubMed  CAS  Google Scholar 

  • Gy I, Gasciolli V, Lauressergues D, Morel J-B, Gombert J, Proux F, Proux C, Vaucheret H, Mallory AC (2007) Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell 19:3451–3461

    Article  PubMed  CAS  Google Scholar 

  • Henry Y, Wood H, Morrissey JP, Petfalski E, Kearsey S, Tollervey D (1994) The 5′ end of yeast 5.8 S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J 13:2452–2463

    PubMed  CAS  Google Scholar 

  • Houseley J, Tollervey D (2009) The many pathways of RNA degradation. Cell 136:763–776

    Article  PubMed  CAS  Google Scholar 

  • Hsu CL, Stevens A (1993) Yeast cells lacking 5′–>3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Mol Cell Biol 13:4826–4835

    PubMed  CAS  Google Scholar 

  • Hu W, Sweet TJ, Chamnongpol S, Baker KE, Coller J (2009) Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461:225–229

    Article  PubMed  CAS  Google Scholar 

  • Hu W, Petzold C, Coller J, Baker KE (2010) Nonsense-mediated mRNA decapping occurs on polyribosomes in Saccharomyces cerevisiae. Nat Struct Mol Biol 17:244–247

    Article  PubMed  CAS  Google Scholar 

  • Hwang KY, Baek K, Kim H-Y, Cho Y (1998) The crystal structure of flap endonuclease-1 from Methanococcus jannaschii. Nat Struct Biol 5:707–713

    Article  PubMed  CAS  Google Scholar 

  • Interthal H, Bellocq C, Bahler J, Bashkirov VI, Edelstein S, Heyer W-D (1995) A role of Sep1 (=Kem1, Xrn1) as a microtubule-associated protein in Saccharomyces cerevisiae. EMBO J 14:1057–1066

    PubMed  CAS  Google Scholar 

  • Isken O, Maquat LE (2007) Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev 21:1833–1856

    Article  PubMed  CAS  Google Scholar 

  • Jiao X, Xiang S, Oh C-S, Martin CE, Tong L, Kiledjian M (2010) Identification of a quality-control mechanism for mRNA 5′-end capping. Nature 467:608–611

    Article  PubMed  CAS  Google Scholar 

  • Jimeno-Gonzalez S, Haaning LL, Malagon F, Jensen TH (2010) The yeast 5′-3′ exonuclease rat1p functions during transcription elongation by RNA polymerase II. Mol Cell 37:580–587

    Article  PubMed  CAS  Google Scholar 

  • Johnson AW (1997) Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively. Mol Cell Biol 17:6122–6130

    PubMed  CAS  Google Scholar 

  • Johnson AW, Kolodner RD (1995) Synthetic lethality of sep1 (xrn1) ski2 and sep1 (xrn1) ski3 mutants of Saccharomyces cerevisiae is independent of killer virus and suggests a general role for these genes in translation control. Mol Cell Biol 15:2719–2727

    PubMed  CAS  Google Scholar 

  • Jones DM, Domingues P, Targett-Adams P, McLauchlan J (2010) Comparison of U2OS and Huh-7 cells for identifying host factors that affect hepatitis C virus RNA replication. J Gen Virol 91:2238–2248

    Article  PubMed  CAS  Google Scholar 

  • Kaslin E, Heyer W-D (1994) A multifunctional exonuclease from vegetative Schizosaccharomyces pombe cells exhibiting in vitro strand exchange activity. J Biol Chem 269:14094–14102

    PubMed  CAS  Google Scholar 

  • Kastenmayer JP, Green PJ (2000) Novel features of the XRN-family in Arabidopsis: evidence that AtXRN4, one of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm. Proc Natl Acad Sci USA 97:13985–13990

    Article  PubMed  CAS  Google Scholar 

  • Kawauchi J, Mischo H, Braglia P, Rondon A, Proudfoot NJ (2008) Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes Dev 22:1082–1092

    Article  PubMed  CAS  Google Scholar 

  • Kearsey S, Kipling D (1991) Recombination and RNA processing: a common strand? Trends Cell Biol 1:110–112

    Article  PubMed  CAS  Google Scholar 

  • Kenna M, Stevens A, McCammon M, Douglas MG (1993) An essential yeast gene with homology to the exonuclease-encoding XRN1/KEM1 gene also encodes a protein with exoribonuclease activity. Mol Cell Biol 13:341–350

