In Silico Analysis of Protein Disulfide Isomerases in Soybean

Abstract

Protein disulfide isomerases are molecular chaperones containing the thioredoxin domain that are involved in the correct formation of disulfide bonds during the protein folding process. There are many studies investigating the catalytic and chaperone roles of PDI proteins in animals. Studies on the diversity and function of PDI proteins in plants are limited. In this study, the presence of 12 PDI genes in the soybean genome was shown with reference to the Arabidopsis PDI gene. The properties of the proteins belonging to these genes were revealed by in silico approaches. It was found that the active site-WCXXC motif was not conserved in the GmPDI6c and GmPDI6d proteins, but this sequence was present in other proteins. As a result of protein modeling, the protein with the highest GMQE score among soy PDI proteins was taken into consideration and its interaction with the coat protein of Tobacco ringspot virus was revealed through docking. The in silico analysis results obtained from the study need to be verified by experimental approaches.

Keywords

• Soybean
• Protein disulfide isomerase (PDI)
• in silico
• protein-protein docking

Soyada Protein Disülfit İzomeraz’ların İn Silico Analizi

Abstract

Protein disülfit izomerazlar protein katlanma sürecinde disülfit bağlarının doğru bir şekilde oluşmasında görev alan thioredoxin domaini içeren moleküler şaperonlardır. Hayvanlarda PDI proteinlerinin katalitik ve şaperon rollerinin araştırıldığı birçok çalışma mevcuttur. Bitkilerde ise PDI proteinlerinin varyasyonu ve fonksiyonu ile ilgili çalışmalar sınırlıdır. Bu çalışmada Arabidopsis PDI geni referans alınarak soya genomunda 12 PDI geninin varlığı gösterilmiş ve bu genlere ait proteinlerin özellikleri in silico yaklaşımlar ile ortaya konmuştur. WCXXC aktif dizi motifinin GmPDI6c ve GmPDI6d proteinlerinde korunmadığı ve diğer proteinlerde bu dizinin mevcut olduğu tespit edilmiştir. Protein modellemesi sonucunda soya PDI proteinlerinden GMQE skoru en yüksek olanı ele alınarak Tobacco ringspot virus’e ait kılıf proteini arasındaki etkileşim docking ile ortaya konmuştur. Çalışma sonucunda elde edilen in silico analiz sonuçlarının deneysel yaklaşımlar ile doğrulanması gerekmektedir.

Keywords

• Soya
• Protein disülfit izomeraz (PDI)
• in silico
• protein-protein docking

References

1. Alanen, H. I., Salo, K. E., Pekkala, M., Siekkinen, H. M., Pirneskoski, A., and Ruddock, L. W. (2003). Defining the domain boundaries of the human protein disulfide isomerases. Antioxid. Redox Signal. 5, 367–374.
2. Appenzeller-Herzog, C., and Ellgaard, L. (2008). The human PDI family: versatility packed into a single fold. Biochim. Biophys. Acta 1783, 535–548.
3. Aslund F, J Beckwith 1999 Bridge over troubled waters: sensing stress by disulfide bond formation. Cell 96:751–753.
4. Byrne, L. J., Sidhu, A., Wallis, A. K., Ruddock, L. W., Freedman, R. B., Howard, M. J., et al. (2009). Mapping of the ligand-binding site on the b0 domain of human PDI: interaction with peptide ligands and the x-linker region. Biochem. J. 423, 209–217.
5. Cheng SY, QH Gong, C Parkison, EA Robinson, E Appella, GT Merlino, I Pastan 1987 The nucleotide sequence of a human cellular thyroid hormone binding protein present in endoplasmic reticulum. J Biol Chem 262:11221–11227.
6. Chivers P. T., Prehoda K. E., Raines R. T. (1997). The CXXC motif: a rheostat in the active site. Biochemistry 36, 4061–4066.
7. Couet J, S de Bernard, H Loosfelt, B Saunier, E Milgrom, M Misrahi 1996 Cell surface protein disulfide-isomerase is involved in the shedding of human thyrotropin receptor ectodomain. Biochemistry 35:14800–14805.
8. D’Aloisio E., Paolacci A. R., Dhanapal A. P., Tanzarella O. A., Porceddu E., Ciaffi M. (2010). The protein disulfide isomerase gene family in bread wheat (T. aestivum L.). BMC Plant Biol. 10:101.

