Page Header

Home > Vol 15, No 3 (Jul.–Sep. 2022) > Laoong-u-thai

DNA Binding Activity of Marine Shrimp LvProfilin

Yanisa Laoong-u-thai, Warapond Wanna, Autaipohn Kaikaew

Abstract


Shrimp farming is an important business in Thailand and worldwide. The study of molecular biology and biochemical pathway of the key molecules controlling muscle growth is an essential to improve shrimp livestock. Profilin is a pivotal protein in muscle formation, especially actin protein. Its nuclear function has been reported in many species for gene regulation. Here in this work, we characterized the function of LvProfilin, a marine shrimp profilin from Litopenaeus vannamei, both in silico and in vitro. The phylogenetic tree of LvProfilin among organisms and its 3D protein structure showed that LvProfilin was highly conserved among shrimp and arthropods. The homology modeling of its 3D structure revealed 3 alpha-helices and 6 beta-strands similar to most eukaryotic profilins. To interpret its possible function, the gene expression of LvProfilin in various tissues was performed. We found that this gene was expressed in various tissues. This result may imply that LvProfilin could share a common function in all tissues. Nuclear activity has been a promising function of LvProfilin. We performed a DNA/RNA binding prediction analysis using DRNApred. The result indicated that Lysine-90 and Threonine-91 were the putative DNA-binding sites with the probability of 63.12% and 54.16%, respectively. Its binding activity was confirmed in vitro which bound stronger to single strand DNA than double strand DNA. To our best knowledge, this is the first report of DNA binding activity of profilin in invertebrates.

Keywords



[1] L. Carlsson, L. E. Nyström, I. Sundkvist, F. Markey, and U. Lindberg, “Actin polymerizability is influenced by profilin, a low molecular weight protein in non-muscle cells,” Journal of Molecular Biology, vol. 115, no. 3, pp. 465–483, Sep. 1977.
[2] L. Cooley, E. Verheyen, and K. Ayers, “Chickadee encodes a profilin required for intercellular cytoplasm transport during Drosophila oogenesis,” Developmental Biology, vol. 69, no. 1. pp. 173–184, 1992.

[3] A. D. Toit, “Profilin(g) Asgard archaea,” Nature Reviews Microbiology, vol. 16, no. 12, p. 717, Dec. 2018.

[4] C. Akıl and R. C. Robinson, “Genomes of Asgard archaea encode profilins that regulate actin,” Nature, vol. 562, no. 7727, pp. 439–443, Oct. 2018.

[5] C. Butler-Cole, M. J. Wagner, M. Da Silva, G. D. Brown, R. D. Burke, and C. Upton, “An ectromelia virus profilin homolog interacts with cellular tropomyosin and viral A-type inclusion protein,” Virology Journal, vol. 4, 2007, doi: 10.1186/1743- 422X-4-76.

[6] W. Witke, “The role of profilin complexes in cell motility and other cellular processes,” Trends in Cell Biology, vol. 14, no. 8. pp. 461–469, 2004.

[7] J. F. Osorio-Méndez, A. Vizcaíno-Castillo, R. Manning-Cela, R. Hernández, and A. M. Cevallos, “Expression of profilin in Trypanosoma cruzi and identification of some of its ligands,” Biochemical and Biophysical Research Communications, vol. 480, no. 4, pp. 709–714, 2016.

[8] T. Sun, S. Li, and H. Ren, “Profilin as a regulator of the membrane-actin cytoskeleton interface in plant cells,” Frontiers in Plant Science, vol. 4, Dec. 2013, Art. no. 512.

[9] M. Reinhard, K. Giehl, K. Abel, C. Haffner, T. Jarchau, V. Hoppe, B. M. Jockusch, and U. Walter, “The proline-rich focal adhesion and microfilament protein VASP is a ligand for profilins,” EMBO Journal, vol. 14, no. 8, pp. 1583–1589, 1995.

