|
|
|
| Identification and Expression Analysis of 4CL Gene Family in Rubus chingii |
| ZHENG Fei-Xiong, CHEN Jun-Yu, JIANG Lin-Qi, ZHAO Jia-Ying, LYU Jia-Yi, YU Zhen-Ming* |
| School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311403, China |
|
|
|
|
Abstract 4-coumarate coenzyme A ligase (4CL) is the last key enzyme of the phenylpropane pathway, which can regulate the biosynthesis of lignin, anthocyanin, and flavonoids, and has an important effect on stress resistance. In order to reveal the biological role of 4CL gene family in Rubus chingii, the present study identified the 4CL gene family through an approach of bioinformatics, and investigated the physicochemical properties, subcellular localization, chromosomal localization, systematic evolution, gene structure, conserved motifs, protein secondary structure and cis-acting elements of each member. Besides, their expression profiles in different tissues and at different growth stages were detected. The results showed that 6 4CL gene family members were presented in R. chingii, with similar physicochemical properties and conserved gene structure, and were divided into 3 subfamilies. Six 4CL genes were unevenly distributed on chromosomes 2, 3, 4, 5 and 7. The promoter regions of 6 4CL genes harbored auxin, gibberellin, jasmonic acid, abscisic acid, light, anaerobic, and drought responsive cis-acting elements. The 4CL genes differentially expressed in different R. chingii tissues, among them, Rc4CL1, Rc4CL2, Rc4CL3 and Rc4CL4 were highly expressed in roots, while Rc4CL5 and Rc4CL6 were highly expressed in fruits. Simultaneously, they also differentially expressed at different fruit growth stages, among them, Rc4CL1, Rc4CL2 and Rc4CL3 showed a downward trend at the late stage of fruit development. However, Rc4CL2, Rc4CL5 and Rc4CL6 were highly expressed at the late stage of fruit development, indicating that they might play a crucial role in fruit ripening. The results provide a reference for in-depth study of the 4CL gene and its biological role in R. chingii.
|
|
Received: 11 April 2023
|
|
|
|
Corresponding Authors:
*yuzhenming@zcmu.edu.cn
|
|
|
|
[1] 陈夏晔, 彭宣翔. 2018. 普通烟草Nt4CL基因家族的生物信息学分析[J]. 贵州农业科学. 46(8): 11-15.
(Chen X Y, Peng X X.2018. Bioinformatics analysis on tobacco Nt4CL gene family[J]. Guizhou Agricultural Sciences, 46(8): 11-15.)
[2] 何磊, 严希, 袁圆, 等. 2022. 辣椒4CL基因家族成员的鉴定与生物信息学分析[J]. 分子植物育种. 20(8): 2478-2484.
(He L, Yan X, Yuan Y, et al.2022. Identification and bioinformatics analysis of family members of 4CL gene of cayenne pepper[J]. Molecular Plant Breeding, 20(8): 2478-2484.)
[3] 俞振明, 赵聪慧, 张明泽, 等. 2021. 益智不同组织多糖含量及其生物合成途径分析[J]. 热带亚热带植物学报. 29(6): 669-677.
(Yu Z M, Zhao C H, Zhang M Z, et al.2021. Analysis of polysaccharide content and biosynthesis pathway in different tissues of Alpinia oxyphylla[J]. Journal of Tropical and Subtropical Botany, 29(6): 669-677.)
[4] Afifi O A, Tobimatsu Y, Lam P Y, et al.2022. Genome-edited rice deficient in two 4-coumarate coenzyme a ligase genes displays diverse lignin alterations[J]. Plant Physiology, 190(4): 2155-2172.
[5] Cesarino I.2019. Structural features and regulation of lignin deposited upon biotic and abiotic stresses[J]. Current Opinion in Biotechnology, 56: 209-214.
[6] Chen C, Chen H, Zhang Y, et al.2020. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 13(8): 1194-1202.
[7] De Azevedo Souza C, Barbazuk B, Ralph S G, et al.2008. Genome-wide analysis of a land plant-specific acyl coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella[J]. New Phytologist, 179(4): 987-1003.
[8] Dong N Q, Lin H X.2021. Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions[J]. Journal of Integrative Plant Biology, 63(1): 180-209.
