In silico promoter and expression analyses of rice Auxin Binding Protein 57 (ABP57)
DOI:
https://doi.org/10.14719/pst.2021.8.3.1208Keywords:
abiotic stress, auxin Binding Protein, Expression analysis, promoter analysis, RiceAbstract
Auxin Binding Protein 57 (ABP57) is one of the molecular components involved in rice response to abiotic stress. The ABP57 gene encodes an auxin receptor which functions in activating the plasma membrane H+-ATPase. Biochemical properties of ABP57 have been characterized; however, the function of ABP57, particularly on stress and hormone responses is still limited. This study was conducted to understand the regulation of ABP57 expression under abiotic stress. Thus, in silico identification of cis-acting regulatory elements (CAREs) in the promoter region of ABP57 was performed. Several motifs and transcription factor binding site (TFBS) that are involved in abiotic stress such as ABRE, DRE, AP2/EREBP, WRKY and NAC were identified. Next, expression analysis of ABP57 under drought, salt, auxin (IAA) and abscisic acid (ABA) was conducted by reverse transcription-PCR (RT-PCR) to verify the effect of these treatments on ABP57 transcript level. ABP57 was expressed at different levels in the shoot and root under drought conditions, and its expression was increased under IAA and ABA treatments. Moreover, our results showed that ABP57 expression in the root was more responsive to drought, auxin and ABA treatments compared to its transcript in the shoot. This finding suggests that ABP57 is a drought-responsive gene and possibly regulated by IAA and ABA.
Downloads
References
Kohli A, Sreenivasulu N, Lakshamanan P, Kumar PP. The phytohormone crosstalk paradigm takes center stage in understanding how plants respond to abiotic stresses. Plant Cell Rep. 2013; 32(7): 945-57. https://doi.org/10.1007/s00299-013-1461-y
Ng LM, Melcher K, Teh BT, Xu HE. Abscisic acid perception and signaling: Structural mechanisms and applications. Acta Pharmacol Sin. 2014;35:567–84. https://doi.org/10.1038/aps.2014.5
Sah SK, Reddy KR, Li J. Abscisic acid and abiotic stress tolerance in crop plants. Front. Plant Sci. 2016;7(571):1–26. https://doi.org/10.3389/fpls.2016.00571
Harris, JM. Abscisic acid: Hidden architect of root system structure. Plants (Basel.) 2015;4(3):548-72. https://doi.org/10.3390/plants4030548
Gómez-Porras JL, Riaño-Pachón DM, Dreyer I, Mayer JE, Mueller-Roeber B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics. 2007;8(260) https://doi.org/10.1186/1471-2164-8-260
Zou C, Sun K, Mackaluso JD, Seddon AE, Jin R, Thomashow MF, Shiu S-H. Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana. Proc Nat Acad USA. 2011; 108(36): 14992-97. https://doi.org/10.1073/pnas.1103202108
Hernandez-Gracia CM, Finer JJ. Identification and validation of promoters and cis-acting regulatory elements. Plant Sc. 2014;218:109-19. https://doi.org/10.1016/j.plantsci.2013.12.007
Hobo T, Asada M, Kowyama Y, Hattori T. ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent. Plant J. 1999;19(6):679-89. https://doi.org/10.1046/j.1365-313x.1999.00565.x
Choi HI, Hong JH, Ha JO, Kang JY, Kim SY. ABFs, a family of ABA-responsive element binding factors. J Biol Chem. 2000;275(3):1723-30. https://doi.org/10.1074/jbc.275.3.1723
Uno Y, Furihata T, Abe H, Yoshida R, Shinozaki K, Yamaguchi-Shinozaki K. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proc Nat Acad. USA. 2000;97(21):11632-37. https://doi.org/10.1073/pnas.190309197
Singh D, Laxmi A. Transcriptional regulation of drought response: a tortuous network of transcriptional factors. Front Plant Sci. 2015;6:895. https://doi.org/10.3389/fpls.2015.00895
Zhao, Y. Auxin biosynthesis and its role in plant development. Annu Rev Plant Biol. 2010;61:49-64. https://doi.org/10.1146/annurev-arplant-042809-112308
Liu J, Rowe J, Lindsey K. Hormonal crosstalk for root development: A combined experimental and modeling perspective. Front Plant Sci. 2014;5(116):1-8. https://doi.org/10.3389/fpls.2014.00116