[10] M. J. Deeks, J. R. Calcutt, E. K. S. Ingle, T. J. Hawkins, S. Chapman, A. C. Richardson, D. A. Mentlak, M. R. Dixon, F. Cartwright, A. P. Smertenko, K. Oparka, and P. J. Hussey, “A superfamily of actin-binding proteins at the actin-membrane nexus of higher plants,” Current Biology, vol. 22, no. 17, pp. 1595–1600, 2012.

[11] Z. Ding, M. Joy, R. Bhargava, M. Gunsaulus, N. Lakshman, M. Miron-Mendoza, M. Petroll, J. Condeelis, A. Wells, and P. Roy, “Profilin-1 downregulation has contrasting effects on early vs late steps of breast cancer metastasis,” Oncogene, vol. 33, no. 16, pp. 2065–2074, 2014.

[12] L. Zou, M. Jaramillo, D. Whaley, A. Wells, V. Panchapakesa, T. Das, and P. Roy, “Profilin-1 is a negative regulator of mammary carcinoma aggressiveness,” British Journal of Cancer, vol. 97, no. 10, pp. 1361–1371, 2007.

[13] T. Takáč, T. Pechan, H. Richter, J. Müller, C. Eck, N. Böhm, B. Obert, H. Ren, K. Niehaus, and J. Samaj, “Proteomics on brefeldin a-treated Arabidopsis roots reveals profilin 2 as a new protein involvedin the cross-talk between vesicular trafficking and the actin cytoskeleton,” Journal of Proteome Research, vol. 10, no. 2, pp. 488–501, 2011.

[14] B. M. Jockusch, K. Murk, and M. Rothkegel, “The profile of profilins,” Reviews of Physiology, Biochemistry and Pharmacology, vol. 159, pp. 131– 149, 2007.

[15] N. M. Mahoney, D. A. Rozwarski, E. Fedorov, A. A. Fedorov, and S. C. Almo, “Profilin binds proline-rich ligands in two distinct amide backbone orientations,” Nature Structural Biology, vol. 6, no. 7, pp. 666–671, 1999.

[16] P. Skare, J. P. Kreivi, Å. Bergström, and R. Karlsson, “Profilin I colocalizes with speckles and Cajal bodies: A possible role in pre-mRNA splicing,” Experimental Cell Research, vol. 286, no. 1, pp. 12–21, 2003.

[17] R. H. Sohn, J. Chen, K. S. Koblan, P. F. Bray, and P. J. Goldschmidt-Clermont, “Localization of a binding site for phosphatidylinositol 4,5- bisphosphate on human profilin,” Journal of Biological Chemistry, vol. 270, no. 36, pp. 21114– 21120, 1995.

[18] A. H. Valster, L. Vidali, and P. K. Hepler, “Nuclear localization of profilin during the cell cycle in Tradescantia virginiana stamen hair cells,” Protoplasma, vol. 222, no. 1–2, pp. 85–95, 2003.

[19] M. Lederer, “Profilin regulates the activity of p42POP, A novel Myb-related transcription factor,” Journal of Cell Science, vol. 118, no. 2, pp. 331– 341, Jan. 2005.

[20] I. A. Olave, S. L. Reck-Peterson, and G. R. Crabtree, “Nuclear actin and actin-related proteins in chromatin remodeling,” Annual Review of Biochemistry, vol. 71. pp. 755–781, 2002.

[21] V. Hurst, K. Shimada, and S. M. Gasser, “Nuclear actin and actin-binding proteins in DNA repair,” Trends in Cell Biology, vol. 29, no. 6. pp. 462–476, 2019.

[22] Y. Ofran, V. Mysore, and B. Rost, “Prediction of DNA-binding residues from sequence,” Bioinformatics, vol. 23, no. 13, pp. 347–353, 2007.
[23] Y. Laoong-u-thai, A. Nakpradit, and A. Deenumchut, “Molecular cloning and bioinformatics analysis of shrimp lvprofilin implicated in muscle formation and muscle specific gene regulation,” ASEAN Engineering Journal, vol. 1, no. 1, pp. 28– 37, 2012.