[9] Jores T, Tonnies J, Wrightsman T, et al.2021. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters[J]. Nature Plants, 7(6): 842-855.
[10] Kumar S, Stecher G, Li M, et al.2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 35(6): 1547-1549.
[11] Lam P Y, Wang L, Lui A C W, et al.2022. Deficiency in flavonoid biosynthesis genes CHS, CHI, and CHIL alters rice flavonoid and lignin profiles[J]. Plant Physiology, 188(4): 1993-2011.
[12] Lavhale S G, Joshi R S, Kumar Y, et al.2021. Functional insights into two Ocimum kilimandscharicum 4-coumarate-CoA ligases involved in phenylpropanoid biosynthesis[J]. International Journal of Biological Macromolecules, 181: 202-210.
[13] Lavhale S G, Kalunke R M, Giri A P.2018. Structural, functional and evolutionary diversity of 4-coumarate-CoA ligase in plants[J]. Planta, 248(5): 1063-1078.
[14] Li X, Jiang J, Chen Z, et al.2021. Transcriptomic, proteomic and metabolomic analysis of flavonoid biosynthesis during fruit maturation in Rubus chingii Hu[J]. Frontiers in Plant Science, 12: 706667.
[15] Li X, Wu Z, Xiao S, et al.2020. Characterization of abscisic acid (ABA) receptors and analysis of genes that regulate rutin biosynthesis in response to ABA in Fagopyrum tataricum[J]. Plant Physiology and Biochemistry, 157: 432-440.
[16] Li Y, Kim J I, Pysh L, et al.2015. Four isoforms of Arabidopsis 4-coumarate CoA ligase have overlapping yet distinct roles in phenylpropanoid metabolism[J]. Plant Physiology, 169(4): 2409-2421.
[17] Livak K J, Schmittgen T D.2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method[J]. Methods, 25(4): 402-408.
[18] Lu S, Wang J, Chitsaz F, et al.2020. CDD/SPARCLE: The conserved domain database in 2020[J]. Nucleic Acids Research, 48(1): 265-268.
[19] Potter S C, Luciani A, Eddy S R, et al.2018. HMMER web server: 2018 update[J]. Nucleic Acids Research, 46(1): 200-204.
[20] Reinprecht Y, Yadegari Z, Perry G E, et al.2013. In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr[J]. Frontiers in Plant Science, 4: 317.
[21] Renault H, Alber A, Horst N A, et al.2017. A phenol-enriched cuticle is ancestral to lignin evolution in land plants[J]. Nature Communications, 8: 14713.
[22] Sun H, Li Y, Feng S, et al.2013. Analysis of five rice 4-coumarate coenzyme A ligase enzyme activity and stress response for potential roles in lignin and flavonoid biosynthesis in rice[J]. Biochemical and Biophysical Research Communications, 430(3): 1151-1156.
[23] Wang L, Lei T, Han G, et al.2021. The chromosome-scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolyzable tannins[J]. Plant Journal, 107(5): 1466-1477.
[24] Yan X, Liu J, Kim H, et al.2019. CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa[J]. New Phytologist, 222(1): 244-260.
[25] Yao P, Huang Y, Dong Q, et al.2020. FtMYB6, a light-induced SG7 R2R3-MYB transcription factor, promotes flavonol biosynthesis in tartary buckwheat (Fagopyrum tataricum)[J]. Journal of Agricultural and Food Chemistry, 68(47): 13685-13696.
[26] Yu G, Luo Z, Wang W, et al.2019. Rubus chingii Hu: A review of the phytochemistry and pharmacology[J]. Frontiers in Pharmacology, 10: 799.
[27] Yu Z, Dong W, Teixeira da Silva J A, et al.2021. Ectopic expression of DoFLS1 from Dendrobium officinale enhances flavonol accumulation and abiotic stress tolerance in Arabidopsis thaliana[J]. Protoplasma, 258(4): 803-815.
[28] Zhang G, Yu Z, Yao B, et al.2022. SsMYB113, a Schima superba MYB transcription factor, regulates the accumulation of flavonoids and functions in drought stress tolerance by modulating ROS generation[J]. Plant and Soil, 478, 427-444. |
|
|
|
