Sequence-Structure Comparative and Network-Based Prediction of Drought Gene Candidate Regulator in Elaeis guineensis

https://doi.org/10.22146/jtbb.90808

Galuh Wening Permatasari(1*), Riza Arief Putranto(2), Larasati Dena Mardhika(3), Annisa Aulia Aksa(4), Yuli Setiawati(5), Hayati Minarsih(6), Imron Riyadi(7), Ernayunita Ernayunita(8)

(1) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(2) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(3) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(4) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(5) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(6) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(7) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(8) Indonesian Oil Palm Research Institute (IOPRI), Brigjend Katamso St. No.51, Kp. Baru, Kec. Medan Maimun, Medan, North Sumatera 20158
(*) Corresponding Author

Abstract


Drought poses a significant threat to global food security, particularly impacting crops like oil palm. Selecting genes for genome editing to enhance drought tolerance presents formidable challenges. To ensure that the target gene is chosen correctly and results in the desired character, a pilot study is necessary to determine the target gene for knockout. Two genes drought-related, AtBRL3 and AtOST2, were scrutinized in this context. Aligned with the Elaeis guineensis genome, their neighbouring proteins and gene ontology were analysed to identify potential targets for genome editing. AtBRL3, identified as BRL1 (XP_010913986.1) in E. guineensis, exhibited 58.48% identity and 100% coverage. It interacts with 12 nodes, including BIR1, BRI1, and AT2G20050, crucial for signalling pathways and cellular responses. Molecular function analysis revealed kinase activity. AtOST2 showed high similarity to plasma membrane ATPase/HA1 (XP_010913679.1) in E. guineensis, with 87.46% identity and 100% query cover. It correlated with 14 genes associated with ABA stimulus, stomatal movement, and hormone response. EgBRL1 and EgHA1, resembling AtBRL3 and AtOST2, respectively, emerge as promising targets for developing drought-tolerant oil palm cultivars through gene editing. Nonetheless, further validation through in vitro gRNA target selection and in vivo conversion of OST2/BRL3-containing plasmids in oil palm calluses is indispensable to demonstrate their efficacy in conferring novel drought resistance traits.

 


Keywords


Alignment; Biological Process; Gene Target; Genome Editing; Networking Analysis

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References

Adam, H. et al., 2011. Environmental regulation of sex determination inoil palm : current knowledge and insights from other species. Annals of Botany, 108, 8, pp.1529-1537. doi: 10.1093/aob/mcr151.

Baek, M. et al., 2021. Accurate prediction of protein structures and interactions using a 3-track network. Science, 373(6557), pp.871-876. doi: 10.1126/science.abj8754.

Baxter, I. et al., 2003. Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice. Plant Physiol., 132, pp.618–628. doi: 10.1104/pp.103.021923

Corley, R.H.V. & Tinker, P.B, 2008. The Oil Palm, New York: Wiley.

Fàbregas, N. et al., 2018. Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth. Nature Communications, 9(1), 4680.

Feng, Y. et al., 2015. Down-regulation of BdBRI1, a putative brassinosteroid receptor gene produces a dwarf phenotype with enhanced drought tolerance in Brachypodium distachyon. Plant Sci., 234, pp.163–173. doi: 10.1016/j.plantsci.2015.02.015.

Gou, X. et al., 2012. Genetic evidence for an indispensable role of somatic embryogenesis receptor kinases in brassinosteroid signaling. PLoS Genet., 8, e1002452. doi: 10.1371/journal.pgen.1002452.

Gao, X. et al., 2013. Cotton GhBAK1 mediates verticillium wilt resistance and cell death. Journal of Integrative Plant Biology, 55(7), pp.586–596. doi: 10.1111/jipb.12064

Gao, X. et al., 2019. BAKing up to survive a battle: Functional dynamics of BAK1 in plant programmed cell death. Frontiers in Plant Science, 9, 1913. doi: 10.3389/FPLS.2018.01913/BIBTEX

Gui, J. et al., 2016. OsREM4.1 interacts with OsSERK1 to coordinate the interlinking between abscisic acid and brassinosteroid signaling in rice. Dev. Cell., 38, pp.201–213. doi: 10.1016/j.devcel.2016.06.011.

He, J.-X. et al., 2002. The GSK3-like kinase BIN2 phosphorylates and destabilizes BZR1, a positive regulator of the brassinosteroid signaling pathway in Arabidopsis. Proceedings of the National Academy of Sciences, 99(15), pp.10185–10190. doi: 10.1073/pnas.152342599.

Hothorn, M. et al., 2011. Structural basis of steroid hormone perception by the receptor kinase BRI1. Nature, 474, pp.467–471. doi: 10.1038/nature10153.

Joshi, R.K, Bharat, S.S. & Mishra, R., 2020. Engineering drought tolerance in plants through CRISPR/Cas genome editing. 3 Biotech, 10(9), 400. doi: 10.1007/s13205-020-02390-3.

