Intracellular ribonucleases involved in transcript processing and decay: Precision tools for RNA

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1829, Issue 6-7, 2013, Pages 491-513

  Arraiano, Cecília Maria ^a   Mauxion, Fabienne ^b   Viegas, Sandra Cristina ^a   Matos, Rute Gonçalves ^a   Séraphin, Bertrand ^b  

^a INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Protein domains; Protein families; Ribonucleases; RNA decay; RNA processing; Structure

Indexed keywords

CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR; DIS3 PROTEIN; DIS3L2 PROTEIN; DNA; ENDONUCLEASE EXONUCLEASE PHOSPHATASE; EUKARYOTIC PROTEIN; EXORIBONUCLEASE; FERREDOXIN; INTRACELLULAR RIBONUCLEASE; MESSENGER RNA; PHOSPHATASE; PHOSPHOLIPASE D; PNPASE PROTEIN; PROTEIN; REG B PROTEIN; RIBONUCLEASE; RIBONUCLEASE E; RIBONUCLEASE G; RIBONUCLEASE H; RIBONUCLEASE II; RIBONUCLEASE III; RIBONUCLEASE J; RIBONUCLEASE Y; RIBONUCLEASE Z; RIBOSOME RNA; RNA; TRANSFER RNA; UNCLASSIFIED DRUG; ZUCCHINI PROTEIN;

BIOLOGICAL FUNCTIONS; ENZYME ACTIVE SITE; ENZYME STRUCTURE; EXOSOME; HUMAN; NONHUMAN; PH; PRIORITY JOURNAL; REVIEW; RNA PROCESSING;

ARCHAEA; DNA; ENDORIBONUCLEASES; ESCHERICHIA COLI; EXORIBONUCLEASES; HUMANS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RNA STABILITY; RNA, MESSENGER;

EID: 84877796956     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2013.03.009     Document Type: Review

References (378)

1. Aravind L., Koonin E.V. A natural classification of ribonucleases. Methods Enzymol. 2001, 341:3-28.
2. Thore S., Mauxion F., Seraphin B., Suck D. X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep. 2003, 4:1150-1155.
3. Horiuchi M., Takeuchi K., Noda N., Muroya N., Suzuki T., Nakamura T., Kawamura-Tsuzuku J., Takahasi K., Yamamoto T., Inagaki F. Structural basis for the antiproliferative activity of the Tob-hCaf1 complex. J. Biol. Chem. 2009, 284:13244-13255.
4. Jonstrup A.T., Andersen K.R., Van L.B., Brodersen D.E. The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme. Nucleic Acids Res. 2007, 35:3153-3164.
5. Zuo Y., Wang Y., Malhotra A. Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing. Structure 2005, 13:973-984.
6. Januszyk K., Liu Q., Lima C.D. Activities of human RRP6 and structure of the human RRP6 catalytic domain. RNA 2011, 17:1566-1577.
7. Midtgaard S.F., Assenholt J., Jonstrup A.T., Van L.B., Jensen T.H., Brodersen D.E. Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:11898-11903.
8. Steitz T.A., Steitz J.A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. 1993, 90:6498-6502.
9. Cudny H., Deutscher M.P. Apparent involvement of ribonuclease D in the 3' processing of tRNA precursors. Proc. Natl. Acad. Sci. U. S. A. 1980, 77:837-841.
10. Zhang J.R., Deutscher M.P. Transfer RNA is a substrate for RNase D in vivo. J. Biol. Chem. 1988, 263:17909-17912.
11. Viswanathan M., Dower K.W., Lovett S.T. Identification of a potent DNase activity associated with RNase T of Escherichia coli. J. Biol. Chem. 1998, 273:35126-35131.
12. Zuo Y., Zheng H., Wang Y., Chruszcz M., Cymborowski M., Skarina T., Savchenko A., Malhotra A., Minor W. Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover. Structure 2007, 15:417-428.
13. Zuo Y., Deutscher M.P. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res. 2001, 29:1017-1026.
14. Ghosh S., Deutscher M.P. Oligoribonuclease is an essential component of the mRNA decay pathway. Proc. Natl. Acad. Sci. U. S. A. 1999, 96:4372-4377.
15. Zhang X., Zhu L., Deutscher M.P. Oligoribonuclease is encoded by a highly conserved gene in the 3'-5' exonuclease superfamily. J. Bacteriol. 1998, 180:2779-2781.
16. Mechold U., Ogryzko V., Ngo S., Danchin A. Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells. Nucleic Acids Res. 2006, 34:2364-2373.
17. Ohnishi Y., Nishiyama Y., Sato R., Kameyama S., Horinouchi S. An oligoribonuclease gene in Streptomyces griseus. J. Bacteriol. 2000, 182:4647-4653.
18. 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.
19. Liu M.F., Cescau S., Mechold U., Wang J., Cohen D., Danchin A., Boulouis H.J., Biville F. Identification of a novel nanoRNase in Bartonella. Microbiology 2012, 158:886-895.
20. Hanekamp T., Thorsness P.E. YNT20, a bypass suppressor of yme1 yme2, encodes a putative 3'-5' exonuclease localized in mitochondria of Saccharomyces cerevisiae. Curr. Genet. 1999, 34:438-448.
21. van Hoof A., Lennertz P., Parker R. Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. EMBO J. 2000, 19:1357-1365.
22. Nguyen L.H., Erzberger J.P., Root J., Wilson D.M. The human homolog of Escherichia coli Orn degrades small single-stranded RNA and DNA oligomers. J. Biol. Chem. 2000, 275:25900-25906.
23. Boeck R., Tarun S., Rieger M., Deardorff J.A., Muller-Auer S., Sachs A.B. The yeast Pan2 protein is required for poly(A)-binding protein-stimulated poly(A)-nuclease activity. J. Biol. Chem. 1996, 271:432-438.
24. Daugeron M.C., Mauxion F., Seraphin B. The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation. Nucleic Acids Res. 2001, 29:2448-2455.
25. Tucker M., Valencia-Sanchez M.A., Staples R.R., Chen J., Denis C.L., Parker R. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 2001, 104:377-386.
26. Basquin J., Roudko V.V., Rode M., Basquin C., Seraphin B., Conti E. Architecture of the nuclease module of the Yeast Ccr4-Not complex: the Not1-Caf1-Ccr4 interaction. Mol. Cell 2012, 48:207-218.
27. Petit A.P., Wohlbold L., Bawankar P., Huntzinger E., Schmidt S., Izaurralde E., Weichenrieder O. The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex. Nucleic Acids Res. 2012, 40:11058-11072.
28. Wiederhold K., Passmore L.A. Cytoplasmic deadenylation: regulation of mRNA fate. Biochem. Soc. Trans. 2010, 38:1531-1536.
29. Collart M.A., Panasenko O.O. The Ccr4-not complex. Gene 2012, 492:42-53.
30. Chen J., Chiang Y.C., Denis C.L. CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. EMBO J. 2002, 21:1414-1426.
31. Tucker M., Staples R.R., Valencia-Sanchez M.A., Muhlrad D., Parker R. Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO J. 2002, 21:1427-1436.
32. Bianchin C., Mauxion F., Sentis S., Seraphin B., Corbo L. Conservation of the deadenylase activity of proteins of the Caf1 family in human. RNA 2005, 11:487-494.
33. Mauxion F., Faux C., Seraphin B. The BTG2 protein is a general activator of mRNA deadenylation. EMBO J. 2008, 27:1039-1048.
34. Sandler H., Kreth J., Timmers H.T., Stoecklin G. Not1 mediates recruitment of the deadenylase Caf1 to mRNAs targeted for degradation by tristetraprolin. Nucleic Acids Res. 2011, 39:4373-4386.
35. Brown C.E., Tarun S.Z., Boeck R., Sachs A.B. PAN3 encodes a subunit of the Pab1p-dependent poly(A) nuclease in Saccharomyces cerevisiae. Mol. Cell. Biol. 1996, 16:5744-5753.
36. Yamashita A., Chang T.C., Yamashita Y., Zhu W., Zhong Z., Chen C.Y., Shyu A.B. Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat. Struct. Mol. Biol. 2005, 12:1054-1063.
37. Albert T.K., Lemaire M., van Berkum N.L., Gentz R., Collart M.A., Timmers H.T. Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits. Nucleic Acids Res. 2000, 28:809-817.
38. Berthet C., Morera A.M., Asensio M.J., Chauvin M.A., Morel A.P., Dijoud F., Magaud J.P., Durand P., Rouault J.P. CCR4-associated factor CAF1 is an essential factor for spermatogenesis. Mol. Cell. Biol. 2004, 24:5808-5820.
39. Nakamura T., Yao R., Ogawa T., Suzuki T., Ito C., Tsunekawa N., Inoue K., Ajima R., Miyasaka T., Yoshida Y., Ogura A., Toshimori K., Noce T., Yamamoto T., Noda T. Oligo-astheno-teratozoospermia in mice lacking Cnot7, a regulator of retinoid X receptor beta. Nat. Genet. 2004, 36:528-533.
