Predicting sub-cellular localization of tRNA synthetases from their primary structures

Amino Acids

Volumn 42, Issue 5, 2012, Pages 1703-1713

  Panwar, Bharat ^a   Raghava, G P S ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

MARSpred; Mitochondrial tRNA synthetase; Prediction; Support vector machine

Indexed keywords

AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; DIPEPTIDE;

ACCURACY; AMINO ACID COMPOSITION; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELLULAR DISTRIBUTION; CORRELATION COEFFICIENT; CYTOSOL; ENZYME LOCALIZATION; ENZYME STRUCTURE; HUMAN; MITOCHONDRION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SCORING SYSTEM; SUPPORT VECTOR MACHINE; VALIDATION PROCESS;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; CELL NUCLEUS; COMPUTATIONAL BIOLOGY; CYTOSOL; EUKARYOTIC CELLS; INTERNET; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; POSITION-SPECIFIC SCORING MATRICES; RIBOSOMES; SOFTWARE; SUPPORT VECTOR MACHINES;

EUKARYOTA;

EID: 84862763897     PISSN: 09394451     EISSN: 14382199     Source Type: Journal    
DOI: 10.1007/s00726-011-0872-8     Document Type: Article

References (35)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 (Pubitemid 27359211)
2. Antonellis A, Green ED (2008) The role of aminoacyl-tRNA synthetases in genetic diseases. Annu Rev Genomics Hum Genet 9:87-107
3. Baker MJ, Frazier AE, Gulbis JM, Ryan MT (2007) Mitochondrial protein-import machinery: correlating structure with function. Trends Cell Biol 17:456-464 (Pubitemid 47499044)
4. Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16:412-424 (Pubitemid 30487963)
5. Berg P (1961) Specificity in protein synthesis. Annu Rev Biochem 30:293-324
6. Bhasin M, Raghava GPS (2004) Classification of nuclear receptors based on amino acid composition and dipeptide composition. J Biol Chem 279:23262-23266 (Pubitemid 38685634)
7. Bhasin M, Raghava GPS (2005) GPCRsclass: a web tool for classification of amine type of G-protein coupled receptors. Nucleic Acids Res 33:W143-W147 (Pubitemid 44529897)
8. Brindefalk B, Viklund J, Larsson D, Thollesson M, Andersson SG (2007) Origin and evolution of the mitochondrial aminoacyltRNA synthetases. Mol Biol Evol 24:743-756 (Pubitemid 46355798)
9. Chou KC, Shen HB (2007) Recent progresses in protein subcellular location prediction. Anal Biochem 370:1-16
10. Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241:779-786 (Pubitemid 26379380)
11. Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14:307-311
12. Duchêne AM, Pujol C, Maréchal-Drouard L (2009) Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet 55:1-18
13. Español Y, Thut D, Schneider A, de Pouplana LR (2009) A mechanism for functional segregation of mitochondrial and cytosolic genetic codes. Proc Natl Acad Sci USA 106(46): 19420-19425
14. Garg A, Bhasin M, Raghava GPS (2005) SVM-based method for subcellular localization of human proteins using amino acid compositions, their order and similarity search. J Biol Chem 280(15):14427-14432 (Pubitemid 40562782)
15. Guda C, Guda P, Fahy E, Subramaniam S (2004) MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Res 32:W372-W374 (Pubitemid 38997361)
16. Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH (2009) The WEKA Data Mining Software: an update. SIGKDD Explorations 11(1):10-18
17. Joachims T (1999) Making large-scale SVM learning particles. In: Scholkopf B, Berges C, Smola A (eds) Advances in kernel methods support vector learning. MIT Press, Cambridge, pp 42-56
18. Kaur H, Raghava GPS (2004) A neural network method for prediction of beta-turn types in proteins using evolutionary information. Bioinformatics 20:2751-2758 (Pubitemid 39530161)
19. Kumar M, Raghava GPS (2009) Prediction of nuclear proteins using SVM and HMM models. BMC Bioinformatics 10:22
20. Kumar M, Bhasin M, Natt NK, Raghava GPS (2005) BhairPred: a webserver for prediction of beta-hairpins in proteins from multiple alignment information using ANN and SVM techniques. Nucleic Acids Res 33:W154-W159 (Pubitemid 44529899)
21. Kumar M, Verma R, Raghava GPS (2006) Prediction of mitochondrial proteins using support vector machine and hidden Markov model. J Biol Chem 281(9):5357-5363 (Pubitemid 43847629)
22. Kumar M, Gromiha MM, Raghava GPS (2007) Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics 8:463
23. Lee JW, Beebe K, Nangle LA, Jang J, Longo-Guess CM, Cook SA, Muriel TD, Sundberg JP, Schimmel P, Ackerman SL (2006) Editing-defective tRNA synthetase causes protein misfolding and neurodegeration. Nature 443:50-55 (Pubitemid 44344044)
24. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large datasets of proteins or nucleotide sequences. Bioinformatics 22:1658-1659 (Pubitemid 43985301)
25. Miyaki M, Iijima T, Shiba K, Aki T, Kita Y, Yasuno M, Mori T, Kuroki T, Iwama T (2001) Alterations of repeated sequences in 50 upstream and coding regions in colorectal tumors from patients with hereditary nonpolyposis colorectal cancer and Turcot syndrome. Oncogene 20:5215-5218 (Pubitemid 32844051)
26. Panwar B, Raghava GPS (2010) Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains. BMC Genomics 11:507
27. Park SG, Schimmel P, Kim S (2008) Aminoacyl tRNA synthetases and their connections to disease. Proc Natl Acad Sci USA 105:11043-11049
28. Raghava GPS, Han JH (2005) Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein. BMC Bioinformatics 6:59
29. Rajbhandary UL (1997) Once there were twenty. Proc Natl Acad Sci USA 94:11761-11763
30. Scheper GC, van der Klok T, van Andel RJ, van Berkel CG, Sissler M, Smet J, Muravina TI, Serkov SV, Uziel G, Bugiani M, Schiffmann R, Krägeloh-Mann I, Smeitink JA, Florentz C, Van Coster R, Pronk JC, van der Knaap MS (2007) Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation. Nat Genet 39:534-539 (Pubitemid 46514784)
31. Schimmel P (2008) Development of tRNA synthetases and connection to genetic code and disease. Protein Sci 17:1643-1652
32. Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4(6):1581-1590 (Pubitemid 38738317)
33. t Hart LM, Hansen T, Rietveld I, Dekker JM, Nijpels G, Janssen GM, Arp PA, Uitterlinden AG, Jørgensen T, Borch-Johnsen K, Pols HA, Pedersen O, van Duijn CM, Heine RJ, Maassen JA (2005) Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene. Diabetes 54:1892-1895 (Pubitemid 40770782)
34. Unseld M, Marienfeld JR, Brandt P, Brennicke A (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides. Nat Genet 15:57-61
35. Vapnik VN (1999) An overview of statistical learning theory. IEEE Trans Neural Netw 10:988-999