Intrinsically disordered proteins (IDPs) in trypanosomatids

BMC Genomics

Jeronimo Conceição Ruiz³  Angela Kaysel Cruz¹  Viviane de Souza Alves²  Juliano Simões Toledo¹  Raul Torrieri³  Patrícia de Cássia Ruy³ 

[1] Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil;Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil;Informática de Biossistemas, Centro de Pesquisas René Rachou – Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, MG, Brasil

关键词: IDP prediction;    Trypanosomatids;    Intrinsically disordered proteins (IDPs);   

Others  :  1127352
DOI  :  10.1186/1471-2164-15-1100

 received in 2014-06-20, accepted in 2014-12-04,  发布年份 2014

【 摘 要 】

Background

Proteins are composed of one or more amino acid chains and exhibit several structure levels. IDPs (intrinsically disordered proteins) represent a class of proteins that do not fold into any particular conformation and exist as dynamic ensembles in their native state. Due to their intrinsic adaptability, IDPs participate in many regulatory biological processes, including parasite immune escape. Using the information from trypanosomatids proteomes, we developed a pipeline for the identification, characterization and analysis of IDPs. The pipeline employs six disorder prediction methodologies and integrates structural and functional annotation information, subcellular location prediction and physicochemical properties. At the core of the IDP pipeline, there is a relational database that describes the protein disorder knowledge in a logically consistent manner.

Results

The results obtained from the IDP pipeline showed that Leishmania and Trypanosoma species have approximately 70% and 55% IDPs, respectively. Our results indicate that IDPs in trypanosomatids contain disorder-promoting amino acids and order-promoting amino acids. The functional annotation analysis demonstrated enrichment of selected Gene Ontology terms. A relevant association was observed between the disordered residue numbers within predicted IDPs and their subcellular location, lack of transmembrane domains and lack of predicted function. We validated our computational findings with 2D electrophoresis designed for IDP identification and found that 100% of the identified protein spots were predicted in silico.

Conclusions

Because there is no pipeline or database addressing IDPs in trypanosomatids, the pipeline described here represents the first attempt to establish possible correlations between protein function and structural disorder in these eukaryotes. Interestingly, all significant associations detected in the contingency analysis were observed when the protein disorder content reached approximately 40%. The exploratory data analysis allowed us to develop hypotheses regarding the IDPs’ association with key biological features of these parasites, including transcription and transcriptional regulation, RNA processing and splicing, and cytoskeleton.

【 授权许可】

   
2014 Ruy et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 1.

Figure 6.

Figure 7.