40. Washio-Oikawa K., Nakamura T., Usui M., Yoneda M., Ezura Y., Ishikawa I., Nakashima K., Noda T., Yamamoto T., Noda M. Cnot7-null mice exhibit high bone mass phenotype and modulation of BMP actions. J. Bone Miner. Res. 2007, 22:1217-1223.
41. Wagner E., Clement S.L., Lykke-Andersen J. An unconventional human Ccr4-Caf1 deadenylase complex in nuclear cajal bodies. Mol. Cell. Biol. 2007, 27:1686-1695.
42. Korner C.G., Wahle E. Poly(A) tail shortening by a mammalian poly(A)-specific 3'-exoribonuclease. J. Biol. Chem. 1997, 272:10448-10456.
43. Wu M., Reuter M., Lilie H., Liu Y., Wahle E., Song H. Structural insight into poly(A) binding and catalytic mechanism of human PARN. EMBO J. 2005, 24:4082-4093.
44. Dehlin E., Wormington M., Korner C.G., Wahle E. Cap-dependent deadenylation of mRNA. EMBO J. 2000, 19:1079-1086.
45. Martinez J., Ren Y.G., Nilsson P., Ehrenberg M., Virtanen A. The mRNA cap structure stimulates rate of poly(A) removal and amplifies processivity of degradation. J. Biol. Chem. 2001, 276:27923-27929.
46. Nagata T., Suzuki S., Endo R., Shirouzu M., Terada T., Inoue M., Kigawa T., Kobayashi N., Guntert P., Tanaka A., Hayashizaki Y., Muto Y., Yokoyama S. The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition. Nucleic Acids Res. 2008, 36:4754-4767.
47. Wu M., Nilsson P., Henriksson N., Niedzwiecka A., Lim M.K., Cheng Z., Kokkoris K., Virtanen A., Song H. Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease. Structure 2009, 17:276-286.
48. Monecke T., Schell S., Dickmanns A., Ficner R. Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode. J. Mol. Biol. 2008, 382:827-834.
49. Berndt H., Harnisch C., Rammelt C., Stohr N., Zirkel A., Dohm J.C., Himmelbauer H., Tavanez J.P., Huttelmaier S., Wahle E. Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming. RNA 2012, 18:958-972.
50. Briggs M.W., Burkard K.T., Butler J.S. Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8S rRNA 3' end formation. J. Biol. Chem. 1998, 273:13255-13263.
51. Bernstein D.A., Keck J.L. Conferring substrate specificity to DNA helicases: role of the RecQ HRDC domain. Structure 2005, 13:1173-1182.
52. Wyers F., Rougemaille M., Badis G., Rousselle J.C., Dufour M.E., Boulay J., Regnault B., Devaux F., Namane A., Seraphin B., Libri D., Jacquier A. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 2005, 121:725-737.
53. Lebreton A., Tomecki R., Dziembowski A., Seraphin B. Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 2008, 456:993-996.
54. Wasmuth E.V., Lima C.D. Exo- and endoribonucleolytic activities of yeast cytoplasmic and nuclear RNA exosomes are dependent on the noncatalytic core and central channel. Mol. Cell 2012, 48:133-144.
55. Gabel H.W., Ruvkun G. The exonuclease ERI-1 has a conserved dual role in 5.8S rRNA processing and RNAi. Nat. Struct. Mol. Biol. 2008, 15:531-533.
56. Kennedy S., Wang D., Ruvkun G. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 2004, 427:645-649.
57. Cheng Y., Patel D.J. Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP. J. Mol. Biol. 2004, 343:305-312.
58. Iida T., Kawaguchi R., Nakayama J. Conserved ribonuclease, Eri1, negatively regulates heterochromatin assembly in fission yeast. Curr. Biol. 2006, 16:1459-1464.
59. Yang X.C., Purdy M., Marzluff W.F., Dominski Z. Characterization of 3'hExo, a 3' exonuclease specifically interacting with the 3' end of histone mRNA. J. Biol. Chem. 2006, 281:30447-30454.
60. Kupsco J.M., Wu M.J., Marzluff W.F., Thapar R., Duronio R.J. Genetic and biochemical characterization of Drosophila Snipper: a promiscuous member of the metazoan 3'hExo/ERI-1 family of 3' to 5' exonucleases. RNA 2006, 12:2103-2117.
61. Horio T., Murai M., Inoue T., Hamasaki T., Tanaka T., Ohgi T. Crystal structure of human ISG20, an interferon-induced antiviral ribonuclease. FEBS Lett. 2004, 577:111-116.
62. Frazão C., McVey C.E., Amblar M., Barbas A., Vonrhein C., Arraiano C.M., Carrondo M.A. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature 2006, 443:110-114.
63. Mian I.S. Comparative sequence analysis of ribonucleases HII, III, II PH and D. Nucleic Acids Res. 1997, 25:3187-3195.
64. Arraiano C.M., Andrade J.M., Domingues S., Guinote I.B., Malecki M., Matos R.G., Moreira R.N., Pobre V., Reis F.P., Saramago M., Silva I.J., Viegas S.C. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol. Rev. 2010, 34:883-923.
65. Barbas A., Matos R.G., Amblar M., Lopez-Vinas E., Gomez-Puertas P., Arraiano C.M. Determination of key residues for catalysis and RNA cleavage specificity: one mutation turns RNase II into a "SUPER-ENZYME". J. Biol. Chem. 2009, 284:20486-20498.
66. Cannistraro V.J., Kennell D. The processive reaction mechanism of ribonuclease II. J. Mol. Biol. 1994, 243:930-943.
67. Spickler C., Mackie G.A. Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J. Bacteriol. 2000, 182:2422-2427.
68. Marujo P.E., Hajnsdorf E., Le Derout J., Andrade R., Arraiano C.M., Régnier P. RNase II removes the oligo(A) tails that destabilize the rpsO mRNA of Escherichia coli. RNA 2000, 6:1185-1193.
69. Matos R.G., Fialho A.M., Giloh M., Schuster G., Arraiano C.M. The rnb gene of Synechocystis PCC6803 encodes a RNA hydrolase displaying RNase II and not RNase R enzymatic properties. PLoS One 2012, 7:e32690.
70. Rott R., Zipor G., Portnoy V., Liveanu V., Schuster G. RNA polyadenylation and degradation in cyanobacteria are similar to the chloroplast but different from Escherichia coli. J. Biol. Chem. 2003, 278:15771-15777.
71. Amblar M., Barbas A., Fialho A.M., Arraiano C.M. Characterization of the functional domains of Escherichia coli RNase II. J. Mol. Biol. 2006, 360:921-933.
72. Schmier B.J., Seetharaman J., Deutscher M.P., Hunt J.F., Malhotra A. The structure and enzymatic properties of a novel RNase II family enzyme from Deinococcus radiodurans. J. Mol. Biol. 2012, 415:547-559.
73. Amblar M., Arraiano C.M. A single mutation in Escherichia coli ribonuclease II inactivates the enzyme without affecting RNA binding. FEBS J. 2005, 272:363-374.
74. Barbas A., Matos R.G., Amblar M., Lopez-Viñas E., Goméz-Puertas P., Arraiano C.M. New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product. J. Biol. Chem. 2008, 283:13070-13076.
75. Dziembowski A., Lorentzen E., Conti E., Seraphin B. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat. Struct. Mol. Biol. 2007, 14:15-22.
76. Matos R.G., Barbas A., Arraiano C.M. RNase R mutants elucidate the catalysis of structured RNA: RNA-binding domains select the RNAs targeted for degradation. Biochem. J. 2009, 423:291-301.
77. Arraiano C.M., Matos R.G., Barbas A. RNase II: the finer details of the Modus operandi of a molecular killer. RNA Biol. 2010, 7:276-281.
78. Awano N., Rajagopal V., Arbing M., Patel S., Hunt J., Inouye M., Phadtare S. Escherichia coli RNase R has dual activities, helicase and RNase. J. Bacteriol. 2010, 192:1344-1352.
79. Charpentier X., Faucher S.P., Kalachikov S., Shuman H.A. Loss of RNase R induces competence development in Legionella pneumophila. J. Bacteriol. 2008, 190:8126-8136.
80. Vincent H.A., Deutscher M.P. Substrate recognition and catalysis by the exoribonuclease RNase R. J. Biol. Chem. 2006, 281:29769-29775.
81. Matos R.G., Barbas A., Goméz-Puertas P., Arraiano C.M. Swapping the domains of exoribonucleases RNase II and RNase R: conferring upon RNase II the ability to degrade ds RNA. Proteins 2011, 79:1853-1867.
82. Vincent H.A., Deutscher M.P. 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. 2009, 284:486-494.
83. Vincent H.A., Deutscher M.P. Insights into how RNase R degrades structured RNA: analysis of the nuclease domain. J. Mol. Biol. 2009, 387:570-583.
84. Cairrão F., Arraiano C.M. The role of endoribonucleases in the regulation of RNase R. Biochem. Biophys. Res. Commun. 2006, 343:731-737.
85. Andrade J.M., Cairrão F., Arraiano C.M. RNase R affects gene expression in stationary phase: regulation of ompA. Mol. Microbiol. 2006, 60:219-228.
