Hidden Markov models and the Viterbi algorithm applied to integrated bioinformatics analyses of putative flagellar actin-interacting proteins in Leishmania spp.

International Journal of Computer Aided Engineering and Technology

Volumn 1, Issue 4, 2009, Pages 420-436

  Pacheco, Ana Carolina L ^a   Araújo, Fabiana F ^a   Kamimura, Michel T ^a   Silva, Samara C ^a   Diniz, Michely C ^a   Oliveira, Fátima de Cássia E ^a   Filho, Raimundo Araújo ^a   Costa, Marcília P ^a   Oliveira, Diana M ^a  

^a STATE UNIVERSITY OF CEARÁ   (Brazil)

Author keywords

actin interacting proteins; AIP; bioinformatics; cofilin; flagellar proteins; hidden Markov models; HMMs; Leishmania; twinfilin; Viterbi algorithm

Indexed keywords

EID: 77957924618     PISSN: 17572657     EISSN: 17572665     Source Type: Journal    
DOI: 10.1504/IJCAET.2009.028550     Document Type: Article

References (54)

1. Acestor, N., Masina, S., Walker, J. et al. (2002) ‘Establishing two-dimensional gels for the analysis of Leishmania proteomes’, Proteomics, Vol. 2, pp.877–879.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) ‘Gapped BLAST and PSI-BLAST: a new generation of protein database search programs’, Nucleic Acids Res., Vol. 25, pp.3389–3402.
3. Avidor-Reiss, T., Maer, A.M., Koundakjian, E., Polyanovsky, A., Keil, T., Subramaniam, S. and Zuker, C.S. (2004) ‘Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis’, Cell, Vol. 117, pp.527–539.
4. Bamburg, J.R. and Bernstein, B.W. (2008) ‘ADF/Cofilin’, Curr. Biol., Vol. 18, pp.R273–R275.
5. Baron, D.M., Ralston, K.S., Kabututu, Z.P. and Hill, K.L. (2007) ‘Functional genomics in Trypanosoma brucei identifies evolutionarily conserved components of motile flagella’, J. Cell Sci., Vol. 120, No. 3, pp.478–491.
6. Berriman, M., Ghedin, E., Hertz-Fowler, C. et al. (2005) ‘The genome of the African trypanosome Trypanosoma brucei’, Science, Vol. 309, No. 5733, pp.416–422.
7. Black, P.E. (2004) ‘Viterbi algorithm’, in P.E. Black (Ed.): Dictionary of Algorithms and Data Structures, U.S. National Institute of Standards and Technology, online.
8. Broadhead, R., Dawe, H.R. et al. (2006) ‘Flagellar motility is required for the viability of the bloodstream trypanosome’, Nature, Vol. 440, pp.224–227.
9. Chauduri, O., Parekh, S.H. and Fletcher, D.A. (2007) ‘Reversible stress softening of actin networks’, Nature, Vol. 445, pp.295–298.
10. Drummelsmith, J., Brochu, V., Girard, I., Messier, N. and Ouellette, M. (2003) ‘Proteome mapping of the protozoan parasite Leishmania and application to the study of drug targets and resistance mechanisms’, Mol. Cell. Proteomics, Vol. 2, pp.146–155.
11. Eddy, S.R. (1998) ‘Profile hidden Markov models’, Bioinformatics, Vol. 14, pp.755–763.
12. Edgar, R.C. (2004) ‘MUSCLE: multiple sequence alignment with high accuracy and high throughput’, Nucleic Acids Res., Vol. 32, pp.1792–1797.
13. El Fakhry, Y., Ouellette, M. and Papadopoulou, B. (2002) ‘A proteomic approach to identify developmentally regulated proteins in Leishmania infantum’, Proteomics, Vol. 2, pp.1007–1017.
14. El-Sayed, N.M., Myler, P.J., Blandin, G. et al. (2005) ‘Comparative genomics of trypanosomatid parasitic protozoa’, Science, Vol. 309, No. 5733, pp.404–409.
15. Emanuelsson, O., Nielsen, H., Brunak, S. and Heijne, G.V. (2000) ‘Predicting subcellular localization of proteins based on their N-terminal amino acid sequence’, J. Mol. Biol., Vol. 300, pp.1005–1016.
16. Fedorov, A.A., Lappalainen, P., Fedorov, E.V., Drubin, D.G. and Almo, S.C. (1997) ‘Structure determination of yeast cofilin’, Nat. Struct. Biol., Vol. 4, pp.366–369.
17. Forney, D.G., Jr. (1973) ‘The Viterbi algorithm’, Proceedings of the IEEE, Vol. 61, No. 3, pp.268–278.