    PubMed  CAS  Google Scholar 

  • Kim J, Ljungdahl PO, Fink GR (1990) Kem mutations affect nuclear fusion in Saccharomyces cerevisiae. Genetics 126:799–812

    PubMed  CAS  Google Scholar 

  • Kim Y, Eom SH, Wang J, Lee D-S, Suh SW, Steitz TA (1995) Crystal structure of Thermus aquaticus DNA polymerase. Nature 376:612–616

    Article  PubMed  CAS  Google Scholar 

  • Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S (2004) The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432:517–522

    Article  PubMed  CAS  Google Scholar 

  • Kipling D, Tambini C, Kearsey SE (1991) Rar mutations which increase artificial chromosome stability in Saccharomyces cerevisiae identify transcription and recombination proteins. Nucleic Acids Res 19:1385–1391

    Article  PubMed  CAS  Google Scholar 

  • Kulkarni M, Ozgur S, Stoecklin G (2010) On track with P-bodies. Biochem Soc Trans 38:242–251

    Article  PubMed  CAS  Google Scholar 

  • Larimer FW, Stevens A (1990) Disruption of the gene XRN1, coding for a 5′-3′ exoribonuclease, restricts yeast cell growth. Gene 95:85–90

    Article  PubMed  CAS  Google Scholar 

  • Larimer FW, Hsu CL, Maupin MK, Stevens A (1992) Characterization of the XRN1 gene encoding 5′->3′ exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of gene-disrupted yeast cells. Gene 120:51–57

    Article  PubMed  CAS  Google Scholar 

  • Lee CY, Lee A, Chanfreau G (2003) The roles of endonucleolytic cleavage and exonucleolytic digestion in the 5′-end processing of S. cerevisiae box C/D snoRNAs. RNA 9:1362–1370

    Article  PubMed  CAS  Google Scholar 

  • Li C-H, Irmer H, Gudjonsdottir-Planck D, Freese S, Salm H, Haile S, Estevez AM, Clayton C (2006) Roles of a Trypanosoma brucei 5′-3′ exoribonuclease homolog in mRNA degradation. RNA 12:2171–2186

    Article  PubMed  CAS  Google Scholar 

  • Liu Z, Gilbert W (1994) The yeast KEM1 gene encodes a nuclease specific for G4 tetraplex DNA: implication of in vivo functions for this novel DNA structure. Cell 77:1083–1092

    Article  PubMed  CAS  Google Scholar 

  • Liu Z, Lee A, Gilbert W (1995) Gene disruption of a G4-DNA-dependent nuclease in yeast leads to cellular senescence and telomere shortening. Proc Natl Acad Sci USA 92:6002–6006

    Article  PubMed  CAS  Google Scholar 

  • Lu Y, Liu P, James M, Vikis HG, Liu H, Wen W, Franklin A, You M (2010) Genetic variants cis-regulating Xrn2 expression contribute to the risk of spontaneous lung tumor. Oncogene 29:1041–1049

    Article  PubMed  CAS  Google Scholar 

  • Luke B, Panza A, Redon S, Iglesias N, Li Z, Lingner J (2008) The Rat1p 5′ to 3′ exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae. Mol Cell 32:465–477

    Article  PubMed  CAS  Google Scholar 

  • Luo W, Bentley D (2004) A ribonucleolytic rat torpedoes RNA polymerase II. Cell 119:911–914

    Article  PubMed  CAS  Google Scholar 

  • Luo W, Johnson AW, Bentley DL (2006) The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev 20:954–965

    Article  PubMed  CAS  Google Scholar 

  • Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L (2006) Polyadenylation factor CPSF-73 is the pre-mRNA 3′-end-processing endonuclease. Nature 444:953–956

    Article  PubMed  CAS  Google Scholar 

  • Mandel CR, Bai Y, Tong L (2008) Protein factors in pre-mRNA 3′-end processing. Cell Mol Life Sci 65:1099–1122

    Article  PubMed  CAS  Google Scholar 

  • 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  PubMed  CAS  Google Scholar 

  • Mueser TC, Nossal NG, Hyde CC (1996) Structure of bacteriophage T4 RNase H, a 5′ to 3′ RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins. Cell 85:1101–1112