9. DuPont F., Hurkman W., Vensel W., Chan R., Lopez R., Tanaka C. & Altenbach S. 2006. Differential accumulation of sulfurrich and sulfur-poor wheat flour proteins is affected by temperature and mineral nutrition during grain development. J. Cereal Sci. 44: 101–112.
10. Ellgaard L. & Ruddock L. 2005. The human protein disulphide isomerase family: substrate interactions and functional properties. EMBO Rep. 6: 28–32.
11. Ferrari, D.M., Soling, H.D., 1999. The protein disulphide-isomerase family: unravelling a string of folds. Biochem. J. 339 (Pt 1), 1–10.
12. Fornes MW, E Bustos-Obregon 1994 Study of nuclear decondensation of the rat spermatozoa by reducing agents during epididymal transit. Andrologia 26:87–92.
13. Frand AR, CA Kaiser 1998 The ERO1 gene of yeast is required for oxidation of protein dithiols in the endoplasmic reticulum. Mol Cell 1:161–170.
14. Freedman RB, TR Hirst, MF Tuite 1994 Protein disulphide isomerase: building bridges in protein folding. Trends Biochem Sci 19: 331–336.
15. Galligan J. J., Petersen D. R. (2012). The human protein disulfide isomerase gene family. Hum. Genomics 6, 1–15.
16. Gruber C. W., Cemazar M., Clark R. J., Horibe T., Renda R. F., Anderson M. A., et al. (2007). A novel plant protein-disulfide isomerase involved in the oxidative folding of cystine knot defense proteins. J. Biol. Chem. 282 20435–20446.
17. Herman E. & Schmidt M. 2004. Endoplasmic reticulum to vacuole trafficking of endoplasmic reticulum bodies provides an alternate pathway for protein transfer to the vacuole. Plant Physiol. 136: 3440–3446.
18. Holmgren A. 1985. Thioredoxin. Annu. Rev. Biochem. 54: 237–271.
19. Honscha W, M Ottallah, A Kistner, H Platte, E Petzinger 1993 A membrane-bound form of protein disulfide isomerase (PDI) and the hepatic uptake of organic anions. Biochim Biophys Acta 1153: 175–183.
20. Houston N. L., Fan C., Xiang J. Q., Schulze J. M., Jung R., Boston R. S. (2005). Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins. Plant Physiol. 137 762–778.
21. Houston N., Fan C., Xiang Q. & Schulze J. 2005. Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins. Plant Physiol. 137: 762–778.
22. Houston, N. L., Fan, C., Schulze, J. M., Jung, R., & Boston, R. S. (2005). Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins. Plant Physiology, 137(2), 762-778.
23. Irvine, A. G.,Wallis, A. K., Sanghera, N., Rowe,M. L., Ruddock, L.W., Howard, M. J., et al. (2014). Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway. PLoS ONE 9:e82511.
24. Jacquot J., Gelhaye E., Rouhier N., Corbier C., Didierjean C. & Aubry A. 2002. Thioredoxins and related proteins in photosynthetic organisms: molecular basis for thiol dependent regulation. Biochem. Pharmacol. 64: 1065–1069.
25. Jacquot J., Gelhaye E., Rouhier N., Corbier C., Didierjean C. & Aubry A. 2002. Thioredoxins and related proteins in photosynthetic organisms: molecular basis for thiol dependent regulation. Biochem. Pharmacol. 64: 1065–1069.
26. Kanai S, H Toh, T Hayano, M Kikuchi 1998 Molecular evolution of the domain structures of protein disulfide isomerases. J Mol Evol 47:200–210.
27. Kayum M. A., Park J. I., Nath U. K., Saha G., Biswas M. K., Kim H. T., et al. (2017). Genome-wide characterization and expression profiling of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 18:885.
28. Kayum M. A., Park J. I., Nath U. K., Saha G., Biswas M. K., Kim H. T., et al. (2017). Genome-wide characterization and expression profiling of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 18:885.
29. Kemmink J., Darby N., Dijkstra K., Nilges M. & Creighton T. 1997. The folding catalyst protein disulfide isomerase is constructed of active and inactive thioredoxin modules. Curr. Biol. 7: 239–245.
30. Kemmink, J., Darby, N. J., Dijkstra, K., Nilges,M., and Creighton, T. E. (1997). The folding catalyst protein disulfide isomerase is constructed of active and inactive thioredoxin modules. Curr. Biol. 7, 239–245.
31. Kimura S., Higashino Y., Kitao Y., Masuda T., Urade R. (2015). Expression and characterization of protein disulfide isomerase family proteins in bread wheat. BMC Plant Biol. 15:73.
32. Lahav J, N Gofer-Dadosh, J Luboshitz, O Hess, M Shaklai 2000 Protein disulfide isomerase mediates integrin-dependent adhesion. FEBS Lett 475:89–92.
