Genome-Wide Identification and Characterization of Maize Long-Chain Acyl-CoA Synthetases and Their Expression Profiles in Different Tissues and in Response to Multiple Abiotic Stresses

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2024 Aug 29

PMID 39202344

Authors

Zhenwei Yan

Jing Hou

Bingying Leng

Guoqi Yao

Changle Ma

Yue Sun

Qiantong Liu

Fajun Zhang

Chunhua Mu

Xia Liu

Affiliations

Soon will be listed here.

Abstract

Long-chain acyl-CoA synthetases (LACSs) are essential enzymes that activate free fatty acids to fatty acyl-CoA thioesters, playing key roles in fatty acid (FA) catabolism, lipid synthesis and storage, epidermal wax synthesis, and stress tolerance. Despite their importance, comprehensive information about genes in maize, a primary food crop, remains scarce. In the present work, eleven maize genes were identified and mapped across five chromosomes. Three pairs of segmentally duplicated genes were detected in the maize gene family, which underwent significant purifying selection (Ka/Ks < 1). Subsequently, phylogenetic analysis indicated that genes were divided into four subclasses, as supported by highly conserved motifs and gene structures. On the basis of the PlantCARE database, analysis of the promoter regions revealed various cis-regulatory elements related to tissue-specific expression, hormonal regulation, and abiotic stress response. RT-qPCR analysis showed that genes exhibit tissue-specific expression patterns and respond to diverse abiotic stresses including drought and salt, as well as phytohormone abscisic acid. Furthermore, using the STRING database, several proteins involved in fatty acid and complex lipid synthesis were identified to be the potential interaction partners of ZmLACS proteins, which was also confirmed by the yeast two-hybrid (Y2H) assay, enhancing our understanding of wax biosynthesis and regulatory mechanisms in response to abiotic stresses in maize. These findings provide a comprehensive understanding of genes and offer a theoretical foundation for future research on the biological functions of genes in maize environmental adaptability.

References

Kumar S, Stecher G, Peterson D, Tamura K . MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics. 2012; 28(20):2685-6. PMC: 3467750. DOI: 10.1093/bioinformatics/bts507. View

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

Petricka J, Winter C, Benfey P . Control of Arabidopsis root development. Annu Rev Plant Biol. 2012; 63:563-90. PMC: 3646660. DOI: 10.1146/annurev-arplant-042811-105501. View

Grevengoed T, Klett E, Coleman R . Acyl-CoA metabolism and partitioning. Annu Rev Nutr. 2014; 34:1-30. PMC: 5881898. DOI: 10.1146/annurev-nutr-071813-105541. View

Ma W, Zhu K, Zhao J, Chen M, Wei L, Qiao Z . Genome-Wide Identification, Characterization, and Expression Analysis of Long-Chain Acyl-CoA Synthetases in under Different Treatments. Int J Mol Sci. 2023; 24(14). PMC: 10380667. DOI: 10.3390/ijms241411558. View

Jiang Y, Peng D, Bai L, Ma H, Chen L, Zhao M . Molecular switch for cold acclimation -- anatomy of the cold-inducible promoter in plants. Biochemistry (Mosc). 2013; 78(4):342-54. DOI: 10.1134/S0006297913040032. View

Zhang C, Mao K, Zhou L, Wang G, Zhang Y, Li Y . Genome-wide identification and characterization of apple long-chain Acyl-CoA synthetases and expression analysis under different stresses. Plant Physiol Biochem. 2018; 132:320-332. DOI: 10.1016/j.plaphy.2018.09.004. View

Flagel L, Wendel J . Gene duplication and evolutionary novelty in plants. New Phytol. 2009; 183(3):557-564. DOI: 10.1111/j.1469-8137.2009.02923.x. View

Zhao L, Katavic V, Li F, Haughn G, Kunst L . Insertional mutant analysis reveals that long-chain acyl-CoA synthetase 1 (LACS1), but not LACS8, functionally overlaps with LACS9 in Arabidopsis seed oil biosynthesis. Plant J. 2010; 64(6):1048-58. DOI: 10.1111/j.1365-313X.2010.04396.x. View

10.

Zhao L, Haslam T, Sonntag A, Molina I, Kunst L . Functional Overlap of Long-Chain Acyl-CoA Synthetases in Arabidopsis. Plant Cell Physiol. 2019; 60(5):1041-1054. DOI: 10.1093/pcp/pcz019. View

11.

Weng H, Molina I, Shockey J, Browse J . Organ fusion and defective cuticle function in a lacs1 lacs2 double mutant of Arabidopsis. Planta. 2010; 231(5):1089-100. DOI: 10.1007/s00425-010-1110-4. View

12.

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

13.

Ding L, Gu S, Zhu F, Ma Z, Li J, Li M . Long-chain acyl-CoA synthetase 2 is involved in seed oil production in Brassica napus. BMC Plant Biol. 2020; 20(1):21. PMC: 6958636. DOI: 10.1186/s12870-020-2240-x. View

14.

Madeira F, Pearce M, Tivey A, Basutkar P, Lee J, Edbali O . Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 2022; 50(W1):W276-W279. PMC: 9252731. DOI: 10.1093/nar/gkac240. View

15.

Kitajima-Koga A, Baslam M, Hamada Y, Ito N, Taniuchi T, Takamatsu T . Functional Analysis of Rice Long-Chain Acyl-CoA Synthetase 9 () in the Chloroplast Envelope Membrane. Int J Mol Sci. 2020; 21(6). PMC: 7139535. DOI: 10.3390/ijms21062223. View

16.

Watkins P, Maiguel D, Jia Z, Pevsner J . Evidence for 26 distinct acyl-coenzyme A synthetase genes in the human genome. J Lipid Res. 2007; 48(12):2736-50. DOI: 10.1194/jlr.M700378-JLR200. View

17.

Bailey T . Discovering novel sequence motifs with MEME. Curr Protoc Bioinformatics. 2008; Chapter 2:Unit 2.4. DOI: 10.1002/0471250953.bi0204s00. View

18.

Chen C, Chen H, Zhang Y, Thomas H, Frank M, He Y . TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020; 13(8):1194-1202. DOI: 10.1016/j.molp.2020.06.009. View

19.

Zhong Y, Wang Y, Li P, Gong W, Wang X, Yan H . Genome-Wide Analysis and Functional Characterization of Gene Family Associated with Lipid Synthesis in Cotton ( spp.). Int J Mol Sci. 2023; 24(10). PMC: 10218317. DOI: 10.3390/ijms24108530. View

20.

Watkins P, Ellis J . Peroxisomal acyl-CoA synthetases. Biochim Biophys Acta. 2012; 1822(9):1411-20. PMC: 3382043. DOI: 10.1016/j.bbadis.2012.02.010. View