    Article  PubMed  CAS  Google Scholar 

  • Murali R, Sharkey DJ, Daiss JL, Murthy HMK (1998) Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: The Fab is directed against an intermediate in the helix-coil dynamics of the enzyme. Proc Natl Acad Sci USA 95:12562–12567

    Article  PubMed  CAS  Google Scholar 

  • Newbury S, Woollard A (2004) The 5′-3′ exoribonuclease xrn-1 is essential for ventral epithelial enclosure during C. elegans embryogenesis. RNA 10:59–65

    Article  PubMed  CAS  Google Scholar 

  • Oeffinger M, Zenklusen D, Ferguson A, Wei KE, El Hage A, Tollervey D, Chait BT, Singer RH, Rout MP (2009) Rrp17p is a eukaryotic exonuclease required for 5′ end processing of pre-60S ribosomal RNA. Mol Cell 36:768–781

    Article  PubMed  CAS  Google Scholar 

  • Olmedo G, Guo H, Gregory BD, Nourizadeh SD, Aguilar-Henonin L, Li H, An F, Guzman P, Ecker JR (2006) Ethylene-insensitive5 encodes a 5′->3′ exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2. Proc Natl Acad Sci USA 103:13286–13293

    Article  PubMed  CAS  Google Scholar 

  • Orban TI, Izaurralde E (2005) Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA 11:459–469

    Article  PubMed  CAS  Google Scholar 

  • Page AM, Davis K, Molineux C, Kolodner RD, Johnson AW (1998) Mutational analysis of exoribonuclease I from Saccharomyces cerevisiae. Nucleic Acids Res 26:3707–3716

    Article  PubMed  CAS  Google Scholar 

  • Park MH, Cho SA, Yoo KH, Yang MH, Ahn JY, Lee HS, Lee KE, Mun YC, Cho DH, Seong CM et al (2007) Gene expression profile related to prognosis of acute myeloid leukemia. Oncol Rep 18:1395–1402

    PubMed  CAS  Google Scholar 

  • Parker R, Sheth U (2007) P bodies and the control of mRNA translation and degradation. Mol Cell 25:635–646

    Article  PubMed  CAS  Google Scholar 

  • Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11:121–127

    Article  PubMed  CAS  Google Scholar 

  • Petfalski E, Dandekar T, Henry Y, Tollervey D (1998) Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol Cell Biol 18:1181–1189

    PubMed  CAS  Google Scholar 

  • Poole TL, Stevens A (1997) Structural modifications of RNA influence the 5′ exoribonucleolytic hydrolysis by XRN1 and HKE1 of Saccharomyces cerevisiae. Biochem Biophys Res Commun 235:799–805

    Article  PubMed  CAS  Google Scholar 

  • Potuschak T, Vansiri A, Binder BM, Lechner E, Vierstra RD, Genschik P (2006) The exoribonuclease XRN4 is a component of the ethylene response pathway in Arabidopsis. Plant Cell 18:3047–3057

    Article  PubMed  CAS  Google Scholar 

  • Proudfoot NJ (2004) New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr Opin Cell Biol 16:272–278

    Article  PubMed  CAS  Google Scholar 

  • Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry L, Caizergues-Ferrer M, Bachellerie JP (1999) Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast. Mol Cell Biol 19:1144–1158

    PubMed  CAS  Google Scholar 

  • Richard P, Manley JL (2009) Transcription termination by nuclear RNA polymerases. Genes Dev 23:1247–1269

    Article  PubMed  CAS  Google Scholar 

  • Rondon AG, Mischo HE, Kawauchi J, Proudfoot NJ (2009) Fail-safe transcriptional termination for protein-encoding genes in S. cerevisiae. Mol Cell 36:88–98

    Article  PubMed  CAS  Google Scholar 

  • Sakurai S, Kitano K, Yamaguchi H, Hamada K, Okada K, Fukuda K, Uchida M, Ohtsuka E, Morioka H, Hakoshima T (2005) Structural basis for recruitment of human flap endonuclease 1 to PCNA. EMBO J 24:683–693

    Article  PubMed  CAS  Google Scholar 

  • Sato Y, Shimamoto A, Shobuike T, Sugimoto M, Ikeda H, Kuroda S, Furuichi Y (1998) Cloning and characterization of human Sep1 (hSEP1) gene and cytoplasmic localization of its product. DNA Res 5:241–246