18. Gadelha, C., Wickstead, B. and Gull, K. (2007) ‘Flagellar and ciliary beating in trypanosome motility’, Cell. Motil. Cytoskeleton, Vol. 64, pp.629–643.
19. Ghedin, E., Bringaud, F., Peterson, J. et al. (2004) ‘Gene synteny and evolution of genome architecture in trypanosomatids’, Mol. Biochem. Parasitol., Vol. 134, pp.183–191.
20. Girão, K.T., Araújo, F.F., Costa, M.P. et al. (2007) ‘Mining genes of WD-40 superfamily in Leishmania through hidden Markov models and natural clustering’, Very Large Databases VLDB Workshop on Data Mining in Bioinformatics-DMB2007, 33rd International Conference Proceedings VLDB, Vienna, Austria.
21. Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001) ‘Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure’, J. Mol. Biol., Vol. 313, pp.903–919.
22. Gouveia, J.J.S., Vasconcelos, E.J.R., Pacheco, A.C.L. et al. (2007) ‘Intraflagellar transport (IFT) complex in Leishmania spp.: in silico genome-wide screening and annotation of gene function’, Genet. Mol. Res., Vol. 7, pp.784–799.
23. Hellman, M., Paavilainen, V., Naumanen, P., Lappalainen, P., Annila, A. and Permi, P. (2004) ‘Solution structure of coactosin reveals structural homology to ADF/cofilin family proteins’, FEBS Letters, Vol. 576, pp.91–96.
24. Higa, R.H., Togawa, R.C., Montagner, A.J. et al. (2004) ‘STING millennium suite: integrated software for extensive analyses of 3D structures of proteins and their complexes’, BMC Bioinformatics, Vol. 5, pp.107–111.
25. Iida, K., Matsumoto, S. and Yahara, I. (1992) ‘The KKRKK sequence is involved in heat shock-induced nuclear translocation of the 18-kDa actin-binding protein, cofilin’, Cell Struct. Funct., Vol. 17, pp.39–46.
26. Ivens, A.C., Peacock, C.S., Worthey, E.A. et al. (2005) ‘The genome of the kinetoplastid parasite, Leishmania major’, Science, Vol. 309, No. 5733, pp.436–442.
27. Kohl, L., Robinson, D. and Bastin, P. (2003) ‘Novel roles for the flagellum in cell morphogenesis and cytokinesis of trypanosomes’, EMBO J., Vol. 22, pp.5336–5346.
28. Lambert, C., Leonard, N., De Bolle, X. and Depiereux, E. (2002) ‘ESyPred3D: prediction of proteins 3D structures’, Bioinformatics, Vol. 18, pp.1250–1256.
29. Lappalainen, P., Kessels, M.M., Cope, M.J.T.V. and Drubin, D.G. (1998) ‘The ADF homology (ADF-H) domain: a highly exploited actin-binding module’, Mol. Biol. Cell, Vol. 9, pp.1951–1959.
30. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) ‘PROCHECK: a program to check the stereochemical quality of protein structures’, J. Appl. Cryst., Vol. 26, pp.283–291.
31. Letunic, L., Copley, R.C., Pils, B., Pinkert, S., Schultz, J. and Bork, P. (2006) ‘SMART 5: domains in the context of genomes and networks’, Nucleic Acids Research, Vol. 34, pp.D257–D260.
32. Loisel, T.P., Boujemaa, R., Pantaloni, D. and Carlier, M.F. (1999) ‘Reconstitution of actin-based motility of Listeria and Shigella using pure proteins’, Nature, Vol. 401, pp.613–616.
33. Maciver, S.K. and Hussey, P.J. (2002) ‘The ADF/cofilin family: actin-remodeling proteins’, Genome Biol., Vol. 3, pp.3007.1–3007.12.
34. Majoros, W.H., Pertea, M. and Salzberg, S.L. (2004) ‘TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders’, Bioinformatics, Vol. 20, pp.2878–2879.
35. Marchler-Bauer, A., Anderson, J.B., Cherukuri, P.F. et al. (2005) ‘CDD: a conserved domain database for protein classification’, Nucleic Acids Research, Vol. 33, pp.D192–D196.
36. Marti-Renom, M.A., Stuart, A., Fiser, A., Sánchez, R., Melo, F. and Sali, A. (2000) ‘Comparative protein structure modeling of genes and genomes’, Annu. Rev. Biophys. Biomol. Struct., Vol. 29, pp.291–325.
37. Mcconville, M.J., Mullin, K.A., Ilgoutz, S.C. and Teasdale, R.D. (2002) ‘Secretory pathway of trypanosomatid parasites’, Microbiol. Mol. Biol. Rev., Vol. 66, pp.122–154.
