Volume 11, Issue 29 (3-2019)                   jcb 2019, 11(29): 143-152 | Back to browse issues page

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Ghorbani H, Samizadeh Lahiji H, Nematzadeh G A. In Silico Characterization of Proteins Containing ARID-PHD Domain and Its Expression in Aeluropus littoralis Halophyte. jcb. 2019; 11 (29) :143-152
URL: http://jcb.sanru.ac.ir/article-1-786-en.html
Faculty of Agricultural Sciences, University of Guilan
Abstract:   (729 Views)
Abiotic stresses are the most important factors that reduce the yield of crops. In this case, Bioinformatics analysis plays an important role to study genes, and their relatedness as well as prediction their function in response to abiotic stresses. Among all domains, ARID-PHD domain has been identified in plants and animals and has a very significant role in growth regulation, cell cycle, and expression of specific genes in each tissue. In this study, we looked for the conserved sequences of the ARID family in various plant species from the NCBI database to evaluate its expression in Aeluropus littoralis. Based on the result, 10 plants that had protein containing the ARID-PHD domain were identified. Then, sequences alignment, designing phylogenetic tree, protein characterization and relative expression assessment of ARID gene in Aeluropus littoralis were done. The results showed that in addition to the similarity of amino acid sequences, proteins were divided into two groups of monocotyledons and di-cotyledons plants. Protein characteristics and structure investigation indicated a high degree of conserved sequences in proteins from different plant species. Regarding gene expression analysis, the maximum level of transcripts belongs to this gene expressed in plant aerial tissue after 6 hours of salinity stress and did not show a significant decrease until 24 hours, which probably suggested the probable role of this protein in plant tolerance to various stresses. Also, in the root, the gene expression was not significantly different from control treatment. This study was the first report to investigate protein characteristics and changing in ARID gene expression in halophyte plant (Aeluropus littoralis) under salt stress conditions and could be used as a useful reference to make plants tolerable specifically to salinity in using this gene family to modify plants to tolerate abiotic stresses especially salinity.
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Type of Study: Research | Subject: بيوتكنولوژي گياهي
Received: 2017/07/23 | Revised: 2019/05/14 | Accepted: 2017/09/10 | Published: 2019/05/8

References
1. Artimo, P., M. Jonnalagedda, K. Arnold, D. Baratin, G. Csardi, E. De Castro, S. Duvaud, V. Flegel, A. Fortier and E. Gasteiger. 2012. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 40: 597-603. [DOI:10.1093/nar/gks400]
2. Ding, Z., L. Gillespie and G. Pate. 2003. Human MI-ER1 alpha and beta function as transcriptional repressors by recruitment of histone deacetylase 1 to their conserved ELM2 domain. Molecular and Cellular Biology, 23: 250-258. [DOI:10.1128/MCB.23.1.250-258.2003]
3. Felsenstein, J. 1985. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39 (4): 783-791. [DOI:10.1111/j.1558-5646.1985.tb00420.x]
4. Fleischer, T.C., U,J. Yun and D.E. Ayer. 2003. Identification and characterization of three new components of the mSin3A corepressor complex. Molecular and Cellular Biology, 23: 3456-3467. [DOI:10.1128/MCB.23.10.3456-3467.2003]
5. Gasteiger, E., C. Hoogland, A. Gattiker and S. Duvaud. 2005. Protein identification and analysis tools on the ExPASyserver. In: Walker JM. The proteomics protocols handbook, Humana Press, New Jersey (USA), 571-607. [DOI:10.1385/1-59259-890-0:571]
6. Geourjon, C. and G. Deléage. 1995. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics, 11(6): 681-684. [DOI:10.1093/bioinformatics/11.6.681]
7. Ghasemi Omran, V., A. R. Bagheri, GH. Nematzadeh and A. Mirshamsi. 2012. Evaluation of the Expression Pattern of AlSOS1and AlNHX Genes Under NaCl Stress in Halophyte Grass Aeluropus littoralis Parl. Crop Biotechnology. 2(2): 27-37.