【 参考文献 】

• [1]Lynch WP, Riseman VM, Bretscher A: Smooth muscle caldesmon is an extended flexible monomeric protein in solution that can readily undergo reversible intra- and intermolecular sulfhydryl cross-linking. A Mech caldesmon’s F-actin bundling activity. J Biol Chem 1987, 262(15):7429-7437.
• [2]Barlow PN, Vidal JC, Lister MD, Hancock AJ, Sigler PB: Synthesis and some properties of constrained short-chain phosphatidylcholine analogues: (+)- and (-)-(1,3/2)-1-O-(phosphocholine)2,3-O- dihexanoylcyclopentane-1,2,3-triol. Chem Phys Lipids 1988, 46(3):157-164.
• [3]Wright PE, Dyson HJ: Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 1999, 293(2):321-331.
• [4]Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM: Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr Opin Struct Biol 2013, 23(3):443-450.
• [5]Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J: The Protein Data Bank and the challenge of structural genomics. Nat Struct Biol 2000, 7(Suppl):957-959.
• [6]Obradovic Z, Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK: Predicting intrinsic disorder from amino acid sequence. Proteins 2003, 53(Suppl 6):566-572.
• [7]Dunker AK, Obradovic Z: The protein trinity–linking function and disorder. Nat Biotechnol 2001, 19(9):805-806.
• [8]Dunker AK, Obradovic Z, Romero P, Garner EC, Brown CJ: Intrinsic protein disorder in complete genomes. Genome Inform Ser Workshop Genome Inform 2000, 11:161-171.
• [9]Mohan A, Sullivan WJ, Radivojac P, Dunker AK, Uversky VN: Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes. Mol Biosyst 2008, 4(4):328-340.
• [10]Uversky VN: The mysterious unfoldome: structureless, underappreciated, yet vital part of any given proteome. J Biomed Biotechnol 2010, 2010:568068.
• [11]Ishida N, Hara T, Kamura T, Yoshida M, Nakayama K, Nakayama KI: Phosphorylation of p27Kip1 on serine 10 is required for its binding to CRM1 and nuclear export. J Biol Chem 2002, 277(17):14355-14358.
• [12]Blain SW, Massagué J: Breast cancer banishes p27 from nucleus. Nat Med 2002, 8(10):1076-1078.
• [13]Tsvetkov LM, Yeh KH, Lee SJ, Sun H, Zhang H: p27(Kip1) ubiquitination and degradation is regulated by the SCF(Skp2) complex through phosphorylated Thr187 in p27. Curr Biol 1999, 9(12):661-664.
• [14]Kriwacki RW, Hengst L, Tennant L, Reed SI, Wright PE: Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proc Natl Acad Sci U S A 1996, 93(21):11504-11509.
• [15]Dyson HJ, Wright PE: Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 2002, 12(1):54-60.
• [16]Lacy ER, Filippov I, Lewis WS, Otieno S, Xiao L, Weiss S, Hengst L, Kriwacki RW: p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding. Nat Struct Mol Biol 2004, 11(4):358-364.
• [17]Feng Z, Zhang X, Han P, Arora N, Anders R, Norton R: Abundance of intrinsically unstructured proteins in P. falciparum and other apicomplexan parasite proteomes. Mol Biochem Parasitol 2006, 150(2):256-267.
• [18]Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, et al.: TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res 2010, 38(Database issue):D457-462.
• [19]Cox FE: History of sleeping sickness (African trypanosomiasis). Infect Dis Clin North Am 2004, 18(2):231-245.
• [20]Hotez PJ, Bottazzi ME, Franco-Paredes C, Ault SK, Periago MR: The neglected tropical diseases of Latin America and the Caribbean: a review of disease burden and distribution and a roadmap for control and elimination. PLoS Negl Trop Dis 2008, 2(9):e300.
• [21]El-On J: Current status and perspectives of the immunotherapy of leishmaniasis. Isr Med Assoc J 2009, 11(10):623-628.
• [22]Dyson HJ, Wright PE: Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005, 6(3):197-208.
• [23]Dunker A, Brown C, Lawson J, Iakoucheva L, Obradović Z: Intrinsic disorder and protein function. Biochemistry 2002, 41(21):6573-6582.
• [24]Namba K: Roles of partly unfolded conformations in macromolecular self-assembly. Genes Cells 2001, 6(1):1-12.
• [25]Tompa P: Intrinsically unstructured proteins. Trends Biochem Sci 2002, 27(10):527-533.
• [26]Tompa P, Csermely P: The role of structural disorder in the function of RNA and protein chaperones. FASEB J 2004, 18(11):1169-1175.
