Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases

BMC Structural Biology

Volumn 3, Issue , 2003, Pages 1-23

  Iyer, Lakshminarayan M ^a   Koonin, Eugene V ^a   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIVALENT CATION; DNA DEPENDENT PROTEIN KINASE; RIBOZYME; RNA DIRECTED RNA POLYMERASE; RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; PROTEIN SUBUNIT;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BACTERIOPHAGE; BETA CHAIN; CATALYSIS; CRYSTAL STRUCTURE; DNA SEQUENCE; ENZYME ACTIVE SITE; EUKARYOTIC CELL; EVOLUTIONARY HOMOLOGY; PROTEIN DATABASE; PROTEIN DOMAIN; RNA BINDING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES COMPARISON; STRUCTURE ANALYSIS; BACTERIUM; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

AMINO ACID SEQUENCE; BACTERIA; BACTERIOPHAGES; BINDING SITES; CATALYTIC DOMAIN; CONSERVED SEQUENCE; DNA-DIRECTED RNA POLYMERASES; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; RNA REPLICASE; SEQUENCE ALIGNMENT;

EID: 0037791613     PISSN: 14726807     EISSN: None     Source Type: Journal    
DOI: 10.1186/1472-6807-3-1     Document Type: Article

References (112)

1. Anantharaman V, Koonin EV and Aravind L Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 2002, 30:1427-1464
2. Nelson DL and Cox MM InLehninger Principles of Biochemistry. Worth Publishers Inc 2000,
3. Goodman MF and Tippin B The expanding polymerase universe. Nat Rev Mol Cell Biol 2000, 1:101-109
4. Burgers PM, Koonin EV, Bruford E, Blanco L, Burtis KC, Christman MF, Copeland WC, Friedberg EC, Hanaoka F and Hinkle DC Eukaryotic DNA polymerases: proposal for a revised nomenclature. J Biol Chem 2001, 276:43487-43490
5. Cheetham GM and Steitz TA Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases. Curr Opin Struct Biol 2000, 10:117-123
6. Steitz TA A mechanism for all polymerases. Nature 1998, 391:231-232
7. Cramer P Multisubunit RNA polymerases. Curr Opin Struct Biol 2002, 12:89-97
8. Kamer G and Argos P Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 1984, 12:7269-7282
9. Delarue M, Poch O, Tordo N, Moras D and Argos P An attempt to unify the structure of polymerases. Protein Eng 1990, 3:461-467
10. Poch O, Sauvaget I, Delarue M and Tordo N Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. Embo J 1989, 8:3867-3874
11. Aravind L, Mazumder R, Vasudevan S and Koonin EV Trends in protein evolution inferred from sequence and structure analysis. Curr Opin Struct Biol 2002, 12:392-399
12. Pei J and Grishin NV GGDEF domain is homologous to adenylyl cyclase. Proteins 2001, 42:210-216
13. Makarova KS, Aravind L, Grishin NV, Rogozin IB and Koonin EV A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 2002, 30:482-496
14. Koonin EV, Wolf YI, Kondrashov AS and Aravind L Bacterial homologs of the small subunit of eukaryotic DNA primase. J Mol Microbiol Biotechnol 2000, 2:509-512
15. Artymiuk PJ, Poirrette AR, Rice DW and Willett P A polymerase I palm in adenylyl cyclase? Nature 1997, 388:33-34
16. Murzin AG How far divergent evolution goes in proteins. Curr Opin Struct Biol 1998, 8:380-387
17. Aravind L, Leipe DD and Koonin EV Toprim - a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res 1998, 26:4205-4213
18. Keck JL, Roche DD, Lynch AS and Berger JM Structure of the RNA polymerase domain of E. coli primase. Science 2000, 287:2482-2486
19. Podobnik M, McInerney P, O'Donnell M and Kuriyan J A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases. J Mol Biol 2000, 300:353-362
20. Bushnell DA, Cramer P and Kornberg RD Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci U S A 2002, 99:1218-1222
21. Gnatt AL, Cramer P, Fu J, Bushnell DA and Kornberg RD Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 2001, 292:1876-1882
22. Cramer P, Bushnell DA and Kornberg RD Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 2001, 292:1863-1876
23. Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S and Yokoyama S Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 2002, 417:712-719
24. Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K and Darst SA Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell 1999, 98:811-824
25. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S and Picault N Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 2000, 101:533-542
26. Schiebel W, Pelissier T, Riedel L, Thalmeir S, Schiebel R, Kempe D, Lottspeich F, Sanger HL and Wassenegger M Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 1998, 10:2087-2101
27. Vaistij FE, Jones L and Baulcombe DC Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell 2002, 14:857-867
28. Dracheva S, Koonin EV and Crute JJ Identification of the primase active site of the herpes simplex virus type I helicase-primase. J Biol Chem 1995, 270:14148-14153
29. Holm L and Sander C DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci 1995, 20:345-347
30. Aravind L and Koonin EV DNA polymerase beta-like nucleoti-dyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res 1999, 27:1609-1618
31. Sweetser D, Nonet M and Young RA Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc Natl Acad Sci U S A 1987, 84:1192-1196
32. Ebright RH RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 2000, 304:687-698
33. Passarelli AL, Todd JW and Miller LK A baculovirus gene involved in late gene expression predicts a large polypeptide with a conserved motif of RNA polymerases. J Virol 1994, 68:4673-4678
34. Passarelli AL and Miller LK Identification of genes encoding late expression factors located between 56.0 and 65.4 map units of the Autographa californica nuclear polyhedrosis virus genome. Virology 1993, 197:704-714
35. Iyer LM, Aravind L and Koonin EV Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 2001, 75:11720-11734
36. Dieci G, Hermann-Le Denmat S, Lukhtanov E, Thuriaux P, Werner M and Sentenac A A universally conserved region of the largest subunit participates in the active site of RNA polymerase III. Embo J 1995, 14:3766-3776
37. Iyer LM, Kumpatla SP, Chandrasekharan MB and Hall TC Transgene silencing in monocots. Plant Mol Biol 2000, 43:323-346
38. Cogoni C and Macino G Post-transcriptional gene silencing across kingdoms. Curr Opin Genet Dev 2000, 10:638-643
39. Grishok A and Mello CC RNAi (Nematodes: Caenorhabditis elegans). Adv Genet 2002, 46:339-360
40. Fire A RNA-triggered gene silencing. Trends Genet 1999, 15:358-363
41. Montgomery MK and Fire A Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 1998, 14:255-258
42. Parrish S, Fleenor J, Xu S, Mello C and Fire A Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. Mol Cell 2000, 6:1077-1087
43. Zamore PD, Tuschl T, Sharp PA and Bartel DP RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000, 101:25-33
44. Hamilton AJ and Baulcombe DC A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999, 286:950-952
45. Hammond SM, Bernstein E, Beach D and Hannon GJ An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000, 404:293-296
46. Hutvagner G and Zamore PD A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002, 297:2056-2060
47. Astier-Manifacier S and Cornuet P [RNA-dependent RNA-polymerase in Brassica chinensis L]. C R Acad Sci Hebd Seances Acad Sci D 1970, 270:2587-2590
48. Astier-Manifacier S and Cornuet P RNA-dependent RNA polymerase in Chinese cabbage. Biochim Biophys Acta 1971, 232:484-493
49. Ikegami M and Fraenkel-Conrat H Characterization of the RNA-dependent RNA polymerase of tobacco leaves. J Biol Chem 1979, 254:149-154
50. Schiebel W, Haas B, Marinkovic S, Klanner A and Sanger HL RNA-directed RNA polymerase from tomato leaves. I. Purification and physical properties. J Biol Chem 1993, 268:11851-11857
51. Cogoni C and Macino G Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 1999, 399:166-169