Xu W, Jia L, Shi W, Liang J, Zhou F, Li Q, Zhang J. Abscisic acid accumulation modulates auxin transport in the root tip to enhance proton secretion for maintaining root growth under moderate water stress. New Phytol. 2013;197(1):139–50. https://doi.org/10.1111/nph.12004
Rowe JH, Topping JF, Liu J, Lindsey K. Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin. New Phytol. 2016;211(1):225–39. https://doi.org/10.1111/nph.13882
Abel S, Theologis A. Early genes and auxin action. Plant Physiol. 1996;111:9–17. https://doi.org/10.1104/pp.111.1.9
Leyser, O. Auxin signalling. Plant Physiol. 2018;176(1):465-79. https://doi.org/10.1104/pp.17.00765
Sauer M, Kleine-Vehn J. Auxin Binding Protein 1: The outsider. Plant Cell. 2011;23(6):2033–43. https://doi.org/10.1105/tpc.111.087064
Yamagami M, Haga K, Napier RM, Iino M. Two distinct signaling pathway participate in auxin-induced swelling of pea epidermal protoplast. Plant Physiol. 2004;134:735–47. https://doi.org/10.1104/pp.103.031294
Kim YS, Kim D, Jung J. Isolation of a novel auxin receptor from soluble fractions of rice (Oryza sativa L.) shoots. FEBS Letters. 1998;438(3):241-44. https://doi.org/10.1016/S0014-5793(98)01307-6
Kim YS, Min JK, Kim D, Jung J. Soluble auxin-binding protein, ABP57 purification with anti-bovine serum albumin antibody and characterization of its mechanistic role in the auxin effect on plant plasma membrane H+-ATPase. J Biol Chem. 2001;276(14):10730-36. https://doi.org/10.1074/jbc.M009416200
Lee K, Kim MI, Kwon YJ, Kim M, Kim YS, Kim D. Cloning and characterization of a gene encoding ABP57, a soluble auxin-binding protein. Plant Biotechnol Rep. 2009;3:293-99. https://doi.org/10.1007/s11816-009-0101-z
Kamarudin ZS, Shamsudin NAA, Che Othman MH, Shakri T, Tan LW, Sukiran NL, Md Isa N, Ab Rahman Z, Zainal Z. Morpho-physiology and antioxidant enzyme activities of transgenic rice plant overexpressing ABP57 under reproductive stage drought condition. Agronomy 2020; 10(1530):1-14. https://doi.org/10.3390/agronomy10101530
Tan LW, Ab Rahman Z, Goh HH, Hwang DJ, Ismail I, Zainal Z. Production of transgenic rice (indica cv. MR219) overexpressing ABP57 gene through Agrobacterium-mediated transformation. Sains Malaysiana 2017;46:703-11. https://doi.org/10.17576/jsm-2017-4605-04
Tan LW, Tan CS, Ab Rahman Z, Hossein HM, Goh HH, Ismail I, Zainal Z. Overexpression of Auxin Binding Protein 57 from rice (Oryza sativa L.) increased drought and salt tolerance in transgenic Arabidopsis thaliana. IOP Conf. Ser.: Earth Environ Sci. 2018;197:1-9. https://doi.org/10.1088/1755-1315/197/1/012038
Zambrose ZA, Mohd Roszelin SA, Mohd Hazbir NA, Chew BL, Jasmali SS, Wan Yahya WA, Md Isa N. Effect of rice Auxin Binding Protein 57 (OsABP57) overexpression in response to flooding. 2020;125-33. https://doi.org/10.17265/2161-6264/2020.03.001
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS. Phytozome: a comparative platform for green plant genomics. 2012;40:1178-86. https://doi.org/10.1093/nar/gkr944
Higo K, Ugawa Y, Iwamoto M, Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res. 1999;27(1):297-300. https://doi.org/10.1093/nar/27.1.297
Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouze P, Rombauts. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325-27. https://doi.org/10.1093/nar/30.1.325
Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, Kuo PL, Zheng HQ, Chang WC. PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Res. 2019;8(47):1155-63. https://doi.org/10.1093/nar/gky1081
Baharuddin FA, Zainal Z, Sukiran NL. Morphological changes analysis of rice cv. IR64 under drought stress. AIP Conference Proceedings. 2019;2111(1):040003. https://doi.org/10.1063/1.5111242
Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics. 2017;18(529):1–26. https://doi.org/10.1186/s12859-017-1934-z
Duncan DB. Multiple range and multiple F-tests. Biometrics. 1955;11(1):1-42.