[24] L. Bordoli, F. Kiefer, K. Arnold, P. Benkert, J. Battey, and T. Schwede, “Protein structure homology modeling using SWISS-MODEL workspace,” Nature Protocols, vol. 4, no. 1, pp. 1–13, 2009.
[25] J. Silvester, H. U. A. Lindang, L. P. Chin, L. T. Ying, and C. Budiman, “Structure and molecular dynamic regulation of FKBP35 from Plasmodium knowlesi by structural homology modeling and electron microscopy,” Journal of Biological Sciences, vol. 17, no. 8, pp. 369–380, 2017.

[26] A. Waterhouse, M. Bertoni, S. Bienert, G. Studer, G. Tauriello, R. Gumienny, F. T. Heer, T. A. P. de Beer, C. Rempfer, L. Bordoli, R. Lepore, and T. Schwede, “SWISS-MODEL: Homology modelling of protein structures and complexes,” Nucleic Acids Research, vol. 46, no. W1, pp. W296–W303, 2018.
[27] P. Benkert, M. Künzli, and T. Schwede, “QMEAN server for protein model quality estimation,” Nucleic Acids Research, vol. 37, pp. W510–W514, 2009.

[28] J. Yan and L. Kurgan, “DRNApred, fast sequence-based method that accurately predicts and discriminates DNA-and RNA-binding residues,” Nucleic Acids Research, vol. 45, no. 10, p. e84, 2017.

[29] Y. Laoong-u-thai, B. Zhao, A. Phongdara, and J. Yang, “Correction: Molecular characterizations of a novel putative DNA-binding protein LvDBP23 in marine shrimp L. vannamei tissues and molting stages,” PLoS One, vol. 6, no. 7, 2011, doi: 10.1371/ journal.pone.0019959.

[30] T. Kamitani, H. P. Nguyen, and E. T. H. Yeh, “Preferential modification of nuclear proteins by a novel ubiquitin-like molecule,” Journal of Biological Chemistry, vol. 272, no. 22, pp. 14001– 14004, 1997.

[31] P. J. Goldschmidt-Clermont, M. I. Furman, D. Wachsstock, D. Safer, V. T. Nachmias, and T. D. Pollard, “The control of actin nucleotide exchange by thymosinβ4 and profilin. A potential regulatory mechanism for actin polymerization in cells,” Molecular Biology of the Cell, vol. 3, no. 9, pp. 1015–1024, 1992.

[32] A. D. Nardo, R. Gareus, D. Kwiatkowski, and W. Witke, “Alternative splicing of the mouse profilin II gene generates functionally different profilin isoforms,” Journal of Cell Science, vol. 113, no. 21, pp. 3795–3803, 2000.

[33] A. Fateen, S. A. Ali, D. N. Baig, and Z. Basharat, “Profilin (pfn) isoforms transcriptional and bioinformatic exploration and Mus musculus brain tissues development,” Gene Reports, vol. 10, pp. 177–183, 2018.

[34] R. Rao, S. Bhassu, R. Z. Y. Bing, T. Alinejad, S. S. Hassan, and J. Wang, “A transcriptome study on Macrobrachium rosenbergii hepatopancreas experimentally challenged with white spot syndrome virus (WSSV),” Journal of Invertebrate Pathology, vol. 136, pp. 10–22, 2016.

[35] Y. Shui, Z-H. Xu, H-S. Shen, and X. Zhou, “Molecular cloning and expression analysis of profilin in red swamp crayfish Procambarus clarkii.,” Journal of Chemical and Pharmaceutical Research, vol. 6, no. 7, pp. 425–431, 2014.

[36] S. Müller, C. Hoege, G. Pyrowolakis, and S. Jentsch, “Sumo, ubiquitin’s mysterious cousin,” Nature Reviews Molecular Cell Biology, vol. 2, no. 3. pp. 202–210, Mar. 2001.

[37] J. S. Seeler and A. Dejean, “Nuclear and unclear functions of sumo,” Nature Reviews Molecular Cell Biology, vol. 4, no. 9. pp. 690–699, 2003.