52. Pickford AS, Catalanotto C, Cogoni C and Macino G Quelling in Neurospora crassa. Adv Genet 2002, 46:277-303
53. Litiere K, van Eldik GJ, Jacobs JJ, Van Montagu M and Cornelissen M Posttranscriptional gene silencing of gn1 in tobacco triggers accumulation of truncated gn1-derived RNA species. Rna 1999, 5:1364-1373
54. Martens H, Novotny J, Oberstrass J, Steck TL, Postlethwait P and Nellen W RNAi in Dictyostelium: the role of RNA-directed RNA polymerases and double-stranded RNase. Mol Biol Cell 2002, 13:445-453
55. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH and Fire A On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 2001, 107:465-476
56. Meins F Jr RNA degradation and models for post-transcriptional gene-silencing. Plant Mol Biol 2000, 43:261-273
57. Nishikura K A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst. Cell 2001, 107:415-418
58. Ahlquist P RNA-dependent RNA polymerases, viruses, and RNA silencing. Science 2002, 296:1270-1273
59. Argos P A sequence motif in many polymerases. Nucleic Acids Res 1988, 16:9909-9916
60. Zhang Z, Schaffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV and Altschul SF Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res 1998, 26:3986-3990
61. Holm L and Sander C Touring protein fold space with Dali/FSSP. Nucleic Acids Res 1998, 26:316-319
62. Castillo RM, Mizuguchi K, Dhanaraj V, Albert A, Blundell TL and Murzin AG A six-stranded double-psi beta barrel is shared by several protein superfamilies. Structure Fold Des 1999, 7:227-236
63. Mizuguchi K, Dhanaraj V, Blundell TL and Murzin AG N-ethylmale-imide-sensitive fusion protein (NSF) and CDC48 confirmed as members of the double-psi beta-barrel aspartate decarboxylase/formate dehydrogenase family. Structure Fold Des 1999, 7:R215-216
64. Coles M, Diercks T, Liermann J, Groger A, Rockel B, Baumeister W, Koretke KK, Lupas A, Peters J and Kessler H The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Curr Biol 1999, 9:1158-1168
65. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C and Murzin AG SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002, 30:264-267
66. Leipe DD, Wolf YI, Koonin EV and Aravind L Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol 2002, 317:41-72
67. Wang B, Jones DN, Kaine BP and Weiss MA High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure 1998, 6:555-569
68. Aravind L and Koonin EV DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res 1999, 27:4658-4670
69. Hard T, Rak A, Allard P, Kloo L and Garber M The solution structure of ribosomal protein L36 from Thermus thermophilus reveals a zinc-ribbon-like fold. J Mol Biol 2000, 296:169-180
70. Chen HT, Legault P, Glushka J, Omichinski JG and Scott RA Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Protein Sci 2000, 9:1743-1752
71. Ferri ML, Peyroche G, Siaut M, Lefebvre O, Carles C, Conesa C and Sentenac A A novel subunit of yeast RNA polymerase III interacts with the TFIIB-related domain of TFIIIB70. Mol Cell Biol 2000, 20:488-495
72. Bell SD and Jackson SP The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius. J Biol Chem 2000, 275:12934-12940
73. Hahn S and Roberts S The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation. Genes Dev 2000, 14:719-730
74. Aravind L and Landsman D AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res 1998, 26:4413-4421
75. Neuwald AF, Liu JS, Lipman DJ and Lawrence CE Extracting protein alignment models from the sequence database. Nucleic Acids Res 1997, 25:1665-1677
76. Anantharaman V, Koonin EV and Aravind L Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol 2001, 307:1271-1292
77. Van Duyne GD, Ghosh G, Maas WK and Sigler PB Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli. J Mol Biol 1996, 256:377-391
78. Aravind L and Koonin EV Novel predicted RNA-binding domains associated with the translation machinery. J Mol Evol 1999, 48:291-302