86. Cairrão F., Cruz A., Mori H., Arraiano C.M. Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Mol. Microbiol. 2003, 50:1349-1360.
87. Chen C., Deutscher M.P. Elevation of RNase R in response to multiple stress conditions. J. Biol. Chem. 2005, 280:34393-34396.
88. Chen C., Deutscher M.P. RNase R is a highly unstable protein regulated by growth phase and stress. RNA 2010, 16:667-672.
89. Liang W., Deutscher M.P. A novel mechanism for ribonuclease regulation: transfer-messenger RNA (tmRNA) and its associated protein SmpB regulate the stability of RNase R. J. Biol. Chem. 2010, 285:29054-29058.
90. Liang W., Malhotra A., Deutscher M.P. Acetylation regulates the stability of a bacterial protein: growth stage-dependent modification of RNase R. Mol. Cell 2011, 44:160-166.
91. Cheng Z.F., Deutscher M.P. Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:6388-6393.
92. Li Z., Reimers S., Pandit S., Deutscher M.P. RNA quality control: degradation of defective transfer RNA. EMBO J. 2002, 21:1132-1138.
93. Andrade J.M., Hajnsdorf E., Régnier P., Arraiano C.M. The poly(A)-dependent degradation pathway of rpsO mRNA is primarily mediated by RNase R. RNA 2009, 15:316-326.
94. Ge Z., Mehta P., Richards J., Karzai A.W. Non-stop mRNA decay initiates at the ribosome. Mol. Microbiol. 2010, 78:1159-1170.
95. Jacob A.I., Kohrer C., Davies B.W., Rajbhandary U.L., Walker G.C. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol. Cell 2013, 49:427-438.
96. Strader M.B., Hervey W.J.t., Costantino N., Fujigaki S., Chen C.Y., Akal-Strader A., Ihunnah C.A., Makusky A.J., Court D.L., Markey S.P., Kowalak J.A. A coordinated proteomic approach for identifying proteins that interact with the E. coli ribosomal protein S12. J. Proteome Res. 2013, 12:1289-1299.
97. Alluri R.K., Li Z. Novel one-step mechanism for tRNA 3'-end maturation by the exoribonuclease RNase R of Mycoplasma genitalium. J. Biol. Chem. 2012, 287:23427-23433.
98. Matos R.G., Lopez-Vinas E., Gomez-Puertas P., Arraiano C.M. The only exoribonuclease present in Haloferax volcanii has an unique response to temperature changes. Biochim. Biophys. Acta 2012, 1820:1543-1552.
99. Erova T.E., Kosykh V.G., Fadl A.A., Sha J., Horneman A.J., Chopra A.K. Cold shock exoribonuclease R (VacB) is involved in Aeromonas hydrophila pathogenesis. J. Bacteriol. 2008, 190:3467-3474.
100. Purusharth R.I., Klein F., Sulthana S., Jager S., Jagannadham M.V., Evguenieva-Hackenberg E., Ray M.K., Klug G. Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudomonas syringae Lz4W. J. Biol. Chem. 2005, 280:14572-14578.
101. Cairrão F., Arraiano C., Newbury S. Drosophila gene tazman, an orthologue of the yeast exosome component Rrp44p/Dis3, is differentially expressed during development. Dev. Dyn. 2005, 232:733-737.
102. Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G., Sanchez-Rotunno M., Arraiano C.M., van Hoof A. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat. Struct. Mol. Biol. 2009, 16:56-62.
103. Schneider C., Leung E., Brown J., Tollervey D. The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome. Nucleic Acids Res. 2009, 37:1127-1140.
104. Schaeffer D., Reis F.P., Johnson S.J., Arraiano C.M., van Hoof A. The CR3 motif of Rrp44p is important for interaction with the core exosome and exosome function. Nucleic Acids Res. 2012, 40:9298-9307.
105. Bonneau F., Basquin J., Ebert J., Lorentzen E., Conti E. The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 2009, 139:547-559.
106. Lee G., Bratkowski M.A., Ding F., Ke A., Ha T. Elastic coupling between RNA degradation and unwinding by an exoribonuclease. Science 2012, 336:1726-1729.
107. Houseley J., LaCava J., Tollervey D. RNA-quality control by the exosome. Nat. Rev. 2006, 7:529-539.
108. Lebreton A., Seraphin B. Exosome-mediated quality control: substrate recruitment and molecular activity. Biochim. Biophys. Acta 2008, 1779:558-565.
109. Chlebowski A., Tomecki R., Lopez M.E., Seraphin B., Dziembowski A. Catalytic properties of the eukaryotic exosome. Adv. Exp. Med. Biol. 2011, 702:63-78.
110. Liu Q., Greimann J.C., Lima C.D. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 2006, 127:1223-1237.
111. Chekanova J.A., Shaw R.J., Wills M.A., Belostotsky D.A. Poly(A) tail-dependent exonuclease AtRrp41p from Arabidopsis thaliana rescues 5.8S rRNA processing and mRNA decay defects of the yeast ski6 mutant and is found in an exosome-sized complex in plant and yeast cells. J. Biol. Chem. 2000, 275:33158-33166.
112. Makino D.L., Baumgartner M., Conti E. Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Nature 2013, 495:70-75.
113. Lorentzen E., Basquin J., Tomecki R., Dziembowski A., Conti E. Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Mol. Cell 2008, 29:717-728.
114. Gudipati R.K., Xu Z., Lebreton A., Seraphin B., Steinmetz L.M., Jacquier A., Libri D. Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol. Cell 2012, 48:409-421.
115. Schneider C., Kudla G., Wlotzka W., Tuck A., Tollervey D. Transcriptome-wide analysis of exosome targets. Mol. Cell 2012, 48:422-433.
116. Staals R.H., Bronkhorst A.W., Schilders G., Slomovic S., Schuster G., Heck A.J., Raijmakers R., Pruijn G.J. Dis3-like 1: a novel exoribonuclease associated with the human exosome. EMBO J. 2010, 29:2358-2367.
117. Tomecki R., Kristiansen M.S., Lykke-Andersen S., Chlebowski A., Larsen K.M., Szczesny R.J., Drazkowska K., Pastula A., Andersen J.S., Stepien P.P., Dziembowski A., Jensen T.H. The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L. EMBO J. 2010, 29:2342-2357.
118. Gas M.E., Seraphin B. Twins take the job. EMBO J. 2010, 29:2260-2261.
119. Dziembowski A., Malewicz M., Minczuk M., Golik P., Dmochowska A., Stepien P.P. The yeast nuclear gene DSS1, which codes for a putative RNase II, is necessary for the function of the mitochondrial degradosome in processing and turnover of RNA. Mol. Gen. Genet. 1998, 260:108-114.
120. Chen C.Y., Rosamond J. Candida albicans SSD1 can suppress multiple mutations in Saccharomyces cerevisiae. Microbiology 1998, 144(Pt 11):2941-2950.
121. Luukkonen B.G., Seraphin B. A conditional U5 snRNA mutation affecting pre-mRNA splicing and nuclear pre-mRNA retention identifies SSD1/SRK1 as a general splicing mutant suppressor. Nucleic Acids Res. 1999, 27:3455-3465.
122. Astuti D., Morris M.R., Cooper W.N., Staals R.H., Wake N.C., Fews G.A., Gill H., Gentle D., Shuib S., Ricketts C.J., Cole T., van Essen A.J., van Lingen R.A., Neri G., Opitz J.M., Rump P., Stolte-Dijkstra I., Muller F., Pruijn G.J., Latif F., Maher E.R. Germline mutations in DIS3L2 cause the Perlman syndrome of overgrowth and Wilms tumor susceptibility. Nat. Genet. 2012, 44:277-284.
123. Zhang W., Murphy C., Sieburth L.E. Conserved RNase II domain protein functions in cytoplasmic mRNA decay and suppresses Arabidopsis decapping mutant phenotypes. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:15981-15985.
124. Malecki M., Viegas S.C., Carneiro T., Golik P., Dressaire C., Ferreira M.G., Arraiano C.M. Characterization of Dis3L2 exoribonuclease discloses a novel RNA degradation pathway in eukaryotes. EMBO J. 2013 Mar15, (Epub ahead of print).
125. Nurmohamed S., Vaidialingam B., Callaghan A.J., Luisi B.F. Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. J. Mol. Biol. 2009, 389:17-33.
126. Deutscher M.P., Marshall G.T., Cudny H. RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase. Proc. Natl. Acad. Sci. U. S. A. 1988, 85:4710-4714.
127. Grumberg-Manago M. Polynucleotide phosphorylase. Prog. Nucleic Acid Res. Mol. Biol. 1963, 1:93-133.
128. Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'→5' exoribonucleases. Cell 1997, 91:457-466.
129. Choi J.M., Park E.Y., Kim J.H., Chang S.K., Cho Y. Probing the functional importance of the hexameric ring structure of RNase PH. J. Biol. Chem. 2004, 279:755-764.
130. Harlow L.S., Kadziola A., Jensen K.F., Larsen S. Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding. Protein Sci. 2004, 13:668-677.
131. Ishii R., Nureki O., Yokoyama S. Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. J. Biol. Chem. 2003, 278:32397-32404.