[38] D. Wen, J. Wu, L. Wang, and Z. Fu, “SUMOylation promotes nuclear import and stabilization of Polo-like Kinase 1 to support its mitotic function,” Cell Reports, vol. 21, no. 8, pp. 2147–2159, 2017.

[39] F. Buss and B.M. Jockusch,, “Tissue-specific expression of profilin,” FEBS Letters, vol. 249, no. 1, pp. 31–34, 1989.

[40] S. C. Mockrin and E. D. Korn, “Acanthamoeba profilin interacts with G-Actin to Increase the rate of exchange of actin-bound adenosine 5’-Triphosphate,” Biochemistry, vol. 19, no. 23, pp. 5359–5362, 1980.

[41] L. G. Tilney, E. M. Bonder, L. M. Coluccio, and M. S. Mooseker, “Actin from Thyone sperm assembles on only one end of an actin filament: A behavior regulated by profilin,” The Journal of Cell Biology, vol. 97, no. 1, pp. 112–124, 1983.

[42] M. Pring, A. Weber, and M. R. Bubb, “Profilinactin complexes directly elongate actin filaments at the barbed end,” Biochemistry, vol. 31, no. 6, pp. 1827–1836, 1992.

[43] D. Pantaloni and M. F. Carlier, “How profilin promotes actin filament assembly in the presence of thymosin β4,” Cell, vol. 75, no. 5, pp. 1007– 1014, 1993.

[44] E. S. Chang, M. J. Bruce, and S. L. Tamone, “Regulation of crustacean molting: A multihormonal system,” Integrative and Comparative Biology, vol. 33, no. 3, pp. 324–329, 1993.

[45] E. S. Chang and D. L. Mykles, “Regulation of crustacean molting: A review and our perspectives,” General and Comparative Endocrinology, vol. 172, no. 3. pp. 323–330, 2011.

[46] Y. Laoong-u-thai, B. Zhao, A. Phongdara, H. Ako, and J. Yang, “Identifications of SUMO-1 cDNA and its expression patterns in pacific white shrimp Litopeanaeus vannamei,” International Journal of Biological Sciences, vol. 5 , no. 2, pp. 205–214, 2009.

[47] K.-K. K. H. J. Kong, G-E. Hong, H. K. Cho, B-H. Nam, Y-O. Kim, W-J. Kim, and S-J. Lee , “Cloning of profilin (FcPFN) from the shrimp Fenneropenaeus chinensis, a highly expressed protein in white spot syndrome virus (WSSV)- infected shrimp,” Journal of Applied Genetics, vol. 50, no. 3, pp. 245–250, 2009.

[48] A. Clavero-Salas, R. R. Sotelo-Mundo, T. Gollas-Galván, J. Hernández-López, A. B. Peregrino-Uriarte, A. Muhlia-Almazán, and G. Yepiz-Plascencia, “Transcriptome analysis of gills from the white shrimp Litopenaeus vannamei infected with white spot syndrome virus,” Fish and Shellfish Immunology, vol. 23, no. 2, pp. 459–472, 2007.

[49] Y. H. Zhu, J. Hu, X. N. Song, and D. J. Yu, “DNAPred: Accurate identification of DNAbinding sites from protein sequence by ensembled hyperplane-distance-based support vector machines,” Journal of Chemical Information and Modeling, vol. 59, no. 6, pp. 3057–3071, 2019.

[50] N. M. Luscombe, S. E. Austin, H. M. Berman, and J. M. Thornton, “An overview of the structures of protein-DNA complexes,” Genome Biology, vol. 1, no. 1, 2000, doi: 10.1186/gb-2000-1-1- reviews001.

[51] S. Zhang, H. Yang, L. Li, Y. Tian, and H. Tan, “Novel ssDNA-binding properties of SSB2 and SSB3 from Thermoanaerobacter tengcongensis,” Wei Sheng Wu Xue Bao = Acta Microbiologica Sinica, vol. 49, no. 4, pp. 453–459, 2009.

