In Silico Analysis of Phalaenopsis Orchid Homeobox1 (POH1) Functional Gene for Shoot Development in Phalaenopsis Orchid

https://doi.org/10.22146/jtbb.83934

Nuzlan Rasjid(1), Febri Yuda Kurniawan(2), Saifa Usni Putri(3), Aviesta Linggabuwana(4), Ireneus Seno Prasojo(5), Endang Semiarti(6*)

(1) Department of Tropical Biology. Faculty of Biology, Universitas Gadjah Mada. Sleman, D.I. Yogyakarta 55281, Republic of Indonesia.
(2) Study Program of Biotechnology, Graduate School, Universitas Gadjah Mada. Sleman, D.I. Yogyakarta 55281, Republic of Indonesia.
(3) Department of Tropical Biology. Faculty of Biology, Universitas Gadjah Mada. Sleman, D.I. Yogyakarta 55281, Republic of Indonesia.
(4) Department of Tropical Biology. Faculty of Biology, Universitas Gadjah Mada. Sleman, D.I. Yogyakarta 55281, Republic of Indonesia.
(5) Department of Tropical Biology. Faculty of Biology, Universitas Gadjah Mada. Sleman, D.I. Yogyakarta 55281, Republic of Indonesia.
(6) Department of Tropical Biology. Faculty of Biology, Universitas Gadjah Mada. Sleman, D.I. Yogyakarta 55281, Republic of Indonesia.
(*) Corresponding Author

Abstract


The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved.  Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11.

 


Keywords


POH1; Conserved Domain; Transcription Factor; Protein Modelling; Phalaenopsis

Full Text:

PDF


References

Arnold, K. et al., 2006. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22(2), pp.195–201. doi: 10.1093/bioinformatics/bti770.

Arro, J. et al., 2019. RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines. BMC Plant Biology, 19(1), p.80. doi: 10.1186/s12870-019-1675-4.

Bailey, T.L. et al., 2015. The MEME suite. Nucleic acids research, 43(W1), pp.W39–W49. doi: 10.1093/nar/gkv416.

Benkert, P., Künzli, M. & Schwede, T., 2009. QMEAN server for protein model quality estimation. Nucleic acids research, 37 (suppl_2), pp.W510–W514. doi: 10.1093/nar/gkp322.

Chandra De, L. et al., 2014. Commercial orchids, De Gruyter Open.

Colovos, C. & Yeates, T.O., 1993. Verification of protein structures: patterns of nonbonded atomic interactions. Protein science, 2(9), pp.1511–1519. doi: 10.1002/pro.5560020916.

Corpet, F., 1988. Multiple sequence alignment with hierarchical clustering. Nucleic acids research, 16(22), pp.10881–10890. doi: 10.1093/nar/16.22.10881.

Dong, T. et al., 2019. RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.). BMC plant biology, 19(1), pp.1–16.

Ezura, K., Nakamura, A. & Mitsuda, N., 2022. Genome-wide characterization of the TALE homeodomain family and the KNOX-BLH interaction network in tomato. Plant Molecular Biology, 109(6), pp.799–821. doi: 10.1007/s11103-022-01277-6.

Furumizu, C. et al., 2015. Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication. PLoS Genetics, 11(2), e1004980. doi: 10.1371/journal.pgen.1004980.

Gao, J. et al., 2015. Evolution, diversification, and expression of KNOX proteins in plants. Frontiers in plant science, 6, p.882. doi: 10.3389/fpls.2015.00882.

Gao, J. et al., 2014. Molecular phylogenetic characterization and analysis of the WRKY transcription factor family responsive to Rhizoctonia solani in maize. Maydica, 59(1), pp.32–41.

Goddard, T.D. et al., 2018. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Science, 27(1), pp.14–25. doi: 10.1002/pro.3235.