38. Naderer, T., Vince, J.E. and Mcconville, M.J. (2004) ‘Surface determinants of Leishmania parasites and their role in infectivity in the mammalian host’, Curr. Mol. Med., Vol. 4, pp.649–665.
39. Oliveira, D.M., Gouveia, J.J.S., Diniz, N.B. et al. (2005) ‘Pathogenomics analysis of Leishmania spp.: flagellar gene families of putative virulence factors’, OMICS, Vol. 9, pp.171–191.
40. Paavilainen, V.O., Hellman, M., Helfer, E., Bovellan, M., Annila, A., Carlier, M-F., Perm, P. and Lappalainen, P. (2007) ‘Structural basis and evolutionary origin of actin filament capping by twinfilin’, Proc. Nat. Acad. Sci. PNAS, Vol. 104, pp.3113–3118.
41. Parsons, M., Worthey, E.A., Ward, P.N. and Mottram, J.C. (2005) ‘Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi’, BMC Genomics, Vol. 6, p.127.
42. Pazour, G.J., Dickert, B.L., Vucica, Y., Seeley, E.S., Rosenbaum, J.L., Witman, G.B. and Cole, D.G. (2005) ‘Proteomic analysis of a eukaryotic cilium’, J. Cell Biol., Vol. 151, pp.709–718.
43. Peacock, C.S., Seeger, K., Harris, D. et al. (2007) ‘Comparative genomic analysis of three Leishmania species that cause diverse human disease’, Nat. Genet., Vol. 39, pp.839–847.
44. Pope, B.J., Zierler-Gould, K.M., Kuhne, R., Weeds, A.G. and Ball, L.J. (2004) ‘Solution structure of human cofilin: actin binding, pH sensitivity and relationship to actin-depolymerizing factor’, J. Biol. Chem., Vol. 279, pp.4840–4848.
45. Ralston, K.S., Lerner, A.G., Diener, D.R. and Hill, K.L. (2006) ‘Flagellar motility contributes to cytokinesis in Trypanosoma brucei and is modulated by an evolutionarily conserved dynein regulatory system’, Eukaryot Cell., Vol. 5, pp.696–711.
46. Romero, S., Le Clainche, C., Didry, D., Egile, C., Pantalón, D. and Carlier, M.F. (2004) ‘Formin is a processive motor that requires profilin to accelerate actin assembly and associated ATP hydrolysis’, Cell, Vol. 119, pp.419–429.
47. Sahasrabuddhe, A.A., Virendra, K. and Gupta, C.M. (2004) ‘A novel form of actin in Leishmania: molecular characterisation, subcellular localisation and association with subpellicular microtubules’, Mol. Biochem. Parasitol., Vol. 134, pp.105–114.
48. Sali, A. and Blundell, T.L. (1993) ‘Comparative protein modelling by satisfaction of spatial restraints’, J. Mol. Biol., Vol. 234, pp.779–815.
49. Toussaint, G.T. (1978) ‘The use of context in pattern recognition’, Pattern Recognition, Vol. 10, pp.189–204.
50. Tull, D., Vince, J.E., Callaghan, J.M., Naderer, T. et al. (2004) ‘SMP-1, a member of a new family of small myristoylated proteins in kinetoplastid parasites, is targeted to the flagellum membrane in Leishmania’, Mol. Biol. Cell, Vol. 15, pp.4775–4786.
51. Vasconcelos, E.J.R., Pacheco, A.C.L., Gouveia, J.J.S. et al. (2007) ‘Profilins, formins and katanins as flagellar proteins of Leishmania spp.: a genome-based, multi-step bioinformatics-driven description’, in N.G. Bourbakis et al. (Eds.): IEEE 7th International Symposium on Bioinformatics and Bioengineering-2007, IEEE BIBE 2007 Conference Proceedings, Boston, MT, pp.880–887.
52. Vasconcelos, E.J.R., Pacheco, A.C.L., Gouveia, J.J.S. et al. (2008) ‘Actin-interacting proteins in flagellated pathogenic Leishmania spp.: a genome-based bioinformatics report on profilins, formins and katanins’, International Journal of Functional Informatics and Personalised Medicine, Vol. 1, No. 3, pp.234–252.
53. Vavylonis, D., Kovar, D.R., O’Shaughnessy, B. and Pollard, T.D. (2006) ‘Model of formin-associated actin filament elongation’, Mol Cell., Vol. 21, pp.455–466.
54. von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005) ‘STRING: known and predicted protein-protein associations, integrated and transferred across organisms’, Nucleic Acids Research, Vol. 33, pp.D433–D437.