TALE Gene Family: Identification, Evolutionary and Expression Analysis Under Various Exogenous Hormones and Waterlogging Stress in Cucumis Sativus L

Overview

Journal BMC Plant Biol

Publisher Biomed Central

Specialty Biology

Date 2024 Jun 15

PMID 38879470

Authors

Sheraz Ahmad

Khushboo Khan

Ibrahim A Saleh

Mohammad K Okla

Ibrahim A Alaraidh

Hamada AbdElgawad

Muhammad Naeem

Naveed Ahmad

Shah Fahad

Affiliations

Soon will be listed here.

Abstract

Background: Three Amino acid Loop Extension (TALE) belongs to the homeobox group of genes that are important constituents of plant systems. The TALE gene family is instrumental not only in growth and development but also plays an essential role in regulating plant response to environmental adversaries.

Results: In the present study, we isolated 21 CsTALE genes from the cucumber (Cucumis sativus L.) genome database. Bioinformatics tools were put in place to understand the structural and functional components of the CsTALE gene family. The evolutionary analysis dissected them into seven subclades (KNOX-I, KNOX-II, and BELL-I to BELL-V). The cis-acting elements in the promoter region of CsTALE genes disclosed that they are key regulators of hormonal and stress-related processes. Additionally, the STRING database advocated the concerting role of CsTALE proteins with other key transcription factors potent in plant developmental biology. The CsmiR319 and CsmiR167a-3p targeting the CsTALE15 and CsTALE16, respectively, further assert the importance of the CsTALE gene family posttranscriptional-related processes. Tissue-specific gene expression unfolded the fundamental involvement of CsTALE genes as they were expressed throughout the developmental stages. Under waterlogging stress, the CsTALE17 expressed significantly higher values in WL, WL-NAA, and WL-ETH but not in WL-MeJA-treated samples.

Conclusions: The present study reveals the evolution and functions of the CsTALE gene family in cucumber. Our work will provide a platform that will help future researchers address the issue of waterlogging stress in the Yangtze River Delta.

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References

Hou Y, Wang Y, Liu X, Ahmad N, Wang N, Jin L . A Cinnamate 4-HYDROXYLASE1 from Safflower Promotes Flavonoids Accumulation and Stimulates Antioxidant Defense System in Arabidopsis. Int J Mol Sci. 2023; 24(6). PMC: 10049626. DOI: 10.3390/ijms24065393. View

Hamant O, Pautot V . Plant development: a TALE story. C R Biol. 2010; 333(4):371-81. DOI: 10.1016/j.crvi.2010.01.015. View

Ahmad N, Jianyu L, Xu T, Noman M, Jameel A, Na Y . Overexpression of a Novel Cytochrome P450 Promotes Flavonoid Biosynthesis and Osmotic Stress Tolerance in Transgenic . Genes (Basel). 2019; 10(10). PMC: 6826380. DOI: 10.3390/genes10100756. View

Smith H, Hake S . The interaction of two homeobox genes, BREVIPEDICELLUS and PENNYWISE, regulates internode patterning in the Arabidopsis inflorescence. Plant Cell. 2003; 15(8):1717-27. PMC: 167164. DOI: 10.1105/tpc.012856. View

Pan J, Sharif R, Xu X, Chen X . Mechanisms of Waterlogging Tolerance in Plants: Research Progress and Prospects. Front Plant Sci. 2021; 11:627331. PMC: 7902513. DOI: 10.3389/fpls.2020.627331. View

Jia P, Sharif R, Li Y, Sun T, Li S, Zhang X . The BELL1-like homeobox gene MdBLH14 from apple controls flowering and plant height via repression of MdGA20ox3. Int J Biol Macromol. 2023; 242(Pt 2):124790. DOI: 10.1016/j.ijbiomac.2023.124790. View

Wang J, Zhao P, Cheng B, Zhang Y, Shen Y, Wang X . Identification of TALE Transcription Factor Family and Expression Patterns Related to Fruit Chloroplast Development in Tomato ( L.). Int J Mol Sci. 2022; 23(9). PMC: 9104321. DOI: 10.3390/ijms23094507. View

Hong Y, Ahmad N, Zhang J, Lv Y, Zhang X, Ma X . Genome-wide analysis and transcriptional reprogrammings of MYB superfamily revealed positive insights into abiotic stress responses and anthocyanin accumulation in Carthamus tinctorius L. Mol Genet Genomics. 2022; 297(1):125-145. DOI: 10.1007/s00438-021-01839-1. View

Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S . Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res. 2018; 47(D1):D1128-D1136. PMC: 6324010. DOI: 10.1093/nar/gky944. View

10.

Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J . TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining. Mol Plant. 2023; 16(11):1733-1742. DOI: 10.1016/j.molp.2023.09.010. View

11.

Zhang L, Zhang X, Ju H, Chen J, Wang S, Wang H . Ovate family protein1 interaction with BLH3 regulates transition timing from vegetative to reproductive phase in Arabidopsis. Biochem Biophys Res Commun. 2016; 470(3):492-497. DOI: 10.1016/j.bbrc.2016.01.135. View

12.

Li H, Li L, ShangGuan G, Jia C, Deng S, Noman M . Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L. Sci Rep. 2020; 10(1):15521. PMC: 7511407. DOI: 10.1038/s41598-020-72390-z. View

13.

Muhammad I, Jing X, Shalmani A, Ali M, Yi S, Gan P . Comparative in Silico Analysis of Ferric Reduction Oxidase (FRO) Genes Expression Patterns in Response to Abiotic Stresses, Metal and Hormone Applications. Molecules. 2018; 23(5). PMC: 6099960. DOI: 10.3390/molecules23051163. View

14.

Raza A, Mubarik M, Sharif R, Habib M, Jabeen W, Zhang C . Developing drought-smart, ready-to-grow future crops. Plant Genome. 2022; 16(1):e20279. DOI: 10.1002/tpg2.20279. View

15.

Raza A . Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants. Plant Cell Rep. 2020; 41(3):741-763. DOI: 10.1007/s00299-020-02635-8. View

16.

Ullah U, Shalmani A, Ilyas M, Raza A, Ahmad S, Shah A . BZR proteins: identification, evolutionary and expression analysis under various exogenous growth regulators in plants. Mol Biol Rep. 2022; 49(12):12039-12053. DOI: 10.1007/s11033-022-07814-2. View

17.

Zhang X, Ahmad N, Zhang Q, Umar A, Wang N, Zhao X . Safflower Flavonoid 3'5'Hydroxylase Promotes Methyl Jasmonate-Induced Anthocyanin Accumulation in Transgenic Plants. Molecules. 2023; 28(7). PMC: 10095914. DOI: 10.3390/molecules28073205. View

18.

Kim D, Cho Y, Ryu H, Kim Y, Kim T, Hwang I . BLH1 and KNAT3 modulate ABA responses during germination and early seedling development in Arabidopsis. Plant J. 2013; 75(5):755-66. DOI: 10.1111/tpj.12236. View

19.

Hu B, Jin J, Guo A, Zhang H, Luo J, Gao G . GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2014; 31(8):1296-7. PMC: 4393523. DOI: 10.1093/bioinformatics/btu817. View

20.

Burglin T . Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. Nucleic Acids Res. 1997; 25(21):4173-80. PMC: 147054. DOI: 10.1093/nar/25.21.4173. View