8. Gregory, S.L., R.D. Kortschak, B. Kalionis and R. Saint. 1996. Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA binding proteins, Molecular and Cellular Biology, 16: 792-799. [DOI:10.1128/MCB.16.3.792]
9. Hashemi, S.H., Gh. Nematzadeh, Gh. Ahmadian, A. Yamchi, and M. Kuhlmann. 2016. Identification and validation of Aeluropus littoralis reference genes for Quantitative Real-Time PCR Normalization. Journal of Biological Research-Thessaloniki, 23: 18-31. [DOI:10.1186/s40709-016-0053-8]
10. Herrscher R.F., M.H. Kaplan, D.L. Lelsz, C. Das, R. Scheuermann and P.W. Tucker 1995. The Immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family. genes and development, 9: 3067-3082. [DOI:10.1101/gad.9.24.3067]
11. Kim, S., Z. Zhang, S. Upchurch, N. Isern and Y. Chen. 2004. Structure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition. The Journal of Biological Chemistry. 279: 16670-16676. [DOI:10.1074/jbc.M312115200]
12. Kortschak, R.D., P.W. Tucker and R. Saint. 2000. ARID proteins come in from the desert. Trends Biochemical Science, 25: 294-299. [DOI:10.1016/S0968-0004(00)01597-8]
13. Liu, K., L. Wang, Y. Xu, N. Chen, Q. Ma, F. Li and K. Chong. 2007. Overexpression of OsCOIN, a putative cold inducible zinc finger protein, increased tolerance to chilling, salt and drought, and enhanced proline level in rice. Planta, 226:1007-1016. [DOI:10.1007/s00425-007-0548-5]
14. Livak, K.J. and T.D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. methods, 25:402-408. [DOI:10.1006/meth.2001.1262]
15. Marchler-Bauer, A., M.K. Derbyshire, N.R. Gonzales, S. Lu, F. Chitsaz, L.Y. Geer, R.C. Geer, J. He, M. Gwadz, D.I. Hurwitz, C.J. Lanczycki, F. Lu, G.H. Marchler, J.S. Song, N. Thanki, Z. Wang, R.A. Yamashita, D. Zhang, C. Zheng and S.H. Bryant. 2015. CDD: NCBI's conserved domain database. Nucleic Acids Research. 43: 222-226. [DOI:10.1093/nar/gku1221]
16. Modarresi, M., G.A. Nematzadeh and M. Zarein. 2013. Glyceraldehyde-3-phosphate Dehydrogenase Gene from Halophyte Aeluropus lagopoides: Identification and Characterization. Journal of Crop Improvment, 27: 281-290. [DOI:10.1080/15427528.2013.766294]
17. Pandey, A., P. Misra, A. Alok, N. Kaur, S. Sharma, D. Lakhwani, M.H. Asif, S. Tiwari and P.K. Trivedi. 2016. Genome-Wide Identification and Expression Analysis of Homeodomain Leucine Zipper Subfamily IV (HDZ IV) Gene Family from Musa accuminata. Frontiers in Plant Science, 7: 20. [DOI:10.3389/fpls.2016.00020]
18. Pasini, D., P.A. Cloos, J. Walfridsson, L. Olsson, J.P. Bukowski, J.V. Johansen, M. Bak , N. Tommerup, J. Rappsilber and K. Helin. 2010. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature. 464: 306-310. [DOI:10.1038/nature08788]
19. Peng, J.C., A. Valouev, T. Swigut, J. Zhang, Y. Zhao, A. Sidow and J. Wysocka. 2009. JARID2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell, 139: 1290-1302. [DOI:10.1016/j.cell.2009.12.002]
20. Ramon-Maiques, S., A.J. Kuo, D. Carney, A.G. Matthews, M.A. Oettinger, O. Gozani and W. Yang. 2007. The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proceedings of the National Academy of Sciences of the United States, 104: 18993-18998. [DOI:10.1073/pnas.0709170104]
21. Riechmann, J.L., J. Heard, G. Martin, L. Reuber, C.Z. Jiang, J. Keddie, L. Adam, 0. Pineda, 0.J. Ratcliffe, R.R. Samaha, R. Creelman, M. Pilgrim, P. Broun, J.Z. Zhang, D. Ghandehari, B. K. Sherman and G.L. Yu. 2000. Arabidopsis transcription factors: genome wide comparative analysis among eukaryotes. Science, 290: 2105-2110. [DOI:10.1126/science.290.5499.2105]
22. Roy, A., A. Dutta, D. Roy, G. Paye, R. Ghosh, R.K. Kar, A. Bhunia, J. Mukhopadhyay, and S. Chaudhuri. 2016. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. Plant Molecular Biology. 92:371-388. [DOI:10.1007/s11103-016-0519-y]
23. Saitou, N. and M. Nei. 1978. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4): 406-425.
24. Scharf, K.D., M. Siddique and E. Vierling. 2001. The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing alpha-crystallin domains (Acd proteins). Cell Stress Chaperones, 6: 225-237. https://doi.org/10.1379/1466-1268(2001)006<0225:TEFOAT>2.0.CO;2 [DOI:10.1379/1466-1268(2001)0062.0.CO;2]
25. Sharafi, E., A. Dehestani, J. Farmani and A. Pakdin Parizi. 2017. Bioinformatics evaluation of plant chlorophyllase, the key enzyme in chlorophyll degradation. Applied Food Biotechnology, 4(3): 167-178.