• [27]Uversky VN, Permyakov SE, Zagranichny VE, Rodionov IL, Fink AL, Cherskaya AM, Wasserman LA, Permyakov EA: Effect of zinc and temperature on the conformation of the gamma subunit of retinal phosphodiesterase: a natively unfolded protein. J Proteome Res 2002, 1(2):149-159.
• [28]Bracken C, Iakoucheva LM, Romero PR, Dunker AK: Combining prediction, computation and experiment for the characterization of protein disorder. Curr Opin Struct Biol 2004, 14(5):570-576.
• [29]Linderstrom-Lang K, Schellman J: Protein Structure and Enzyme Activity. In The Enzymes. Edited by Boyer PD, Lardy H, Myrback K. New York: Academic Press; 1959:443-510. Vol 1, 2nd Ed
• [30]Pullen RA, Jenkins JA, Tickle IJ, Wood SP, Blundell TL: The relation of polypeptide hormone structure and flexibility to receptor binding: the relevance of X-ray studies on insulins, glucagon and human placental lactogen. Mol Cell Biochem 1975, 8(1):5-20.
• [31]Cary PD, Moss T, Bradbury EM: High-resolution proton-magnetic-resonance studies of chromatin core particles. Eur J Biochem 1978, 89(2):475-482.
• [32]Dunker A, Lawson J, Brown C, Williams R, Romero P, Oh J, Oldfield C, Campen A, Ratliff C, Hipps K, Ausio J, Nissen M, Reeves R, Kang C, Kissinger C, Bailey R, Griswold M, Chiu W, Garner E, Obradovic Z: Intrinsically disordered protein. J Mol Graph Model 2001, 19(1):26-59.
• [33]Daughdrill GW, Pielak GJ, Uversky VN, Cortese MS, Dunker K: Natively Disordered Proteins. In Protein Folding Handbook. vol. Volume 1. Basel, Switzerland: Wiley-VCH; 2005.
• [34]Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK: Sequence complexity of disordered protein. Proteins 2001, 42(1):38-48.
• [35]Vucetic S, Brown C, Dunker A, Obradovic Z: Flavors of protein disorder. Proteins 2003, 52(4):573-584.
• [36]Uversky VN, Gillespie JR, Fink AL: Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 2000, 41(3):415-427.
• [37]Linding R, Jensen L, Diella F, Bork P, Gibson T, Russell R: Protein disorder prediction: implications for structural proteomics. Structure 2003, 11(11):1453-1459.
• [38]Ferron F, Longhi S, Canard B, Karlin D: A practical overview of protein disorder prediction methods. Proteins 2006, 65(1):1-14.
• [39]Dosztányi Z, Mészáros B, Simon I: Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins. Brief Bioinform 2010, 11(2):225-243.
• [40]Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, Dunker AK: Comparing and combining predictors of mostly disordered proteins. Biochemistry 2005, 44(6):1989-2000.
• [41]Brown C, Takayama S, Campen A, Vise P, Marshall T, Oldfield C, Williams C, Dunker A: Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 2002, 55(1):104-110.
• [42]Han P, Zhang X, Feng ZP: Predicting disordered regions in proteins using the profiles of amino acid indices. BMC Bioinformatics 2009, 10(Suppl 1):S42. BioMed Central Full Text
• [43]Pryor EE, Wiener MC: A critical evaluation of in silico methods for detection of membrane protein intrinsic disorder. Biophys J 2014, 106(8):1638-1649.
• [44]Abercrombie BD, Kneale GG, Crane-Robinson C, Bradbury EM, Goodwin GH, Walker JM, Johns EW: Studies on the conformational properties of the high-mobility-group chromosomal protein HMG 17 and its interaction with DNA. Eur J Biochem 1978, 84(1):173-177.
• [45]Penkett CJ, Redfield C, Dodd I, Hubbard J, McBay DL, Mossakowska DE, Smith RA, Dobson CM, Smith LJ: NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein. J Mol Biol 1997, 274(2):152-159.
• [46]Bai Y, Chung J, Dyson HJ, Wright PE: Structural and dynamic characterization of an unfolded state of poplar apo-plastocyanin formed under nondenaturing conditions. Protein Sci 2001, 10(5):1056-1066.
• [47]Lee T, Moran-Gutierrez CR, Deniz AA: Probing protein disorder and complexity at single-molecule resolution. Semin Cell Dev Biol 2014. in press
• [48]Green DM, Swets JM: Signal detection theory and psychophysics. New York: John Wiley and Sons Inc; 1966.
• [49]Linding R, Russell R, Neduva V, Gibson T: GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res 2003, 31(13):3701-3708.
• [50]Dosztányi Z, Csizmók V, Tompa P, Simon I: The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 2005, 347(4):827-839.