79. Fletcher CM, Pestova TV, Hellen CU and Wagner G Structure and interactions of the translation initiation factor eIFI. Embo J 1999, 18:2631-2637
80. Kraulis PJ Similarity of protein G and ubiquitin. Science 1991, 254:581-582
81. Murzin AG Familiar strangers. Nature 1992, 360:635
82. Baumann P, Qureshi SA and Jackson SP Transcription: new insights from studies on Archaea. Trends Genet 1995, 11:279-283
83. Bell SD and Jackson SP Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 2001, 4:208-213
84. Lagos-Quintana M, Rauhut R, Lendeckel W and Tuschl T Identification of novel genes coding for small expressed RNAs. Science 2001, 294:853-858
85. Dennis C The brave new world of RNA. Nature 2002, 418:122-124
86. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B and Bartel DP MicroRNAs in plants. Genes Dev 2002, 16:1616-1626
87. Pasquinelli AE MicroRNAs: deviants no longer. Trends Genet 2002, 18:171-173
88. Grosshans H and Slack FJ Micro-RNAs: small is plentiful. J Cell Biol 2002, 156:17-21
89. Llave C, Kasschau KD, Rector MA and Carrington JC Endogenous and silencing-associated small RNAs in plants. Plant Cell 2002, 14:1605-1619
90. Llave C, Xie Z, Kasschau KD and Carrington JC Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297:2053-2056
91. Wassarman KM, Repoila F, Rosenow C, Storz G and Gottesman S Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 2001, 15:1637-1651
92. Davids W, Amiri H and Andersson SG Small RNAs in Rickettsia: are they functional? Trends Genet 2002, 18:331-334
93. Eddy SR Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001, 2:919-929
94. Rivas E, Klein RJ, Jones TA and Eddy SR Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 2001, 11:1369-1373
95. Woese C The universal ancestor. Proc Natl Acad Sci U S A 1998, 95:6854-6859
96. Leipe DD, Aravind L and Koonin EV Did DNA replication evolve twice independently? Nucleic Acids Res 1999, 27:3389-3401
97. Aravind L, Anantharaman V and Koonin EV Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA. Proteins 2002, 48:1-14
98. Lingner J, Hughes TR, Shevchenko A, Mann M, Lundblad V and Cech TR Reverse transcriptase motifs in the catalytic subunit of telomerase. Science 1997, 276:561-567
99. Nakamura TM, Morin GB, Chapman KB, Weinrich SL, Andrews WH, Lingner J, Harley CB and Cech TR Telomerase catalytic subunit homologs from fission yeast and human. Science 1997, 277:955-959
100. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W and Lipman DJ Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402
101. Aravind L and Koonin EV Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 1999, 287:1023-1040
102. Wootton JC Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 1994, 18:269-285
103. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV and Altschul SF Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29:2994-3005
104. Notredame C, Higgins DG and Heringa J T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-217
105. Neuwald AF, Liu JS and Lawrence CE Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 1995, 4:1618-1632
106. Schuler GD, Altschul SF and Lipman DJ A workbench for multiple alignment construction and analysis. Proteins 1991, 9:180-190
107. Walker DR and Koonin EV SEALS: a system for easy analysis of lots of sequences. Proc Int Conf Intell Syst Mol Biol 1997, 5:333-339
108. Holm L and Sander C Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997, 25:231-234
109. Rost B and Sander C Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993, 232:584-599
110. Rost B, Sander C and Schneider R PHD - an automatic mail server for protein secondary structure prediction. Comput Appl Biosci 1994, 10:53-60
111. Guex N and Peitsch MC SWISS-MODEL and the Swiss-Pdb-Viewer: an environment for comparative protein modeling. Electrophoresis 1997, 18:2714-2723
112. Kraulis PJ MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures. Journal of App Crystallography 1991, 24:946-950