Kinoshita, T. et al., 2005. Binding of brassinosteroids to the extracellular domain of plant receptor kinase BRI1. Nature, 433, pp.167–171. doi: 10.1038/nature03227.

Lamichhane, S. & Sapana, T., 2022. Advances from Conventional to Modern Plant Breeding Methodologies. Plant Breeding and Biotechnology, 10, pp.1-14

Li, J. & Chory J., 1997. A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. Cell, 90, pp.929–938. doi: 10.1016/S0092-8674(00)80357-8.

Li, J. et al., 2002. BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling. Cell, 110(2), pp.213–222. doi: 10.1016/S0092-8674(02)00812-7

Merlot, S. et al., 2007. Constitutive activation of a plasma membrane H(+)-ATPase prevents abscisic acid-mediated stomatal closure. EMBO Journal, 26, pp.3216–3226.

Osakabe, Y. et al., 2014. Response of plants to water stress. Front. Plant Sci., 5, 86. doi: 10.3389/fpls.2014.00086

Osakabe, Y. et al. 2016. Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Scientific Reports, 6, 26685. doi: 10.1038/srep26685

Palmgreen, M.G., 2001. Plant plasma membrane H+-ATPases: powerhouses for nutrient uptake. Annu. Rev. Plant Physiol. Mol. Biol., 52, pp.817–845.

Pearson, W.R, 2013. An introduction to sequence similarity ("homology") searching. Current Protocol Bioinformatics, 3, pp.3.1.1-3.1.8. doi: 10.1002/0471250953.bi0301s42.

Pedersen, B.P. et al., 2007. Crystal structure of the plasma membrane proton pump. Nature, 450, pp.1111–1114. doi: 10.1038/nature06417

Putranto, R.A. et al., 2019. Profiling Akumulasi Transkrip Gen Pada Akar Bibit Kelapa Sawit (Elaeis Guineensis Jacq.) Rentan Dan Toleran Terhadap Ganoderma Boninense. AGRIN, 23(2), pp.155-167. doi: 10.20884/1.agrin.2019.23.2.510

Santiago, J. et al., 2009. Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs. The Plant Journal : For Cell and Molecular Biology, 60(4), pp.575–588. doi: 10.1111/J.1365-313X.2009.03981.X

Shannon, P. et al., 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), pp.2498-2504. doi: 10.1101/gr.1239303

She, J., et al. 2011. Structural insight into brassinosteroid perception by BRI1. Nature, 474, pp.472–476. doi: 10.1038/nature10178.

Skubacz, A., Daszkowska-Golec, A., & Szarejko, I., 2016. The role and regulation of ABI5 (ABA-insensitive 5) in plant development, abiotic stress responses and phytohormone crosstalk. Frontiers in Plant Science, 7, 1884. doi: 10.3389/FPLS.2016.01884/BIBTEX

Svennelid, F. et al., 1999. Phosphorylation of Thr-948 at the C terminus of the plasma membrane H+-ATPase creates a binding site for the regulatory 14-3-3 protein. Plant Cell, 11, pp.2379–2391. Doi: 10.1105/tpc.11.12.2379

Szklarczyk, D. et al., 2023. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Reearch, 51(D1), pp.D638-646. doi: 10.1093/nar/gkac1000

Trenberth, K., 2020, ‘Nino SST Indices (Nino 1+2, 3, 3.4, 4; ONI and TNI)’ in The Climate Data Guide, from https://climatedataguide.ucar.edu/climate-data/nino-sst-indices-nino-12-3-34-4-oni-and-tni

Wang, Z.Y., et al. 2001. BRI1 is a critical component of a plasma-membrane receptor for plant steroids. Nature, 410, pp.380–383. doi: 10.1038/35066597.

Wang, Z.Y., et al. 2002. Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Dev. Cell., 2, pp.505–513. doi: 10.1016/S1534-5807(02)00153-3.

Wang, C. et al., 2017. El Niño and Southern Oscillation (ENSO): A Review. In Coral Reefs of the World. Springer. doi: 10.1007/978-94-017-7499-4

Wlodawer, A., 2017. Stereochemistry and Validation of Macromolecular Structures. Methods in Molecular Biology, 1607, pp.595-610. doi: 10.1007/978-1-4939-7000-1_24

Ye, H. et al., 2017. RD26 mediates crosstalk between drought and brassinosteroid signalling pathways. Nat. Commun., 8, 14573. doi: 10.1038/ncomms14573.

Yin, Y. et al., 2002. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell, 109, pp.181–191. doi: 10.1016/S0092-8674(02)00721-3.

Zhang, S., et al. 2009. The primary signaling outputs of brassinosteroids are regulated by abscisic acid signaling. Proc. Natl Acad. Sci. USA, 106, pp.4543–4548. doi: 10.1073/pnas.0900349106.

Zhang, C., et al. 2018. Transcriptional and physiological data reveal the dehydration memory behavior in switchgrass (Panicum virgatum L.). Biotechnology Biofuels, 11, 91. doi: 10.1186/s13068-018-1088-x



DOI: https://doi.org/10.22146/jtbb.90808

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