[52] S. Sugiman-Marangos and M. S. Junop, “The structure of DdrB from Deinococcus: A new fold for single-stranded DNA binding proteins,” Nucleic Acids Research, vol. 38, no. 10, pp. 3432– 3440, 2010.

[53] K. J. Kwak, J. Y. Kim, Y. O. Kim, and H. Kang, “Characterization of transgenic arabidopsis plants overexpressing high mobility group B proteins under high salinity, drought or cold stress,” Plant and Cell Physiology, vol. 48, no. 2, pp. 221–231, 2007.
[54] M. A. Heine, M. L. Rankin, and P. J. DiMario, “The Gly/Arg-rich (GAR) domain of Xenopus nucleolin facilitates in vitro nucleic acid binding and in vivo nucleolar localization,” Molecular Biology of the Cell, vol. 4, no. 11, pp. 1189–1204, 1993.

[55] R. G. Garces, W. Gillon, and E. F. Pai, “Atomic model of human Rcd-1 reveals an armadillo -likerepeat protein with in vitro nucleic acid binding properties,” Protein Science, vol. 16, no. 2, pp. 176– 188, Feb. 2007.

[56] C. O. Pabo, E. Peisach, and R. A. Grant, “Design and selection of novel Cys2His2 zinc finger proteins,” Annual Review of Biochemistry, vol. 70, no. 1. pp. 313–340, Jun. 2001.

[57] P. A. Reynolds, G. A. Smolen, R. E. Palmer, D. Sgroi, V. Yajnik, W. L. Gerald, and D. A. Haber, “Identification of a DNA- binding site and transcriptional target for the EWS-WT1(+KTS) oncoprotein,” Genes and Development, vol. 17, no. 17, pp. 2094–2107, Sep. 2003.

[58] D. L. Theobald, R. M. Mitton-Fry, and D. S. Wuttke, “Nucleic acid recognition by OB-fold proteins,” Annual Review of Biophysics and Biomolecular Structure, vol. 32. pp. 115–133, 2003.

[59] D. J. Richard, E. Bolderson, and K. K. Khanna, “Multiple human single-stranded DNA binding proteins function in genome maintenance: Structural, biochemical and functional analysis human single-stranded DNA binding proteins,” Critical Reviews in Biochemistry and Molecular Biology, vol. 44, no. 2–3, pp. 98–116, 2009.

[60] R. D. Shereda, A. G. Kozlov, T. M. Lohman, M. M. Cox, and J. L. Keck, “SSB as an organizer/ mobilizer of genome maintenance complexes,” Critical Reviews in Biochemistry and Molecular Biology, vol. 43, no. 5, pp. 289–318, 2008.

[61] H. Rasyid and R. Armunanto, “Molecular docking analysis on epidermal growth factor receptor wild type (EGFR wt) with quinazoline derivative compounds as tyrosine kinase inhibitors,” KMUTNB International Journal of Applied Science and Technology, vol. 10, no. 4, pp. 293– 299, Dec. 2017, doi: 10.14416/j.ijast.2017.12.001.

[62] D. J. Richard, E. Bolderson, L. Cubeddu, R. I. M. Wadsworth, K. Savage, G. G. Sharma, M. L. Nicolette, S. Tsvetanov, M. J. McIlwraith, R. K. Pandita, S. Takeda, R. T. Hay, J. Gautier, S. C. West, T. T. Paull, T. K. Pandita, M. F. White, and K. K. Khanna, “Single-stranded DNA-binding protein hSSB1 is critical for genomic stability,” Nature, vol. 453, no. 7195, pp. 677–681, 2008.

[63] P. Gu, W. Deng, M. Lei, and S. Chang, “Single strand DNA binding proteins 1 and 2 protect newly replicated telomeres,” Cell Research, vol. 23, no. 5, pp. 705–719, 2013.

Full Text: PDF

DOI: 10.14416/j.asep.2021.10.002

Refbacks

  • There are currently no refbacks.


Copyright © 2022 by King Mongkut’s University of Technology North Bangkok. All rights reserved.