Genome Wide Analysis of PHD Finger Family in Soybean (Glycine max)

Abstract:

The PHD finger is a highly conserved structural domain in roles with regulating transcription and modification of chromatin structure. Forty-five PHD finger genes encoding PHD finger protein were identified from soybean (Glycine max) database. And sixty - four unique typical PHD finger domains were retrieved. NJ phylogenetic tree of all 64 PHD finger domains consisted of ten main clades (A-J). Subcellular localization analysis shows that Glyma06g33590.1, Glyma10g05080.1 and Glyma11g11720.1 may localize in Golgi body, chloroplast thylakoid membrane and mitochondrial inner membrane, respectively. The function of domain is loyal to the cause of protein situated in particular site of cell. Eight unique domains have been found concomitant with PHD domain in a certain protein. The cooperative relationship between diverse domains may important for particular biological event.

• Periodical: Advanced Materials Research (Volumes 864-867)
• Pages: 2503-2508
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.864-867.2503
• Online since: December 2013
• Authors: Qi Wu, Chuan Tang Wang*
• Keywords: Glycine max, PHD Finger, Soybean

References

[1] R. Aasland, T.J. Gibson, A.F. Stewart, The PHD finger: implications for chromatinmediated transcriptional regulation, Trends Biochemical Sciences. 20 (1995) 56-59.

DOI: 10.1016/s0968-0004(00)88957-4

[2] G. Farkas, J. Gausz, M. Galloni, G. Reuter, H. Gyurkovics, F. Karch, The Trithorax-like gene encodes the Drosophila GAGA factor, Nature. 371 (1994) 806-808.

DOI: 10.1038/371806a0

[3] A. Lonie, R. D'Andrea, R. Paro, R. Saint, Molecular characterisation of the Polycomblike gene of Drosophila melanogaster, a trans-acting negative regulator of homeotic gene expression, Development. 120 (1994) 2629-2636.

DOI: 10.1242/dev.120.9.2629

[4] R.J. Gibbons, S. Bachoo, D.J. Picketts, S. Aftimos, B. Asenbauer, J. Bergoffen, S.A. Berry, N. Dahl, A. Fryer, K. Keppler, K. Kurosawa, M.L. Levin, M. Masuno, G. Neri, M.E. Pierpont, S.F. Slaney, D.R. Hiqqs, Mutations in transcriptional regulator ATRX establish the functional significance of a PHD-like domain, Nature Genetic, 17 (1997).

DOI: 10.1038/ng1097-146

[5] S. Jacobson, L. Pillus, Modifying chromatin and concepts of cancer, Current Opinion in Genetics and Development. 9 (1999) 175-184.

DOI: 10.1016/s0959-437x(99)80027-6

[6] U. Aapola, K. Shibuya, H.S. Scott, J. Ollila, M. Vihinen, M. Heino, A. Shintani, K. Kawasaki, S. Minoshima, K. Krohn, S.E. Antonarakis, N. Shimizu, J. Kuddoh, P. Peterson, Isolation and initial characterizaion of a novel zinc finger gene, DNMTL3L, on 21q22. 3, related to the cytosine-5-methyltransferase 3 gene family, Genomics. 65 (2000).

DOI: 10.1006/geno.2000.6168

[7] L.C. Wu, Z.W. Wang, J.T. Tsan, M.A. Apillman, A. Phung, X.L. Xu, M.W. Yang, L.Y. Hwang, A.M. Bowcock, R. Baer, Identification of a RING protein that can interact in vivo with the BRCA1 gene product, Nature Genetic. 14 (1996) 430-440.

DOI: 10.1038/ng1296-430

[8] T.A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symposium Series. 41 (1999) 95-98.

[9] J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, D.G. Higgins, The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research. 25 (1997) 4876-4882.

DOI: 10.1093/nar/25.24.4876

[10] T.L. Bailey, M. Gribskov, Combining evidence using p-values: application to sequence homology searches, Bioinformatics. 14 (1998) 48-54.

DOI: 10.1093/bioinformatics/14.1.48

[11] U. Schindler, H. Beckmann, A.R. Cashmore, HAT3. 1, a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region, Plant Journal. 4 (1993) 137-150.

DOI: 10.1046/j.1365-313x.1993.04010137.x

[12] M.R. Kaadige, D.E. Ayer, The polybasic region that follows the plant homeodomain zinc finger1 of Pf1 is necessary and sufficient for specific phosphoinositide binding, Biological Chemistry. 281 (2006) 28831-28836.

DOI: 10.1074/jbc.m605624200

[13] M. Bienz, The PHD f inger, a nuclear protein-interaction domain, Trends Biochemical Sciences. 31 (2006) 35-40.

DOI: 10.1016/j.tibs.2005.11.001

[14] J. Schmutz, S.B. Cannon, J. Schlueter, J.X. Ma, et al., Genome sequence of the palaeopolyploid soybean, Nature. 463 (2010) 178-183.

[15] G.S. Yochum, D.E. Ayer, Pf1, a novel PHD zinc finger protein that links the TLE corepressor to the mSin3A-histone deacetylase complex, Molecular and Cellular Biology. 21 (2001) 4110-4118.

DOI: 10.1128/mcb.21.13.4110-4118.2001

[16] D.C. Schultz, J.R. Friedman, F.J. Rauscher, Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2alpha subunit of NuRD, Genes and Developmen. 15 (2001).

DOI: 10.1101/gad.869501

[17] M. Anderson, K. Fair, S. Amero, S. Nelson, P.J. Harte, M.O. Diaz, A new family of cyclophilins with an RNA recognition motif that interact with members of the trx/MLL protein family in Drosophila and human cells, Development Genes and Evolution. 212 (2002).

DOI: 10.1007/s00427-002-0213-8