    Article  PubMed  CAS  Google Scholar 

  • Sayers JR, Artymiuk PJ (1998) Flexible loops and helical arches. Nat Struct Biol 5:668–670

    Article  PubMed  CAS  Google Scholar 

  • Scholes DT, Banerjee M, Bowen B, Curcio MJ (2001) Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics 159:1449–1465

    PubMed  CAS  Google Scholar 

  • Shimoyama Y, Morikawa Y, Ichihara M, Kodama Y, Fukuda N, Hayashi H, Morinaga T, Iwashita T, Murakumo Y, Takahashi M (2003) Identification of human SEP1 as a glial cell line-derived neurotrophic factor-inducible protein and its expression in the nervous system. Neurosci 121:899–906

    Article  CAS  Google Scholar 

  • Shobuike T, Sugano S, Yamashita T, Ikeda H (1995) Characterization of cDNA encoding mouse homolog of fission yeast dhp1+ gene: structural and functional conservation. Nucleic Acids Res 23:357–361

    Article  PubMed  CAS  Google Scholar 

  • Shobuike T, Sugano S, Yamashita T, Ikeda H (1997) Cloning and characterization of mouse Dhm2 cDNA, a functional homolog of budding yeast SEP1. Gene 191:161–166

    Article  PubMed  CAS  Google Scholar 

  • Shobuike T, Tatebayashi K, Tani T, Sugano S, Ikeda H (2001) The dhp1+ gene, encoding a putative nuclear 5′->3′ exoribonuclease, is required for proper chromosome segregation in fission yeast. Nucleic Acids Res 29:1326–1333

    Article  PubMed  CAS  Google Scholar 

  • Sinturel F, Pellegrini O, Xiang S, Tong L, Condon C, Benard L (2009) Real-time fluorescence detection of exoribonucleases. RNA 15:2057–2062

    Article  PubMed  CAS  Google Scholar 

  • Solinger JA, Pascolini D, Heyer W-D (1999) Active-site mutations in the Xrn1p exoribonuclease of Saccharomyces cerevisiae reveal a specific role in meiosis. Mol Cell Biol 19:5930–5942

    PubMed  CAS  Google Scholar 

  • Souret FF, Kastenmayer JP, Green PJ (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15:173–183

    Article  PubMed  CAS  Google Scholar 

  • Stevens A (1978) An exoribonuclease from Saccharomyces cerevisiae: effect of modifications of 5′ end groups on the hydrolysis of substrates to 5′ mononucleotides. Biochem Biophys Res Commun 81:656–661

    Article  PubMed  CAS  Google Scholar 

  • Stevens A (1980) Purification and characterization of a Saccharomyces cerevisiae exoribonuclease which yields 5′-mononucleotides by a 5′->3′ mode of hydrolysis. J Biol Chem 255:3080–3085

    PubMed  CAS  Google Scholar 

  • Stevens A, Poole TL (1995) 5′-exonuclease-2 of Saccharomyces cerevisiae. Purification and features of ribonuclease activity with comparison to 5′-exonuclease-1. J Biol Chem 270:16063–16069

    Article  PubMed  CAS  Google Scholar 

  • Stevens A, Hsu CL, Isham KR, Larimer FW (1991) Fragments of the internal transcribed spacer 1 of pre-rRNA accumulate in Saccharomyces cerevisiae lacking 5′-3′ exoribonuclease 1. J Bacteriol 173:7024–7028

    PubMed  CAS  Google Scholar 

  • Sugano S, Shobuike T, Takeda T, Sugino A, Ikeda H (1994) Molecular analysis of the dhp1+ gene of Schizosaccharomyces pombe: an essential gene that has homology to the DST2 and RAT1 genes of Saccharomyces cerevisiae. Mol Gen Genet 243:1–8

    Article  PubMed  CAS  Google Scholar 

  • Till DD, Linz B, Seago JE, Elgar SJ, Marujo PE, Elias ML, Arraiano CM, McClellan JA, McCarthy JE, Newbury SF (1998) Identification and developmental expression of a 5′-3′ exoribonuclease from Drosophila melanogaster. Mech Dev 79:51–55

