Molecular evolution of dihydrouridine synthases

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Kasprzak, Joanna M ^b   Czerwoniec, Anna ^b   Bujnicki, Janusz M ^a,b  

^a ADAM MICKIEWICZ UNIVERSITY   (Poland)

^b INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

Author keywords

Dihydrouridine synthases; Enzymes acting on RNA; Fold recognition; Molecular evolution; Protein structure prediction; Remote homology; RNA modification

Indexed keywords

FOLD RECOGNITION; MOLECULAR EVOLUTION; PROTEIN STRUCTURE PREDICTION; REMOTE HOMOLOGY; RNA MODIFICATIONS; SYNTHASES;

BIOINFORMATICS; EVOLUTIONARY ALGORITHMS; MOLECULAR BIOLOGY; PROTEINS; RNA; SEARCH ENGINES;

ENZYMES;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

OXIDOREDUCTASE; TRANSFER RNA;

AMINO ACID SEQUENCE; ANIMAL; ARCHAEON; ARTICLE; BACTERIUM; ENZYMOLOGY; EUKARYOTE; GENETICS; HUMAN; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; ANIMALS; ARCHAEA; BACTERIA; EUKARYOTA; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES; PHYLOGENY; RNA, TRANSFER; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84862756078     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-153     Document Type: Article

References (52)

1. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 1998, 26(1):148-153. 10.1093/nar/26.1.148, 147216, 9399820.
2. Kowalak JA, Bruenger E, McCloskey JA. Posttranscriptional modification of the central loop of domain V in Escherichia coli 23 S ribosomal RNA. J Biol Chem 1995, 270(30):17758-17764. 10.1074/jbc.270.30.17758, 7629075.
3. Dalluge JJ, Hashizume T, Sopchik AE, McCloskey JA, Davis DR. Conformational flexibility in RNA: the role of dihydrouridine. Nucleic Acids Res 1996, 24(6):1073-1079. 10.1093/nar/24.6.1073, 145759, 8604341.
4. Dalluge JJ, Hamamoto T, Horikoshi K, Morita RY, Stetter KO, McCloskey JA. Posttranscriptional modification of tRNA in psychrophilic bacteria. J Bacteriol 1997, 179(6):1918-1923. 178914, 9068636.
5. Kato T, Daigo Y, Hayama S, Ishikawa N, Yamabuki T, Ito T, Miyamoto M, Kondo S, Nakamura Y. A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis. Cancer Res 2005, 65(13):5638-5646. 10.1158/0008-5472.CAN-05-0600, 15994936.
6. Bishop AC, Xu J, Johnson RC, Schimmel P, de Crecy-Lagard V. Identification of the tRNA-dihydrouridine synthase family. J Biol Chem 2002, 277(28):25090-25095. 10.1074/jbc.M203208200, 11983710.
7. Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res 2009, 37(Database issue):D118-D121. 2686465, 18854352.
8. Xing F, Hiley SL, Hughes TR, Phizicky EM. The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J Biol Chem 2004, 279(17):17850-17860. 10.1074/jbc.M401221200, 14970222.
9. Xing F, Martzen MR, Phizicky EM. A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA 2002, 8(3):370-381. 10.1017/S1355838202029825, 1370258, 12003496.
10. Savage DF, de Crecy-Lagard V, Bishop AC. Molecular determinants of dihydrouridine synthase activity. FEBS Lett 2006, 580(22):5198-5202. 10.1016/j.febslet.2006.08.062, 16962594.
11. Dobritzsch D, Ricagno S, Schneider G, Schnackerz KD, Lindqvist Y. Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer. J Biol Chem 2002, 277(15):13155-13166. 10.1074/jbc.M111877200, 11796730.
12. Rowland P, Bjornberg O, Nielsen FS, Jensen KF, Larsen S. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function. Protein Sci 1998, 7(6):1269-1279. 10.1002/pro.5560070601, 2144028, 9655329.
13. Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I. Molecular basis of dihydrouridine formation on tRNA. Proc Natl Acad Sci U S A 2011, 108(49):19593-19598. 10.1073/pnas.1112352108, 3241823, 22123979.
14. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
15. Frickey T, Lupas A. CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 2004, 20(18):3702-3704. 10.1093/bioinformatics/bth444, 15284097.
16. Park F, Gajiwala K, Noland B, Wu L, He D, Molinari J, Loomis K, Pagarigan B, Kearins P, Christopher J, et al. The 1.59 A resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima. Proteins 2004, 55(3):772-774. 10.1002/prot.20086, 15103641.
17. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. NucleicAcids Res 1997, 25(24):4876-4882.
18. Kurowski MA, Bujnicki JM. GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003, 31(13):3305-3307. 10.1093/nar/gkg557, 168964, 12824313.
19. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. The COG database: an updated version includes eukaryotes. BMC Bioinforma 2003, 4(1):41.
20. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574. 10.1093/bioinformatics/btg180, 12912839.
21. Shatkay H, Hoglund A, Brady S, Blum T, Donnes P, Kohlbacher O. SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics 2007, 23(11):1410-1417. 10.1093/bioinformatics/btm115, 17392328.
22. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. WoLF PSORT: protein localization predictor. Nucleic Acids Res 2007, 35(Web Server issue):W585-W587. 1933216, 17517783.
23. Chou KC, Shen HB. Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J Proteome Res 2007, 6(5):1728-1734. 10.1021/pr060635i, 17397210.
24. Hawkins J, Davis L, Boden M. Predicting nuclear localization. J Proteome Res 2007, 6(4):1402-1409. 10.1021/pr060564n, 17319708.
25. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007, 2(4):953-971. 10.1038/nprot.2007.131, 17446895.
26. Yu CS, Lin CJ, Hwang JK. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 2004, 13(5):1402-1406. 10.1110/ps.03479604, 2286765, 15096640.
27. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 2003, 19(1):163-164. 10.1093/bioinformatics/19.1.163, 12499312.
28. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 2001, 98(18):10037-10041. 10.1073/pnas.181342398, 56910, 11517324.
29. DeLano WL. The PyMOL Molecular Graphics System 2002, DeLano Scientific, Palo Alto, CA, USA.
30. Rider LW, Ottosen MB, Gattis SG, Palfey BA. Mechanism of dihydrouridine synthase 2 from yeast and the importance of modifications for efficient tRNA reduction. J Biol Chem 2009, 284(16):10324-10333. 10.1074/jbc.M806137200, 2667719, 19139092.
31. Porter DJ, Chestnut WG, Taylor LC, Merrill BM, Spector T. Inactivation of dihydropyrimidine dehydrogenase by 5-iodouracil. J Biol Chem 1991, 266(30):19988-19994.
32. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092, 17488738.
33. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18(5):691-699. 10.1093/oxfordjournals.molbev.a003851, 11319253.
34. Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001, 10(11):2354-2362. 2374055, 11604541.
35. Wallner B, Elofsson A. Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 2007, 69(Suppl 8):184-193.
36. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234(3):779-815. 10.1006/jmbi.1993.1626, 8254673.
37. Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM. MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinforma 2008, 9(1):403.
38. Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci U S A 2006, 103(14):5361-5366. 10.1073/pnas.0509355103, 1459360, 16567638.
39. Wallner B, Fang H, Elofsson A. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins 2003, 53(Suppl 6):534-541.
40. Kozlowski LP, Bujnicki JM. MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics 2012, 13(13):111-1459.
41. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure 2003, 11(11):1453-1459. 10.1016/j.str.2003.10.002, 14604535.
42. Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z. Intrinsic disorder and protein function. Biochemistry 2002, 41(21):6573-6582. 10.1021/bi012159+, 12022860.
43. Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 2005, 61(Suppl 7):176-182.
44. Dosztanyi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005, 21(16):3433-3434. 10.1093/bioinformatics/bti541, 15955779.
45. Shimizu K, Hirose S, Noguchi T. POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Bioinformatics 2007, 23(17):2337-2338. 10.1093/bioinformatics/btm330, 17599940.
46. Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T. POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics 2007, 23(16):2046-2053. 10.1093/bioinformatics/btm302, 17545177.
47. Ishida T, Kinoshita K. PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res 2007, 35(Web Server issue):W460-W464. 1933209, 17567614.
48. Yang ZR, Thomson R, McNeil P, Esnouf RM. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 2005, 21(16):3369-3376. 10.1093/bioinformatics/bti534, 15947016.
49. Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM. Computational methods for prediction of protein-RNA interactions. J Struct Biol 2011,
50. Murakami Y, Spriggs RV, Nakamura H, Jones S, et al. PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. Nucleic Acids Res 2010, 38(Web Server issue):W412-W416. 2896099, 20507911.
51. Kumar M. Gromiha MM 2007, Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins, Raghava GP.
52. Wang L, Huang C, Yang MQ, Yang JY. BindN + for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst Biol 2010, 4(Suppl 1):S3. 10.1186/1752-0509-4-S1-S3, 2982690, 20840730.