Hirayama, Y. et al., 2007. Expression patterns of class I KNOX and YABBY genes in Ruscus aculeatus (Asparagaceae) with implications for phylloclade homology. Development Genes and Evolution, 217(5), pp.363–372. doi: 10.1007/s00427-007-0149-0.

Holland, P.W.H., 2013. Evolution of homeobox genes. Wiley Interdisciplinary Reviews: Developmental Biology, 2(1), pp.31–45. doi: 10.1002/wdev.78.

Hossain, M.M. et al., 2013. The application of biotechnology to orchids. Critical Reviews in Plant Sciences, 32(2), pp.69–139. doi: 10.1080/07352689.2012.715984.

Howell, S.H., 1998. Molecular Genetics of Plant Development, Cambridge: Cambridge University Press.

Ito, Y., Hirochika, H. & Kurata, N., 2002. Organ-specific alternative transcripts of KNOX family class 2 homeobox genes of rice. Gene, 288(1), pp.41–47. doi: https://doi.org/10.1016/S0378-1119(02)00460-2.

Jumper, J. et al., 2021. Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), pp.583–589. doi: 10.1038/s41586-021-03819-2.

Laskowski, R.A., Furnham, N. & Thornton, J.M., 2013. The Ramachandran plot and protein structure validation. In Biomolecular forms and functions: a celebration of 50 years of the ramachandran map. World Scientific, pp.62–75. doi: 10.1142/9789814449144_0005.

Marsch-Martínez, N. & de Folter, S., 2016. Hormonal control of the development of the gynoecium. Current Opinion in Plant Biology, 29, pp.104–114. doi: https://doi.org/10.1016/j.pbi.2015.12.006.

Mirdita, M. et al., 2022. ColabFold: making protein folding accessible to all. Nature Methods, 19(6), pp.679–682. doi: 10.1038/s41592-022-01488-1.

Mukherjee, K. & Brocchieri, L., 2010. Evolution of Plant Homeobox Genes. In eLS. Wiley. doi: 10.1002/9780470015902.a0022865.

Nagasaki, H. et al., 2001. Functional analysis of the conserved domains of a rice KNOX homeodomain protein, OSH15. The Plant cell, 13(9), pp.2085–2098. doi: 10.1105/tpc.010113.

Niu, X. & Fu, D., 2022. The roles of BLH transcription factors in plant development and environmental response. International Journal of Molecular Sciences, 23(7), 3731. doi: 10.3390/ijms23073731.

Nookaraju, A. et al., 2022. Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis. Plants, 11(4), 493. doi: 10.3390/plants11040493.

Paysan-Lafosse, T. et al., 2023. InterPro in 2022. Nucleic Acids Research, 51(D1), pp.D418–D427.

Razzaq, A. et al., 2020. In silico analyses of TALE transcription factors revealed its potential role for organ development and abiotic stress tolerance in Cotton. Int. J. Agric. Biol, 23, pp.1083–1094. doi: 10.17957/IJAB/15.1389.

Rüscher, D. et al., 2021. Auxin signaling and vascular cambium formation enable storage metabolism in cassava tuberous roots. Journal of Experimental Botany, 72(10), pp.3688–3703. doi: 10.1093/jxb/erab106.

Sakakibara, K. et al., 2013. KNOX2 genes regulate the haploid-to-diploid morphological transition in land plants. Science, 339(6123), pp.1067–1070. doi: 10.1126/science.1230082.

Semiarti, E. et al., 2016. Dynamic expression of POH1 gene in shoot development during in vitro culture of Phalaenopsis orchid. AIP Conference Proceedings, 1744, 020019.. doi: 10.1063/1.4953493.

Semiarti, E. et al., 2015. Induction of In Vitro Flowering of Indonesian Wild Orchid, Phalaenopsis amabilis (L.) Blume. KnE Life Sciences, 2(1), 398. doi: 10.18502/kls.v2i1.182.