    Article  PubMed  CAS  Google Scholar 

  • Tishkoff DX, Johnson AW, Kolodner RD (1991) Molecular and genetic analysis of the gene encoding the Saccharomyces cerevisiae strand exchange protein Sep1. Mol Cell Biol 11:2593–2608

    PubMed  CAS  Google Scholar 

  • Tishkoff DX, Rockmill B, Roeder GS, Kolodner RD (1995) The sep1 mutant of Saccharomyces cerevisiae arrests in pachytene and is deficient in meiotic recombination. Genetics 139:495–509

    PubMed  CAS  Google Scholar 

  • Villa T, Ceradini F, Presutti C, Bozzoni I (1998) Processing of the intron-encoded U18 small nucleolar RNA in the yeast Saccharomyces cerevisiae relies on both exo- and endonucleolytic activities. Mol Cell Biol 18:3376–3383

    PubMed  CAS  Google Scholar 

  • Wahle E, Ruegsegger U (1999) 3′-end processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev 23:277–295

    PubMed  CAS  Google Scholar 

  • West S, Proudfoot NJ (2008) Human Pcf11 enhances degradation of RNA polymerase II-associated nascent RNA and transcriptional termination. Nucleic Acids Res 36:905–914

    Article  PubMed  CAS  Google Scholar 

  • West S, Gromak N, Proudfoot NJ (2004) Human 5′->3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432:522–525

    Article  PubMed  CAS  Google Scholar 

  • Xiang S, Cooper-Morgan A, Jiao X, Kiledjian M, Manley JL, Tong L (2009) Structure and function of the 5′->3′ exoribonuclease Rat1 and its activating partner Rai1. Nature 458:784–788

    Article  PubMed  CAS  Google Scholar 

  • Xue Y, Bai X, Lee I, Kallstrom G, Ho J, Brown J, Stevens A, Johnson AW (2000) Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. Mol Cell Biol 20:4006–4015

    Article  PubMed  CAS  Google Scholar 

  • Yang W, Lee JY, Nowotny M (2006) Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol Cell 22:5–13

    Article  PubMed  CAS  Google Scholar 

  • Yang X-C, Sullivan KD, Marzluff WF, Dominski Z (2009) Studies of the 5′ exonuclease and endonuclease activities of CPSF-73 in histone pre-mRNA processing. Mol Cell Biol 29:31–42

    Article  PubMed  CAS  Google Scholar 

  • Zabolotskaya MV, Grima DP, Lin M-D, Chou T-B, Newbury SF (2008) The 5′-3′ exoribonuclease Pacman is required for normal male fertility and is dynamically localized in cytoplasmic particles in Drosophila testis cells. Biochem J 416:327–335

    Article  PubMed  CAS  Google Scholar 

  • Zakrzewska-Placzek M, Souret FF, Sobczyk GJ, Green PJ, Kufel J (2010) Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Nucleic Acids Res 38:4487–4502

    Article  PubMed  CAS  Google Scholar 

  • Zhang M, Yu L, Xin Y, Hu P, Fu Q, Yu C, Zhao S (1999) Cloning and mapping of the XRN2 gene to human chromosome 20p11.1-p11.2. Genomics 59:252–254

    Article  PubMed  CAS  Google Scholar 

  • Zhang K, Dion N, Fuchs B, Damron T, Gitelis S, Irwin R, O’Connor M, Schwartz H, Scully SP, Rock MG et al (2002) The human homolog of yeast SEP1 is a novel candidate tumor suppressor gene in osteogenic sarcoma. Gene 298:121–127

    Article  PubMed  CAS  Google Scholar 

  • Zhang Z, Fu J, Gilmour DS (2005) CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3′-end processing factor, Pcf11. Genes Dev 19:1572–1580

    Article  PubMed  CAS  Google Scholar 

  • Zhao J, Hyman L, Moore CL (1999) Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 63:405–445

    PubMed  CAS  Google Scholar 

  • Zuo Y, Deutscher MP (2001) Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res 29:1017–1026

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgment

This research is supported in part by grants from the NIH to LT (GM077175).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Liang Tong .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Chang, J.H., Xiang, S., Tong, L. (2011). 5′-3′ Exoribonucleases. In: Nicholson, A. (eds) Ribonucleases. Nucleic Acids and Molecular Biology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21078-5_7

Download citation

Publish with us

Policies and ethics