132. Kelly K.O., Deutscher M.P. Characterization of Escherichia coli RNase PH. J. Biol. Chem. 1992, 267:17153-17158.
133. Wen T., Oussenko I.A., Pellegrini O., Bechhofer D.H., Condon C. Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis. Nucleic Acids Res. 2005, 33:3636-3643.
134. Li Z., Pandit S., Deutscher M.P. 3' exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:2856-2861.
135. Redko Y., Condon C. Maturation of 23S rRNA in Bacillus subtilis in the absence of Mini-III. J. Bacteriol. 2010, 192:356-359.
136. Zhou Z., Deutscher M.P. An essential function for the phosphate-dependent exoribonucleases RNase PH and polynucleotide phosphorylase. J. Bacteriol. 1997, 179:4391-4395.
137. Bralley P., Gust B., Chang S., Chater K.F., Jones G.H. RNA 3'-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase. Microbiology 2006, 152:627-636.
138. Jain C. Novel role for RNase PH in the degradation of structured RNA. J. Bacteriol. 2012, 194:3883-3890.
139. Basturea G.N., Zundel M.A., Deutscher M.P. Degradation of ribosomal RNA during starvation: comparison to quality control during steady-state growth and a role for RNase PH. RNA 2011, 17:338-345.
140. Kelly K.O., Reuven N.B., Li Z., Deutscher M.P. RNase PH is essential for tRNA processing and viability in RNase-deficient Escherichia coli cells. J. Biol. Chem. 1992, 267:16015-16018.
141. Briani F., Del Favero M., Capizzuto R., Consonni C., Zangrossi S., Greco C., De Gioia L., Tortora P., Dehò G. Genetic analysis of polynucleotide phosphorylase structure and functions. Biochimie 2007, 89:145-157.
142. Jarrige A., Brechemier-Baey D., Mathy N., Duche O., Portier C. Mutational analysis of polynucleotide phosphorylase from Escherichia coli. J. Mol. Biol. 2002, 321:397-409.
143. Amblar M., Barbas A., Goméz-Puertas P., Arraiano C.M. The role of the S1 domain in exoribonucleolytic activity: substrate specificity and multimerization. RNA 2007, 13:317-327.
144. Matus-Ortega M.E., Regonesi M.E., Pina-Escobedo A., Tortora P., Dehò G., García-Mena J. The KH and S1 domains of Escherichia coli polynucleotide phosphorylase are necessary for autoregulation and growth at low temperature. Biochim. Biophys. Acta 2007, 1769:194-203.
145. Shi Z., Yang W.Z., Lin-Chao S., Chak K.F., Yuan H.S. Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation. RNA 2008, 14:2361-2371.
146. Symmons M.F., Jones G.H., Luisi B.F. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure 2000, 8:1215-1226.
147. Guarneros G., Portier C. Different specificities of ribonuclease II and polynucleotide phosphorylase in 3'mRNA decay. Biochimie 1991, 73:543-549.
148. De Lay N., Gottesman S. Role of polynucleotide phosphorylase in sRNA function in Escherichia coli. RNA 2011, 17:1172-1189.
149. Andrade J.M., Pobre V., Matos A.M., Arraiano C.M. The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq. RNA 2012, 18:844-855.
150. Grunberg-Manago M., Oritz P.J., Ochoa S. Enzymatic synthesis of nucleic acidlike polynucleotides. Science 1955, 122:907-910.
151. Littauer Y.Z., Soreq H. Polynucleotide phosphorylase 1982, Academic Press, New York.
152. Sohlberg B., Huang J., Cohen S.N. The Streptomyces coelicolor polynucleotide phosphorylase homologue, and not the putative poly(A) polymerase, can polyadenylate RNA. J. Bacteriol. 2003, 185:7273-7278.
153. Cardenas P.P., Carzaniga T., Zangrossi S., Briani F., Garcia-Tirado E., Deho G., Alonso J.C. Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins. Nucleic Acids Res. 2011, 39:9250-9261.
154. Rath D., Mangoli S.H., Pagedar A.R., Jawali N. Involvement of pnp in survival of UV radiation in Escherichia coli K-12. Microbiology 2012, 158:1196-1205.
155. Wang G., Shimada E., Zhang J., Hong J.S., Smith G.M., Teitell M.A., Koehler C.M. Correcting human mitochondrial mutations with targeted RNA import. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:4840-4845.
156. Arraiano C.M., Yancey S.D., Kushner S.R. Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J. Bacteriol. 1988, 170:4625-4633.
157. Cheng Z.F., Zuo Y., Li Z., Rudd K.E., Deutscher M.P. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 1998, 273:14077-14080.
158. Donovan W.P., Kushner S.R. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc. Natl. Acad. Sci. U. S. A. 1986, 83:120-124.
159. Clements M.O., Eriksson S., Thompson A., Lucchini S., Hinton J.C., Normark S., Rhen M. Polynucleotide phosphorylase is a global regulator of virulence and persistency in Salmonella enterica. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:8784-8789.
160. Goverde R.L., Huis in't Veld J.H., Kusters J.G., Mooi F.R. The psychrotrophic bacterium Yersinia enterocolitica requires expression of pnp, the gene for polynucleotide phosphorylase, for growth at low temperature (5 degrees C). Mol. Microbiol. 1998, 28:555-569.
161. Yamanaka K., Inouye M. Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli. J. Bacteriol. 2001, 183:2808-2816.
162. Haddad N., Burns C.M., Bolla J.M., Prevost H., Federighi M., Drider D., Cappelier J.M. Long-term survival of Campylobacter jejuni at low temperatures is dependent on polynucleotide phosphorylase activity. Appl. Environ. Microbiol. 2009, 75:7310-7318.
163. Luttinger A., Hahn J., Dubnau D. Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis. Mol. Microbiol. 1996, 19:343-356.
164. Haddad N., Tresse O., Rivoal K., Chevret D., Nonglaton Q., Burns C.M., Prévost H., Cappelier J.M. Polynucleotide phosphorylase has an impact on cell biology of Campylobacter jejuni. Front. Cell. Infect. Microbiol. 2012, 10.3389/fcimb.2012.00030.
165. Matos R.G., Barria C., Pobre V., Andrade J.M., Arraiano C.M. Exoribonucleases as modulators of virulence in pathogenic bacteria. Front. Cell. Infect. Microbiol. 2012, 2:65.
166. Vanzo N.F., Li Y.S., Py B., Blum E., Higgins C.F., Raynal L.C., Krisch H.M., Carpousis A.J. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 1998, 12:2770-2781.
167. Carpousis A.J., Van Houwe G., Ehretsmann C., Krisch H.M. Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 1994, 76:889-900.
168. Py B., Higgins C.F., Krisch H.M., Carpousis A.J. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 1996, 381:169-172.
169. Iost I., Dreyfus M. DEAD-box RNA helicases in Escherichia coli. Nucleic Acids Res. 2006, 34:4189-4197.
170. Miczak A., Kaberdin V.R., Wei C.L., Lin-Chao S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:3865-3869.
171. Lin P.H., Lin-Chao S. RhlB helicase rather than enolase is the beta-subunit of the Escherichia coli polynucleotide phosphorylase (PNPase)-exoribonucleolytic complex. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:16590-16595.
172. Mohanty B.K., Maples V.F., Kushner S.R. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol. Microbiol. 2004, 54:905-920.
173. Buttner K., Wenig K., Hopfner K.P. Structural framework for the mechanism of archaeal exosomes in RNA processing. Mol. Cell 2005, 20:461-471.
174. Evguenieva-Hackenberg E., Walter P., Hochleitner E., Lottspeich F., Klug G. An exosome-like complex in Sulfolobus solfataricus. EMBO Rep. 2003, 4:889-893.
175. Lorentzen E., Conti E. Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol. Cell 2005, 20:473-481.
176. Witharana C., Roppelt V., Lochnit G., Klug G., Evguenieva-Hackenberg E. Heterogeneous complexes of the RNA exosome in Sulfolobus solfataricus. Biochimie 2012, 94:1578-1587.
177. Lorentzen E., Dziembowski A., Lindner D., Seraphin B., Conti E. RNA channelling by the archaeal exosome. EMBO Rep. 2007, 8:470-476.
178. Portnoy V., Evguenieva-Hackenberg E., Klein F., Walter P., Lorentzen E., Klug G., Schuster G. RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus. EMBO Rep. 2005, 6:1188-1193.
179. Hernandez H., Dziembowski A., Taverner T., Seraphin B., Robinson C.V. Subunit architecture of multimeric complexes isolated directly from cells. EMBO Rep. 2006, 7:605-610.
180. Dlakic M. Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases. Trends Biochem. Sci. 2000, 25:272-273.
181. Wang H., Morita M., Yang X., Suzuki T., Yang W., Wang J., Ito K., Wang Q., Zhao C., Bartlam M., Yamamoto T., Rao Z. Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. EMBO J. 2010, 29:2566-2576.
182. Finoux A.L., Seraphin B. In vivo targeting of the yeast Pop2 deadenylase subunit to reporter transcripts induces their rapid degradation and generates new decay intermediates. J. Biol. Chem. 2006, 281:25940-25947.