• [51]Peng K, Radivojac P, Vucetic S, Dunker A, Obradovic Z: Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 2006, 7:208. BioMed Central Full Text
• [52]Käll L, Krogh A, Sonnhammer EL: A combined transmembrane topology and signal peptide prediction method. J Mol Biol 2004, 338(5):1027-1036.
• [53]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):W585-587.
• [54]Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676.
• [55]Altschul S, Gish W, Miller W, Myers E, Lipman D: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
• [56]Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G: GO::TermFinder–open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20(18):3710-3715.
• [57]Hobohm U, Sander C: Enlarged representative set of protein structures. Protein Sci 1994, 3(3):522-524.
• [58]Agresti A: Categorical Data Analysis. 2nd edition. Hoboken, NJ, USA: John Wiley & Sons, Inc.; 2002.
• [59]Friendly M: Graphical methods for categorical data. In SAS User Group International Conference Proceedings, 17, 190–200: 1992. Canada: York University, Downsview, ONT; 1992.
• [60]Csizmók V, Szollosi E, Friedrich P, Tompa P: A novel two-dimensional electrophoresis technique for the identification of intrinsically unstructured proteins. Mol Cell Proteomics 2006, 5(2):265-273.
• [61]Galea C, Pagala V, Obenauer J, Park C, Slaughter C, Kriwacki R: Proteomic studies of the intrinsically unstructured mammalian proteome. J Proteome Res 2006, 5(10):2839-2848.
• [62]Uversky VN: Natively unfolded proteins: a point where biology waits for physics. Protein Sci 2002, 11(4):739-756.
• [63]Boesch C, Bundi A, Oppliger M, Wüthrich K: 1H nuclear-magnetic-resonance studies of the molecular conformation of monomeric glucagon in aqueous solution. Eur J Biochem 1978, 91(1):209-214.
• [64]Daniels AJ, Williams RJ, Wright PE: The character of the stored molecules in chromaffin granules of the adrenal medulla: a nuclear magnetic resonance study. Neuroscience 1978, 3(6):573-585.
• [65]Iakoucheva L, Brown C, Lawson J, Obradović Z, Dunker A: Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 2002, 323(3):573-584.
• [66]Iakoucheva LM, Radivojac P, Brown CJ, O’Connor TR, Sikes JG, Obradovic Z, Dunker AK: The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 2004, 32(3):1037-1049.
• [67]Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi Z, Uversky VN, Obradovic Z, Kurgan L, Dunker A, Gough J: D2P2: database of disordered protein predictions. Nucleic Acids Res 2013, 41(Database issue):D508-516.
• [68]Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT: Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004, 337(3):635-645.
• [69]El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G, Westenberger SJ, Caler E, Cerqueira GC, Branche C, Haas B, Anupama A, Arner E, Aslund L, Attipoe P, Bontempi E, Bringaud F, Burton P, Cadag E, Campbell DA, Carrington M, Crabtree J, Darban H, da Silveira JF, de Jong P, Edwards K: The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 2005, 309(5733):409-415.
• [70]Williamson MP: The structure and function of proline-rich regions in proteins. Biochem J 1994, 297(Pt 2):249-260.
• [71]Williams RM, Obradovi Z, Mathura V, Braun W, Garner EC, Young J, Takayama S, Brown CJ, Dunker AK: The protein non-folding problem: amino acid determinants of intrinsic order and disorder. Pac Symp Biocomput 2001, 89-100.
• [72]Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK: Protein flexibility and intrinsic disorder. Protein Sci 2004, 13(1):71-80.
• [73]Li X, Romero P, Rani M, Dunker AK, Obradovic Z: Predicting protein disorder for N-, C-, and internal regions. Genome Inform Ser Workshop Genome Inform 1999, 10:30-40.
• [74]Sugase K, Dyson HJ, Wright PE: Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 2007, 447(7147):1021-1025.
• [75]Galea CA, Nourse A, Wang Y, Sivakolundu SG, Heller WT, Kriwacki RW: Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27 Kip1. J Mol Biol 2008, 376(3):827-838.
• [76]Campbell KM, Terrell AR, Laybourn PJ, Lumb KJ: Intrinsic structural disorder of the C-terminal activation domain from the bZIP transcription factor Fos. Biochemistry 2000, 39(10):2708-2713.