Singhal P, Jan AT, Azam M, Haq MR. Plant abiotic stress: A prospective strategy of exploiting promoters as alternative to overcome escalating burden. Front Life Sc. 2016;9(1):52-63. https://doi.org/10.1080/21553769.2015.1077478
Yamaguchi-Shinozaki K, Shinozaki K. Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. Trends Plant Sci. 2006;10:88–94. https://doi.org/10.1016/j.tplants.2004.12.012
Kim JS, Mizoi J, Yoshida T, Fujita Y, Nakajima J, Ohori T, Todaka D, Nakashima K, Hirayama T, Shinozaki K, Yamaguchi-Shinozaki K. An ABRE promoter sequence is involved in osmotic stress-responsive expression of the DREB2A gene, which encodes a transcription factor regulating drought-inducible genes in Arabidopsis. Plant Cell Physiol. 2011; 52(12): 2136-46. https://doi.org/10.1093/pcp/pcr143
Yang X, Yang YN, Xue LJ, Zou MJ, Liu JY, Chen F, Xue HW. Rice ABI5-Like1 regulates abscisic acid and auxin responses by affecting the expression of ABRE-containing genes. Plant Physiol. 2011;156:1397-1409. https://doi.org/10.1104/pp.111.173427
Maruyama K, Sakuma Y, Kasuga M, Ito Y, Seki M, Goda H, Shimada Y, Yoshida S, Shinozaki K, Yamaguchi-Shinozaki K. Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. Plant J. 2004; 38(6):982-93. https://doi.org/10.1111/j.1365-313X.2004.02100.x
Jiang C, Iu B, Singh J. Requirement of a CCGAC cis-acting element for cold induction of the BN115 gene from winter Brassica napus. Plant Mol Biol. 1996;30:679-84. https://doi.org/10.1007/BF00049344
Wang C, Gao G, Cao S, Xie Q, Qi H. Isolation and functional validation of the CmLOX08 promoter associated with signalling molecule and abiotic stress responses in oriental melon, Cucumis melo var. makuwa Makino. BMC Plant Biol. 2019;19:75-89. https://doi.org/10.1186/s12870-019-1678-1
Gujjar RS, Akhtar M, Singh M. Transcription factors in abiotic stress tolerance. Ind. J. Plant Physiol. 2014;19:306-16. https://doi.org/10.1007/s40502-014-0121-8
Xie Z, Nolan TM, Jiang H, Yin Y. AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Front Plant Sci. 2019;10(228):1-17. https://doi.org/10.3389/fpls.2019.00228
Eulgem T, Rushton PJ, Robatzek S, Somssich IE. The WRKY superfamily of plant transcription factors. Trends in Plant Sci. 2000; 5(5): 199-206. https://doi.org/10.1016/S1360-1385(00)01600-9
Powers SK, Strader LC. Regulation of auxin transcriptional responses. Dev Dyn. 2020; 249(4):483-95. https://doi.org/10.1002/dvdy.139
Teale WD, Paponov IA, Palme K. Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol. 2006;7:847-59. https://doi.org/10.1038/nrm2020
Paponov IA, Paponov M, Teale W, Menges M, Chakrabortee S, Murray JAH, Palme K. Comprehensive transcriptome analysis of auxin responses in Arabidopsis. Mol Plant. 2008;1(2):321–37. https://doi.org/10.1093/mp/ssm021
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2021 Farah Afiqah Baharuddin, Zhan Xuan Khong, Zamri Zainal, Noor Liyana Sukiran
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright and Licence details of published articles
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
Open Access Policy
Plant Science Today is an open access journal. There is no registration required to read any article. All published articles are distributed under the terms of the Creative Commons Attribution License (CC Attribution 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited (https://creativecommons.org/licenses/by/4.0/). Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