183. Schwede A., Ellis L., Luther J., Carrington M., Stoecklin G., Clayton C. A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells. Nucleic Acids Res. 2008, 36:3374-3388.
184. F. Mauxion, B. Prève, B. Séraphin, C2ORF29/CNOT11 and CNOT10 form a new module of the CCR4-NOT complex, RNA Biol. (in press).
185. Dupressoir A., Morel A.P., Barbot W., Loireau M.P., Corbo L., Heidmann T. Identification of four families of yCCR4- and Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding. BMC Genomics 2001, 2:9.
186. Faber A.W., Van Dijk M., Raue H.A., Vos J.C. Ngl2p is a Ccr4p-like RNA nuclease essential for the final step in 3'-end processing of 5.8S rRNA in Saccharomyces cerevisiae. RNA 2002, 8:1095-1101.
187. Feddersen A., Dedic E., Poulsen E.G., Schmid M., Van L.B., Jensen T.H., Brodersen D.E. Saccharomyces cerevisiae Ngl3p is an active 3'-5' exonuclease with a specificity towards poly-A RNA reminiscent of cellular deadenylases. Nucleic Acids Res. 2012, 40:837-846.
188. Green C.B., Besharse J.C. Identification of a novel vertebrate circadian clock-regulated gene encoding the protein nocturnin. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:14884-14888.
189. Baggs J.E., Green C.B. Nocturnin, a deadenylase in Xenopus laevis retina: a mechanism for posttranscriptional control of circadian-related mRNA. Curr. Biol. 2003, 13:189-198.
190. Fang M., Zeisberg W.M., Condon C., Ogryzko V., Danchin A., Mechold U. Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis. Nucleic Acids Res. 2009, 37:5114-5125.
191. Aravind L., Koonin E.V. A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease. Trends Biochem. Sci. 1998, 23:17-19.
192. Wakamatsu T., Kim K., Uemura Y., Nakagawa N., Kuramitsu S., Masui R. Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation. J. Biol. Chem. 2011, 286:2807-2816.
193. Mechold U., Fang G., Ngo S., Ogryzko V., Danchin A. YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. Nucleic Acids Res. 2007, 35:4552-4561.
194. Postic G., Dubail I., Frapy E., Dupuis M., Dieppedale J., Charbit A., Meibom K.L. Identification of a novel small RNA modulating Francisella tularensis pathogenicity. PLoS One 2012, 7:e41999.
195. Stevens A. 5'-exoribonuclease 1: Xrn1. Methods Enzymol. 2001, 342:251-259.
196. van Dijk E., Cougot N., Meyer S., Babajko S., Wahle E., Seraphin B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 2002, 21:6915-6924.
197. Wang Z., Jiao X., Carr-Schmid A., Kiledjian M. The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:12663-12668.
198. Lykke-Andersen J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell. Biol. 2002, 22:8114-8121.
199. Chang J.H., Jiao X., Chiba K., Oh C., Martin C.E., Kiledjian M., Tong L. Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity. Nat. Struct. Mol. Biol. 2012, 19:1011-1017.
200. Johnson A.W. Rat1p nuclease. Methods Enzymol. 2001, 342:260-268.
201. Bouveret E., Rigaut G., Shevchenko A., Wilm M., Seraphin B. A Sm-like protein complex that participates in mRNA degradation. EMBO J. 2000, 19:1661-1671.
202. Tharun S., He W., Mayes A.E., Lennertz P., Beggs J.D., Parker R. Yeast Sm-like proteins function in mRNA decapping and decay. Nature 2000, 404:515-518.
203. Xiang S., Cooper-Morgan A., Jiao X., Kiledjian M., Manley J.L., Tong L. Structure and function of the 5'→3' exoribonuclease Rat1 and its activating partner Rai1. Nature 2009, 458:784-788.
204. Till D.D., Linz B., Seago J.E., Elgar S.J., Marujo P.E., Elias M.L., Arraiano C.M., McClellan J.A., McCarthy J.E., Newbury S.F. Identification and developmental expression of a 5'-3' exoribonuclease from Drosophila melanogaster. Mech. Dev. 1998, 79:51-55.
205. Chang J.H., Xiang S., Xiang K., Manley J.L., Tong L. Structural and biochemical studies of the 5'→3' exoribonuclease Xrn1. Nat. Struct. Mol. Biol. 2011, 18:270-276.
206. Dominski Z. Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism. Crit. Rev. Biochem. Mol. Biol. 2007, 42:67-93.
207. Mandel C.R., Kaneko S., Zhang H., Gebauer D., Vethantham V., Manley J.L., Tong L. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Nature 2006, 444:953-956.
208. Mathy N., Benard L., Pellegrini O., Daou R., Wen T., Condon C. 5'-to-3' exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5' stability of mRNA. Cell 2007, 129:681-692.
209. Richards J., Liu Q., Pellegrini O., Celesnik H., Yao S., Bechhofer D.H., Condon C., Belasco J.G. An RNA pyrophosphohydrolase triggers 5'-exonucleolytic degradation of mRNA in Bacillus subtilis. Mol. Cell 2011, 43:940-949.
210. Li de la Sierra-Gallay I., Zig L., Jamalli A., Putzer H. Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol. 2008, 15:206-212.
211. Even S., Pellegrini O., Zig L., Labas V., Vinh J., Brechemmier-Baey D., Putzer H. Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res. 2005, 33:2141-2152.
212. Madhugiri R., Evguenieva-Hackenberg E. RNase J is involved in the 5'-end maturation of 16S rRNA and 23S rRNA in Sinorhizobium meliloti. FEBS Lett. 2009, 583:2339-2342.
213. Durand S., Gilet L., Bessieres P., Nicolas P., Condon C. Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs. PLoS Genet. 2012, 8:e1002520.
214. Mader U., Zig L., Kretschmer J., Homuth G., Putzer H. mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol. Microbiol. 2008, 70:183-196.
215. Condon C. What is the role of RNase J in mRNA turnover?. RNA Biol. 2010, 7:316-321.
216. Lehnik-Habrink M., Lewis R.J., Mader U., Stulke J. RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol. Microbiol. 2012, 84:1005-1017.
217. Newman J.A., Hewitt L., Rodrigues C., Solovyova A., Harwood C.R., Lewis R.J. Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1. Structure 2011, 19:1241-1251.
218. Mathy N., Hebert A., Mervelet P., Benard L., Dorleans A., Li de la Sierra-Gallay I., Noirot P., Putzer H., Condon C. Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol. Microbiol. 2010, 75:489-498.
219. Dorleans A., Li de la Sierra-Gallay I., Piton J., Zig L., Gilet L., Putzer H., Condon C. Molecular basis for the recognition and cleavage of RNA by the bifunctional 5'-3' exo/endoribonuclease RNase J. Structure 2011, 19:1252-1261.
220. Proudfoot N. New perspectives on connecting messenger RNA 3' end formation to transcription. Curr. Opin. Cell Biol. 2004, 16:272-278.
221. West S., Gromak N., Proudfoot N.J. Human 5'→3' exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 2004, 432:522-525.
222. Kolev N.G., Yario T.A., Benson E., Steitz J.A. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation. EMBO Rep. 2008, 9:1013-1018.
223. Baillat D., Hakimi M.A., Naar A.M., Shilatifard A., Cooch N., Shiekhattar R. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 2005, 123:265-276.
224. Schedl P., Roberts J., Primakoff P. In vitro processing of E. coli tRNA precursors. Cell 1976, 8:581-594.
225. Garber R.L., Gage L.P. Transcription of a cloned Bombyx mori tRNA2Ala gene: nucleotide sequence of the tRNA precursor and its processing in vitro. Cell 1979, 18:817-828.
226. Hagenbuchle O., Larson D., Hall G.I., Sprague K.U. The primary transcription product of a silkworm alanine tRNA gene: identification of in vitro sites of initiation, termination and processing. Cell 1979, 18:1217-1229.
227. Schiffer S., Rosch S., Marchfelder A. Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. EMBO J. 2002, 21:2769-2777.
228. Li de la Sierra-Gallay I., Mathy N., Pellegrini O., Condon C. Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA. Nat. Struct. Mol. Biol. 2006, 13:376-377.
229. Pellegrini O., Nezzar J., Marchfelder A., Putzer H., Condon C. Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J. 2003, 22:4534-4543.
230. Asha P.K., Blouin R.T., Zaniewski R., Deutscher M.P. Ribonuclease BN: identification and partial characterization of a new tRNA processing enzyme. Proc. Natl. Acad. Sci. U. S. A. 1983, 80:3301-3304.
231. Kelly K.O., Deutscher M.P. The presence of only one of five exoribonucleases is sufficient to support the growth of Escherichia coli. J. Bacteriol. 1992, 174:6682-6684.
232. Dutta T., Malhotra A., Deutscher M.P. Exoribonuclease and endoribonuclease activities of RNase BN/RNase Z both function in vivo. J. Biol. Chem. 2012, 287:35747-35755.