33. Lu D. P., Christopher D. A. (2008). Endoplasmic reticulum stress activates the expression of a sub-group of protein disulfide isomerase genes and AtbZIP60 modulates the response in Arabidopsis thaliana. Mol. Genet. Genomics 280 199–210.
34. Markus M, R Benezra 1999 Two isoforms of protein disulfide isomerase alter the dimerization status of E2A proteins by a redox mechanism. J Biol Chem 274:1040–1049.
35. Motohashi K, A Kondoh, MT Stumpp, T Hisabori 2001 Comprehensive survey of proteins targeted by chloroplast thioredoxin. Proc Natl Acad Sci USA 98:11224–11229.
36. Ohtani H, H Wakui, T Ishino, A Komatsuda, AB Miura 1993 An isoform of protein disulfide isomerase is expressed in the developing acrosome of spermatids during rat spermiogenesis and is transported into the nucleus of mature spermatids and epididymal spermatozoa. Histochemistry 100:423–429.
37. Onda Y., Kobori Y. (2016). Differential activity of rice protein disulfide isomerase (PDI) family members for disulfide bond formation and reduction. FEBS Open Bio. 4 730–734.
38. Ondzighi C. A., Staehelin L. A. (2008). Arabidopsis protein disulfide isomerase-5 inhibits cysteine proteases during trafficking to vacuoles before programmed cell death of the endothelium in developing seeds W. Plant Cell 20 2205–2220.
39. Pelham HR (1990) The retention signal for soluble proteins of the endoplasmic reticulum. Trends Biochem Sci 15: 483–486
40. Peng R. H., Qiu J., Tian Y. S., Gao J. J., Han H. J., Fu X. Y., et al. (2017). Disulfide isomerase-like protein AtPDIL1–2 is a good candidate for trichlorophenol phytodetoxification. Sci. Rep. 7:40130.
41. Rigobello MP, A Donella-Deana, L Cesaro, A Bindoli 2001 Distribution of protein disulphide isomerase in rat liver mitochondria. Biochem J 356:567–570.
42. Serrato A., Guilleminot J., Meyer Y. & Vignols F. 2008. AtCXXS: atypical members of the Arabidopsis thaliana thioredoxin h family with a remarkably high disulfide isomerase activity. Physiol. Plant. 133: 611–622.
43. Shewry P.R. & Halford N.G. 2002. Cereal seed storage proteins: structures, properties and role in grain utilization. J. Exp. Bot. 53: 947–958.
44. Takemoto Y., Coughlan S. J., Okita T. W., Satoh H., Ogawa M., Kumamaru T. (2002). The rice mutant esp2 greatly accumulates the glutelin precursor and deletes the protein disulfide isomerase. Plant Physiol. 128 1212–1222.
45. Tosi P., Parker M., Gritsch C., Carzaniga R., Martin B. & Shewry S. 2009. Trafficking of storage proteins in developing grain of wheat. J. Exp. Bot. 60: 979–991.
46. Tu B, SC Ho-Schleyer, KJ Travers, JS Weissman 2000 Biochemical basis of oxidative protein folding in the endoplasmic reticulum. Science 290:1571–1574.
47. Turano C, S Coppari, F Altieri, A Ferraro 2002 Proteins of the PDI family: unpredicted non-ER locations and functions. J Cell Physiol 193:154–163.
48. Vitale A. & Ceriotti A. 2004. Protein quality control mechanisms and protein storage in the endoplasmic reticulum. A conflict of interests? Plant Physiol. 136: 3420–3426.
49. Wang H., Boavida L. C., Ron M., Mccormick S. (2008). Truncation of a protein disulfide isomerase, PDIL2-1, delays embryo sac maturation and disrupts pollen tube guidance in Arabidopsis thaliana. Plant Cell 20 3300–3311. 10.1105/tpc.108.062919
50. Wedemeyer WJ, E Welker, M Narayan, HA Scheraga 2000 Disulfide bonds and protein folding. Biochem 39:4207–4216.
51. Wilkinson B. & Gilbert H. 2004. Protein disulfide isomerase. Biochim. Biophys. Acta 1699: 35–44.
52. Wilson R, JF Lees, NJ Bulleid 1998 Protein disulfide isomerase acts as a molecular chaperone during the assembly of procollagen. J Biol Chem 273:9637–9643.
53. Woycechowsky K, Raines R. 2000. Native disulfide bond formation in proteins. Curr. Opin. Chem. Biol. 4: 533–539.
54. Yang, P., Lüpken, T., Habekuss, A., Hensel, G., Steuernagel, B., Kilian, B., ... & Ordon, F. (2014). PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proceedings of the National Academy of Sciences, 111(6), 2104-2109.
55. Zhu C., Luo N., He M., Chen G., Zhu J., Yin G., et al. (2014). Molecular characterization and expression profiling of the protein disulfide isomerase gene family in Brachypodium distachyon L. PLoS One 9:e94704.