Semiarti, E. et al., 2008. Isolation and charaterization of Phalaenopsis Orchid Homeobox1 (POH1) cDNAS, knotted1-like homeobox family of genes in Phalaenopsis amabilis orchid. In Proceedings of The 2nd International Conference on Mathematics and Natural Sciences (ICMNS) ITB, Bandung, Indonesia. pp. 28–30.

Shu, Y. et al., 2015. GmSBH1, a homeobox transcription factor gene, relates to growth and development and involves in response to high temperature and humidity stress in soybean. Plant Cell Reports, 34(11), pp.1927–1937. doi: 10.1007/s00299-015-1840-7.

Tadege, M., 2013. Molecular insight into polarity-mediated lamina outgrowth. International Journal of Plant Biology and Research, 1(1), 1005.

Tamura, K., Stecher, G. & Kumar, S., 2021. MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 38(7), pp.3022–3027. doi: 10.1093/molbev/msab120.

Testone, G. et al., 2015. The KNOTTED-like genes of peach (Prunus persica L. Batsch) are differentially expressed during drupe growth and the class 1 KNOPE1 contributes to mesocarp development. Plant Science, 237, pp.69–79. doi: 10.1016/j.plantsci.2015.05.005.

Townsley, B.T., Sinha, N.R. & Kang, J., 2013. KNOX1 genes regulate lignin deposition and composition in monocots and dicots. Frontiers in Plant Science, 4, 121. doi: 10.3389/fpls.2013.00121.

Viola, I.L. & Gonzalez, D.H., 2016. Structure and evolution of plant homeobox genes. In Plant Transcription Factors. Elsevier, pp.101–112. doi: 10.1016/B978-0-12-800854-6.00006-3.

Wang, S. et al., 2020. The Class II KNOX genes KNAT3 and KNAT7 work cooperatively to influence deposition of secondary cell walls that provide mechanical support to Arabidopsis stems. The Plant Journal, 101(2), pp.293–309. doi: 10.1111/tpj.14541.

Wang, Y. et al., 2022. The cellular basis for synergy between RCO and KNOX1 homeobox genes in leaf shape diversity. Current Biology, 32(17), pp.3773–3784. doi: 10.1016/j.cub.2022.08.020.

Wang, Y. & Jiao, Y., 2020. Keeping leaves in shape. Nature Plants, 6(5), pp.436–437. doi: 10.1038/s41477-020-0660-0.

Wybouw, B. & De Rybel, B., 2019. Cytokinin – A Developing Story. Trends in Plant Science, 24(2), pp.177–185. doi: 10.1016/j.tplants.2018.10.012.

Xu, X. et al., 2019. Identification of homeobox genes associated with lignification and their expression patterns in bamboo shoots. Biomolecules, 9(12), 862. doi: 10.3390/biom9120862.

Yuan, Q. et al., 2018. A genome-wide analysis of GATA transcription factor family in tomato and analysis of expression patterns. International Journal of Agriculture and Biology, 20(6), pp.1274–1282. doi: 10.17957/IJAB/15.0626.

Zahara, M. & Win, C.C., 2019. Morphological and stomatal characteristics of two Indonesian local orchids. Journal of Tropical Horticulture, 2(2), pp.65–69.

Zhang, X. et al., 2022. Identification and responding to exogenous hormone of HB-KNOX family based on transcriptome data of Caucasian clover. Gene, 828, 146469. doi: https://doi.org/10.1016/j.gene.2022.146469.

Zhang, Y. et al., 2021. Hormonal regulatory patterns of laknoxs and label1 transcription factors reveal their potential role in stem bulblet formation in LA hybrid lily. International Journal of Molecular Sciences, 22(24), 13502. doi: 10.3390/ijms222413502



DOI: https://doi.org/10.22146/jtbb.83934

Article Metrics

Abstract views : 965 | views : 831

Refbacks

  • There are currently no refbacks.


Copyright (c) 2023 Journal of Tropical Biodiversity and Biotechnology

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Editoral address:

Faculty of Biology, UGM

Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia

ISSN: 2540-9581 (online)