233. Aravind L., Koonin E.V. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 1998, 23:469-472.
234. Lehnik-Habrink M., Schaffer M., Mader U., Diethmaier C., Herzberg C., Stulke J. RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol. Microbiol. 2011, 81:1459-1473.
235. Shahbabian K., Jamalli A., Zig L., Putzer H. RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J. 2009, 28:3523-3533.
236. Lehnik-Habrink M., Newman J., Rothe F.M., Solovyova A.S., Rodrigues C., Herzberg C., Commichau F.M., Lewis R.J., Stulke J. RNase Y in Bacillus subtilis: a natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. J. Bacteriol. 2011, 193:5431-5441.
237. Kaito C., Kurokawa K., Matsumoto Y., Terao Y., Kawabata S., Hamada S., Sekimizu K. Silkworm pathogenic bacteria infection model for identification of novel virulence genes. Mol. Microbiol. 2005, 56:934-944.
238. Chen Z., Itzek A., Malke H., Ferretti J.J., Kreth J. Dynamics of speB mRNA transcripts in Streptococcus pyogenes. J. Bacteriol. 2012, 194:1417-1426.
239. Kang S.O., Caparon M.G., Cho K.H. Virulence gene regulation by CvfA, a putative RNase: the CvfA-enolase complex in Streptococcus pyogenes links nutritional stress, growth-phase control, and virulence gene expression. Infect. Immun. 2010, 78:2754-2767.
240. Nagata M., Kaito C., Sekimizu K. Phosphodiesterase activity of CvfA is required for virulence in Staphylococcus aureus. J. Biol. Chem. 2008, 283:2176-2184.
241. Bessarab D.A., Kaberdin V.R., Wei C.L., Liou G.G., Lin-Chao S. RNA components of Escherichia coli degradosome: evidence for rRNA decay. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:3157-3161.
242. Commichau F.M., Rothe F.M., Herzberg C., Wagner E., Hellwig D., Lehnik-Habrink M., Hammer E., Volker U., Stulke J. Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics 2009, 8:1350-1360.
243. Meinken C., Blencke H.M., Ludwig H., Stulke J. Expression of the glycolytic gapA operon in Bacillus subtilis: differential syntheses of proteins encoded by the operon. Microbiology 2003, 149:751-761.
244. Condon C. RNA processing and degradation in Bacillus subtilis. Microbiol. Mol. Biol. Rev. 2003, 67:157-174. (table of contents).
245. Oussenko I.A., Sanchez R., Bechhofer D.H. Bacillus subtilis YhaM, a member of a new family of 3'-to-5' exonucleases in gram-positive bacteria. J. Bacteriol. 2002, 184:6250-6259.
246. Carpousis A.J., Luisi B.F., McDowall K.J. Endonucleolytic initiation of mRNA decay in Escherichia coli. Prog. Mol. Biol. Transl. Sci. 2009, 85:91-135.
247. Callaghan A.J., Marcaida M.J., Stead J.A., McDowall K.J., Scott W.G., Luisi B.F. Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 2005, 437:1187-1191.
248. Stead M.B., Marshburn S., Mohanty B.K., Mitra J., Pena Castillo L., Ray D., van Bakel H., Hughes T.R., Kushner S.R. Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res. 2011, 39:3188-3203.
249. Babitzke P., Kushner S.R. The ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 1991, 88:1-5.
250. Melefors O., von Gabain A. Genetic studies of cleavage-initiated mRNA decay and processing of ribosomal 9S RNA show that the Escherichia coli ams and rne loci are the same. Mol. Microbiol. 1991, 5:857-864.
251. Mudd E.A., Krisch H.M., Higgins C.F. RNase E, an endoribonuclease, has a general role in the chemical decay of Escherichia coli mRNA: evidence that rne and ams are the same genetic locus. Mol. Microbiol. 1990, 4:2127-2135.
252. Taraseviciene L., Miczak A., Apirion D. The gene specifying RNase E (rne) and a gene affecting mRNA stability (ams) are the same gene. Mol. Microbiol. 1991, 5:851-855.
253. Apirion D., Lassar A.B. A conditional lethal mutant of Escherichia coli which affects the processing of ribosomal RNA. J. Biol. Chem. 1978, 253:1738-1742.
254. Ono M., Kuwano M. A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of messenger RNA. J. Mol. Biol. 1979, 129:343-357.
255. Misra T.K., Apirion D. RNase E, an RNA processing enzyme from Escherichia coli. J. Biol. Chem. 1979, 254:11154-11159.
256. Li Z., Pandit S., Deutscher M.P. RNase G (CafA protein) and RNase E are both required for the 5' maturation of 16S ribosomal RNA. EMBO J. 1999, 18:2878-2885.
257. Ow M.C., Kushner S.R. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes Dev. 2002, 16:1102-1115.
258. Lin-Chao S., Wei C.L., Lin Y.T. RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity. Proc. Natl. Acad. Sci. U. S. A. 1999, 96:12406-12411.
259. Ko J.H., Han K., Kim Y., Sim S., Kim K.S., Lee S.J., Cho B., Lee K., Lee Y. Dual function of RNase E for control of M1 RNA biosynthesis in Escherichia coli. Biochemistry 2008, 47:762-770.
260. Lundberg U., Altman S. Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli. RNA 1995, 1:327-334.
261. Manasherob R., Miller C., Kim K.S., Cohen S.N. Ribonuclease E modulation of the bacterial SOS response. PLoS One 2012, 7:e38426.
262. Mackie G.A. Secondary structure of the mRNA for ribosomal protein S20. Implications for cleavage by ribonuclease E. J. Biol. Chem. 1992, 267:1054-1061.
263. McDowall K.J., Lin-Chao S., Cohen S.N. A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J. Biol. Chem. 1994, 269:10790-10796.
264. Deana A., Celesnik H., Belasco J.G. The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature 2008, 451:355-358.
265. Baker K.E., Mackie G.A. Ectopic RNase E sites promote bypass of 5'-end-dependent mRNA decay in Escherichia coli. Mol. Microbiol. 2003, 47:75-88.
266. Kime L., Jourdan S.S., Stead J.A., Hidalgo-Sastre A., McDowall K.J. Rapid cleavage of RNA by RNase E in the absence of 5' monophosphate stimulation. Mol. Microbiol. 2010, 76:590-604.
267. Anupama K., Leela J.K., Gowrishankar J. Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol. Microbiol. 2011, 82:1330-1348.
268. Garrey S.M., Mackie G.A. Roles of the 5'-phosphate sensor domain in RNase E. Mol. Microbiol. 2011, 80:1613-1624.
269. Kaberdin V.R., Miczak A., Jakobsen J.S., Lin-Chao S., McDowall K.J., von Gabain A. The endoribonucleolytic N-terminal half of Escherichia coli RNase E is evolutionarily conserved in Synechocystis sp. and other bacteria but not the C-terminal half, which is sufficient for degradosome assembly. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:11637-11642.
270. Callaghan A.J., Aurikko J.P., Ilag L.L., Gunter Grossmann J., Chandran V., Kuhnel K., Poljak L., Carpousis A.J., Robinson C.V., Symmons M.F., Luisi B.F. Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J. Mol. Biol. 2004, 340:965-979.
271. Lopez P.J., Marchand I., Joyce S.A., Dreyfus M. The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Mol. Microbiol. 1999, 33:188-199.
272. Ow M.C., Liu Q., Kushner S.R. Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Mol. Microbiol. 2000, 38:854-866.
273. Khemici V., Poljak L., Luisi B.F., Carpousis A.J. The RNase E of Escherichia coli is a membrane-binding protein. Mol. Microbiol. 2008, 70:799-813.
274. Murashko O.N., Kaberdin V.R., Lin-Chao S. Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:7019-7024.
275. Chandran V., Poljak L., Vanzo N.F., Leroy A., Miguel R.N., Fernandez-Recio J., Parkinson J., Burns C., Carpousis A.J., Luisi B.F. Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. J. Mol. Biol. 2007, 367:113-132.
276. Worrall J.A., Howe F.S., McKay A.R., Robinson C.V., Luisi B.F. Allosteric activation of the ATPase activity of the Escherichia coli RhlB RNA helicase. J. Biol. Chem. 2008, 283:5567-5576.
277. Bouvier M., Carpousis A.J. A tale of two mRNA degradation pathways mediated by RNase E. Mol. Microbiol. 2011, 82:1305-1310.
278. Gao J., Lee K., Zhao M., Qiu J., Zhan X., Saxena A., Moore C.J., Cohen S.N., Georgiou G. Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol. Microbiol. 2006, 61:394-406.
279. Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A., Simons R.W. Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'. Mol. Microbiol. 2004, 54:1409-1421.
280. Aiba H. Mechanism of RNA silencing by Hfq-binding small RNAs. Curr. Opin. Microbiol. 2007, 10:134-139.
281. Morita T., Mochizuki Y., Aiba H. Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:4858-4863.
282. Morita T., Maki K., Aiba H. RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 2005, 19:2176-2186.
283. Callaghan A.J., Redko Y., Murphy L.M., Grossmann J.G., Yates D., Garman E., Ilag L.L., Robinson C.V., Symmons M.F., McDowall K.J., Luisi B.F. "Zn-link": a metal-sharing interface that organizes the quaternary structure and catalytic site of the endoribonuclease, RNase E. Biochemistry 2005, 44:4667-4675.