26. Sinha, S., V.K. Raxwal, B. Joshi, A. Jagannath, S. Katiyar-Agarwal, S. Goel, A. Kumar and M. Agarwal. 2015. De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.). Frontiers in Plant Science, 6: 932-949. [DOI:10.3389/fpls.2015.00932]
27. Stros, M., D. Launholt and K.D. Grasser. 2007. The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins. Cellular and Molecular Life Sciences, 64:2590-2606. [DOI:10.1007/s00018-007-7162-3]
28. Takahashi, M., M. Kojima, K. Nakajima, R. Suzuki-Migishima and T. Takeuchi. 2007. Functions of a jumonji-cyclin D1 pathway in the coordination of cell cycle exit and migration during neurogenesis in the mouse hindbrain. Developmental Biology, 303: 549- 560. [DOI:10.1016/j.ydbio.2006.11.031]
29. Tamura, K., J. Dudley, M. Nei and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24: 1596-1599. [DOI:10.1093/molbev/msm092]
30. Tavallaie, A. 2016. Review of Data mining in Genetics
31. (Clustering of Iranian kinfolks by DNA identification). 2nd International and 14th Iranian Genetics Congress, 1-5 pp., Tehran, Iran.
32. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680. [DOI:10.1093/nar/22.22.4673]
33. Tu, X., J. Wu, Y. Xu and Y. Shi. 2001. 1H, 13C and 15N resonance assignments and secondary structure of ADR6 DNA-binding domain. Journal of Biomolecular NMR, 21: 187- 188.
34. Wilsker, D., A. Patsialou, P.B. Dallas and E. Moran. 2002. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth and Differentiation, 146: 95-106.
35. Wilsker, D., L. Probst, H.M. Wain, L. Maltais, P.W. Tucker and E. Moran, 2005. Nomenclature of the ARID family of DNA-binding proteins. Genomics, 86: 242-251. [DOI:10.1016/j.ygeno.2005.03.013]
36. Wu, R.C., M. Jiang, A.L. Beaudet and M.Y. Wu. 2013. ARID4A and ARID4B regulate male fertility, a functional link to the AR and RB pathways. Proceedings of the National Academy of Sciences of the United States, 110: 4616-4621. [DOI:10.1073/pnas.1218318110]
37. Xia, C., Y.J. Wang, Y. Liang, Q.K. Niu, X.Y. Tan, L.C. Chu, L.Q. Chen, X.Q. Zhang and D. Ye. 2014. The ARID-HMG DNA-binding protein AtHMGB15 is required for pollen tube growth in Arabidopsis thaliana. The Plant Journal. 79: 741-756. [DOI:10.1111/tpj.12582]
38. Xu, Y. W. Zong, X. Hou, J. Yao, H. Liu, X. Li, Y. Zhao and L. Xiong. 2015. OsARID3, an AT-rich Interaction Domain-containing protein, is required for shoot meristem development in rice. The Plant Journal, 83: 806-817. [DOI:10.1111/tpj.12927]
39. Yamaguchi-Shinozaki, K. and K. Shinozaki. 2006. Cross-talk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Current Opinion in Plant Biology, 9: 436-442. [DOI:10.1016/j.pbi.2006.05.014]
40. Yu, C.S., Y.C. Chen, C.H. Lu and J.K. Hwang. 2006. Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3): 643-651. [DOI:10.1002/prot.21018]
41. Zhang, H., X. Mao, C. Wang and R. Jing. 2010. Overexpression of a common wheat gene TaSnRK2.8 enhances tolerance to drought, salt and low temperature in Arabidopsis. PLoS One, 5(12): e16041. [DOI:10.1371/journal.pone.0016041]
42. Zhang, Y., M. Gao, S.D. Singer, Z. Fei, H. Wang and X. Wang. 2012. Genome- Wide Identification and Analysis of the TIFY Gene Family in Grape. PLoS One, 7(9): e44465. [DOI:10.1371/journal.pone.0044465]
43. Zheng, B., H. He, Y. Zheng, W. Wu and S. McCormick. 2014. An ARID Domain-Containing Protein within Nuclear Bodies Is Required for Sperm Cell Formation in Arabidopsis thaliana. PLOS Genetics, 10(7): e1004421. [DOI:10.1371/journal.pgen.1004421]
44. Zhu, H., T. Chen, M. Zhu, Q. Fang, H. Kang, Z. Hong and Z. Zhang. 2008. A novel ARID DNA binding protein interacts with SymRK and is expressed during early nodule development in Lotus japonicus. Plant Physiology, 148: 337-347. [DOI:10.1104/pp.108.119164]

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