284. Koslover D.J., Callaghan A.J., Marcaida M.J., Garman E.F., Martick M., Scott W.G., Luisi B.F. The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation. Structure 2008, 16:1238-1244.
285. Diwa A., Bricker A.L., Jain C., Belasco J.G. An evolutionarily conserved RNA stem-loop functions as a sensor that directs feedback regulation of RNase E gene expression. Genes Dev. 2000, 14:1249-1260.
286. Jain C., Belasco J.G. Autoregulation of RNase E synthesis in Escherichia coli. Nucleic Acids Symp. Ser. 1995, 85-88.
287. Mudd E.A., Higgins C.F. Escherichia coli endoribonuclease RNase E: autoregulation of expression and site-specific cleavage of mRNA. Mol. Microbiol. 1993, 9:557-568.
288. Sousa S., Marchand I., Dreyfus M. Autoregulation allows Escherichia coli RNase E to adjust continuously its synthesis to that of its substrates. Mol. Microbiol. 2001, 42:867-878.
289. Lee K., Zhan X., Gao J., Qiu J., Feng Y., Meganathan R., Cohen S.N., Georgiou G. RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 2003, 114:623-634.
290. Barlow T., Berkmen M., Georgellis D., Bayr L., Arvidson S., von Gabain A. RNase E, the major player in mRNA degradation, is down-regulated in Escherichia coli during a transient growth retardation (diauxic lag). Biol. Chem. 1998, 379:33-38.
291. Georgellis D., Arvidson S., von Gabain A. Decay of ompA mRNA and processing of 9S RNA are immediately affected by shifts in growth rate, but in opposite manners. J. Bacteriol. 1992, 174:5382-5390.
292. Le Derout J., Regnier P., Hajnsdorf E. Both temperature and medium composition regulate RNase E processing efficiency of the rpsO mRNA coding for ribosomal protein S15 of Escherichia coli. J. Mol. Biol. 2002, 319:341-349.
293. Okada Y., Wachi M., Hirata A., Suzuki K., Nagai K., Matsuhashi M. Cytoplasmic axial filaments in Escherichia coli cells: possible function in the mechanism of chromosome segregation and cell division. J. Bacteriol. 1994, 176:917-922.
294. Wachi M., Umitsuki G., Shimizu M., Takada A., Nagai K. Escherichia coli cafA gene encodes a novel RNase, designated as RNase G, involved in processing of the 5' end of 16S rRNA. Biochem. Biophys. Res. Commun. 1999, 259:483-488.
295. McDowall K.J., Hernandez R.G., Lin-Chao S., Cohen S.N. The ams-1 and rne-3071 temperature-sensitive mutations in the ams gene are in close proximity to each other and cause substitutions within a domain that resembles a product of the Escherichia coli mre locus. J. Bacteriol. 1993, 175:4245-4249.
296. Briant D.J., Hankins J.S., Cook M.A., Mackie G.A. The quaternary structure of RNase G from Escherichia coli. Mol. Microbiol. 2003, 50:1381-1390.
297. Mackie G.A. Ribonuclease E is a 5'-end-dependent endonuclease. Nature 1998, 395:720-723.
298. Tock M.R., Walsh A.P., Carroll G., McDowall K.J. The CafA protein required for the 5'-maturation of 16S rRNA is a 5'-end-dependent ribonuclease that has context-dependent broad sequence specificity. J. Biol. Chem. 2000, 275:8726-8732.
299. Kim K.S., Lee Y. Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Res. 2004, 32:6057-6068.
300. Mohanty B.K., Kushner S.R. Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Res. 2007, 35:7614-7625.
301. Mohanty B.K., Kushner S.R. Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli. Nucleic Acids Res. 2008, 36:364-375.
302. Roy-Chaudhuri B., Kirthi N., Culver G.M. Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:4567-4572.
303. Song W.S., Lee M., Lee K. RNase G participates in processing of the 5'-end of 23S ribosomal RNA. J. Microbiol. 2011, 49:508-511.
304. Lee K., Bernstein J.A., Cohen S.N. RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli. Mol. Microbiol. 2002, 43:1445-1456.
305. Umitsuki G., Wachi M., Takada A., Hikichi T., Nagai K. Involvement of RNase G in in vivo mRNA metabolism in Escherichia coli. Genes Cells 2001, 6:403-410.
306. Sakai T., Nakamura N., Umitsuki G., Nagai K., Wachi M. Increased production of pyruvic acid by Escherichia coli RNase G mutants in combination with cra mutations. Appl. Microbiol. Biotechnol. 2007, 76:183-192.
307. Ow M.C., Perwez T., Kushner S.R. RNase G of Escherichia coli exhibits only limited functional overlap with its essential homologue, RNase E. Mol. Microbiol. 2003, 49:607-622.
308. Tamura M., Lee K., Miller C.A., Moore C.J., Shirako Y., Kobayashi M., Cohen S.N. RNase E maintenance of proper FtsZ/FtsA ratio required for nonfilamentous growth of Escherichia coli cells but not for colony-forming ability. J. Bacteriol. 2006, 188:5145-5152.
309. Chung D.H., Min Z., Wang B.C., Kushner S.R. Single amino acid changes in the predicted RNase H domain of Escherichia coli RNase G lead to complementation of RNase E deletion mutants. RNA 2010, 16:1371-1385.
310. Lamontagne B., Larose S., Boulanger J., Elela S.A. The RNase III family: a conserved structure and expanding functions in eukaryotic dsRNA metabolism. Curr. Issues Mol. Biol. 2001, 3:71-78.
311. Meng W., Nicholson A.W. Heterodimer-based analysis of subunit and domain contributions to double-stranded RNA processing by Escherichia coli RNase III in vitro. Biochem. J. 2008, 410:39-48.
312. Blaszczyk J., Tropea J.E., Bubunenko M., Routzahn K.M., Waugh D.S., Court D.L., Ji X. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure 2001, 9:1225-1236.
313. Redko Y., Bechhofer D.H., Condon C. Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis. Mol. Microbiol. 2008, 68:1096-1106.
314. Du Z., Lee J.K., Tjhen R., Stroud R.M., James T.L. Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:2391-2396.
315. Jaskiewicz L., Filipowicz W. Role of Dicer in posttranscriptional RNA silencing. Curr. Top. Microbiol. Immunol. 2008, 320:77-97.
316. Doyle M., Jaskiewicz L., Filipowicz W. Dicer proteins and their role in gene silencing pathways. The enzymes 2012, vol. 32:1-35. Academic Press, Burlington.
317. Gan J., Tropea J.E., Austin B.P., Court D.L., Waugh D.S., Ji X. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 2006, 124:355-366.
318. Gan J., Shaw G., Tropea J.E., Waugh D.S., Court D.L., Ji X. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol. Microbiol. 2008, 67:143-154.
319. Pertzev A.V., Nicholson A.W. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III. Nucleic Acids Res. 2006, 34:3708-3721.
320. Zhang H., Kolb F.A., Jaskiewicz L., Westhof E., Filipowicz W. Single processing center models for human Dicer and bacterial RNase III. Cell 2004, 118:57-68.
321. Babitzke P., Granger L., Olszewski J., Kushner S.R. Analysis of mRNA decay and rRNA processing in Escherichia coli multiple mutants carrying a deletion in RNase III. J. Bacteriol. 1993, 175:229-239.
322. Evguenieva-Hackenberg E., Klug G. RNase III processing of intervening sequences found in helix 9 of 23S rRNA in the alpha subclass of Proteobacteria. J. Bacteriol. 2000, 182:4719-4729.
323. Nicholson A.W. Structure, reactivity, and biology of double-stranded RNA. Prog. Nucleic Acid Res. Mol. Biol. 1996, 52:1-65.
324. Lioliou E., Sharma C.M., Caldelari I., Helfer A.C., Fechter P., Vandenesch F., Vogel J., Romby P. Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet. 2012, 8:e1002782.
325. Aceti D.J., Champness W.C. Transcriptional regulation of Streptomyces coelicolor pathway-specific antibiotic regulators by the absA and absB loci. J. Bacteriol. 1998, 180:3100-3106.
326. Adamidis T., Champness W. Genetic analysis of absB, a Streptomyces coelicolor locus involved in global antibiotic regulation. J. Bacteriol. 1992, 174:4622-4628.
327. Price B., Adamidis T., Kong R., Champness W. A Streptomyces coelicolor antibiotic regulatory gene, absB, encodes an RNase III homolog. J. Bacteriol. 1999, 181:6142-6151.
328. Xu W., Huang J., Lin R., Shi J., Cohen S.N. Regulation of morphological differentiation in S. coelicolor by RNase III (AbsB) cleavage of mRNA encoding the AdpA transcription factor. Mol. Microbiol. 2010, 75:781-791.
329. Huntzinger E., Boisset S., Saveanu C., Benito Y., Geissmann T., Namane A., Lina G., Etienne J., Ehresmann B., Ehresmann C., Jacquier A., Vandenesch F., Romby P. Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression. EMBO J. 2005, 24:824-835.
330. Chanfreau G., Legrain P., Jacquier A. Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. J. Mol. Biol. 1998, 284:975-988.
331. Chanfreau G., Rotondo G., Legrain P., Jacquier A. Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO J. 1998, 17:3726-3737.
332. Elela S.A., Igel H., Ares M. RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell 1996, 85:115-124.
333. Kufel J., Dichtl B., Tollervey D. Yeast Rnt1p is required for cleavage of the pre-ribosomal RNA in the 3' ETS but not the 5' ETS. RNA 1999, 5:909-917.
334. Danin-Kreiselman M., Lee C.Y., Chanfreau G. RNAse III-mediated degradation of unspliced pre-mRNAs and lariat introns. Mol. Cell 2003, 11:1279-1289.
335. Catala M., Tremblay M., Samson E., Conconi A., Abou Elela S. Deletion of Rnt1p alters the proportion of open versus closed rRNA gene repeats in yeast. Mol. Cell. Biol. 2008, 28:619-629.
336. El Hage A., Koper M., Kufel J., Tollervey D. Efficient termination of transcription by RNA polymerase I requires the 5' exonuclease Rat1 in yeast. Genes Dev. 2008, 22:1069-1081.
337. Ghazal G., Gagnon J., Jacques P.E., Landry J.R., Robert F., Elela S.A. Yeast RNase III triggers polyadenylation-independent transcription termination. Mol. Cell 2009, 36:99-109.
338. Prescott E.M., Osheim Y.N., Jones H.S., Alen C.M., Roan J.G., Reeder R.H., Beyer A.L., Proudfoot N.J. Transcriptional termination by RNA polymerase I requires the small subunit Rpa12p. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:6068-6073.
339. Carthew R.W., Sontheimer E.J. Origins and mechanisms of miRNAs and siRNAs. Cell 2009, 136:642-655.
340. Liu Q., Rand T.A., Kalidas S., Du F., Kim H.E., Smith D.P., Wang X. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 2003, 301:1921-1925.
341. Yang W., Hendrickson W.A., Crouch R.J., Satow Y. Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Science 1990, 249:1398-1405.
342. Yang W., Lee J.Y., Nowotny M. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol. Cell 2006, 22:5-13.
343. Ohtani N., Haruki M., Morikawa M., Crouch R.J., Itaya M., Kanaya S. Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families. Biochemistry 1999, 38:605-618.
344. Itaya M., Omori A., Kanaya S., Crouch R.J., Tanaka T., Kondo K. Isolation of RNase H genes that are essential for growth of Bacillus subtilis 168. J. Bacteriol. 1999, 181:2118-2123.
345. Cerritelli S.M., Crouch R.J. Ribonuclease H: the enzymes in eukaryotes. FEBS J. 2009, 276:1494-1505.
346. Davies J.F., Hostomska Z., Hostomsky Z., Jordan S.R., Matthews D.A. Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase. Science 1991, 252:88-95.
347. Kitamura S., Fujishima K., Sato A., Tsuchiya D., Tomita M., Kanai A. Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus. Biochem. J. 2010, 426:337-344.
348. Song J.J., Smith S.K., Hannon G.J., Joshua-Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 2004, 305:1434-1437.
349. Elkayam E., Kuhn C.D., Tocilj A., Haase A.D., Greene E.M., Hannon G.J., Joshua-Tor L. The structure of human argonaute-2 in complex with miR-20a. Cell 2012, 150:100-110.
350. Nakanishi K., Weinberg D.E., Bartel D.P., Patel D.J. Structure of yeast Argonaute with guide RNA. Nature 2012, 486:368-374.
351. Schirle N.T., MacRae I.J. The crystal structure of human Argonaute2. Science 2012, 336:1037-1040.
352. Uzan M. RNA processing and decay in bacteriophage T4. Prog. Mol. Biol. Transl. Sci. 2009, 85:43-89.
353. Durand S., Richard G., Bisaglia M., Laalami S., Bontems F., Uzan M. Activation of RegB endoribonuclease by S1 ribosomal protein requires an 11 nt conserved sequence. Nucleic Acids Res. 2006, 34:6549-6560.
354. Sanson B., Uzan M. Post-transcriptional controls in bacteriophage T4: roles of the sequence-specific endoribonuclease RegB. FEMS Microbiol. Rev. 1995, 17:141-150.
355. Uzan M. Bacteriophage T4 RegB endoribonuclease. Methods Enzymol. 2001, 342:467-480.
356. Sanson B., Hu R.M., Troitskayadagger E., Mathy N., Uzan M. Endoribonuclease RegB from bacteriophage T4 is necessary for the degradation of early but not middle or late mRNAs. J. Mol. Biol. 2000, 297:1063-1074.
357. Durand S., Richard G., Bontems F., Uzan M. Bacteriophage T4 polynucleotide kinase triggers degradation of mRNAs. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:7073-7078.
358. Arcus V.L., McKenzie J.L., Robson J., Cook G.M. The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array. Protein Eng. Des. Sel. 2011, 24:33-40.
359. Levin I., Schwarzenbacher R., Page R., Abdubek P., Ambing E., Biorac T., Brinen L.S., Campbell J., Canaves J.M., Chiu H.J., Dai X., Deacon A.M., DiDonato M., Elsliger M.A., Floyd R., Godzik A., Grittini C., Grzechnik S.K., Hampton E., Jaroszewski L., Karlak C., Klock H.E., Koesema E., Kovarik J.S., Kreusch A., Kuhn P., Lesley S.A., McMullan D., McPhillips T.M., Miller M.D., Morse A., Moy K., Ouyang J., Quijano K., Reyes R., Rezezadeh F., Robb A., Sims E., Spraggon G., Stevens R.C., van den Bedem H., Velasquez J., Vincent J., von Delft F., Wang X., West B., Wolf G., Xu Q., Hodgson K.O., Wooley J., Wilson I.A. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution. Proteins 2004, 56:404-408.
360. Glavan F., Behm-Ansmant I., Izaurralde E., Conti E. Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J. 2006, 25:5117-5125.
361. Mueser T.C., Nossal N.G., Hyde C.C. 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 1996, 85:1101-1112.
362. Eberle A.B., Lykke-Andersen S., Muhlemann O., Jensen T.H. SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nat. Struct. Mol. Biol. 2009, 16:49-55.
363. Fatica A., Tollervey D., Dlakic M. PIN domain of Nob1p is required for D-site cleavage in 20S pre-rRNA. RNA 2004, 10:1698-1701.
364. Lamanna A.C., Karbstein K. Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:14259-14264.
365. Veith T., Martin R., Wurm J.P., Weis B.L., Duchardt-Ferner E., Safferthal C., Hennig R., Mirus O., Bohnsack M.T., Wohnert J., Schleiff E. Structural and functional analysis of the archaeal endonuclease Nob1. Nucleic Acids Res. 2012, 40:3259-3274.
366. Mamolen M., Smith A., Andrulis E.D. Drosophila melanogaster Dis3 N-terminal domains are required for ribonuclease activities, nuclear localization and exosome interactions. Nucleic Acids Res. 2010, 38:5507-5517.
367. Haurwitz R.E., Jinek M., Wiedenheft B., Zhou K., Doudna J.A. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 2010, 329:1355-1358.
368. Wang H.W., Wang J., Ding F., Callahan K., Bratkowski M.A., Butler J.S., Nogales E., Ke A. Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:16844-16849.
369. Marraffini L.A., Sontheimer E.J. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 2010, 11:181-190.
370. Ebihara A., Yao M., Masui R., Tanaka I., Yokoyama S., Kuramitsu S. Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain. Protein Sci. 2006, 15:1494-1499.
371. Carte J., Wang R., Li H., Terns R.M., Terns M.P. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 2008, 22:3489-3496.
372. Ipsaro J.J., Haase A.D., Knott S.R., Joshua-Tor L., Hannon G.J. The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Nature 2012, 491:279-283.
373. Nishimasu H., Ishizu H., Saito K., Fukuhara S., Kamatani M.K., Bonnefond L., Matsumoto N., Nishizawa T., Nakanaga K., Aoki J., Ishitani R., Siomi H., Siomi M.C., Nureki O. Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature 2012, 491:284-287.
374. Voigt F., Reuter M., Kasaruho A., Schulz E.C., Pillai R.S., Barabas O. Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc. RNA 2012, 18:2128-2134.
375. Lu C., Ding F., Ke A. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. PLoS One 2010, 5:e8739.
376. Pellegrini O., Li de la Sierra-Gallay I., Piton J., Gilet L., Condon C. Activation of tRNA maturation by downstream uracil residues in B. subtilis. Structure 2012, 20:1769-1777.
377. Macrae I.J., Zhou K., Li F., Repic A., Brooks A.N., Cande W.Z., Adams P.D., Doudna J.A. Structural basis for double-stranded RNA processing by Dicer. Science 2006, 311:195-198.
378. Chen X., Taylor D.W., Fowler C.C., Galan J.E., Wang H.W., Wolin S.L. An RNA degradation machine sculpted by ro autoantigen and noncoding RNA. Cell Mar 28 2013, 153(1):166-177. 10.1016/j.cell.2013.02.037.