Consensus co-expression network analysis identifies AdZAT5 regulating pectin degradation in ripening kiwifruit

Qiu-Yun Zhang; Jun Ge; Xin-Cheng Liu; Wen-Qiu Wang; Xiao-Fen Liu; Xue-Ren Yin

doi:10.1016/j.jare.2021.11.019

Consensus co-expression network analysis identifies AdZAT5 regulating pectin degradation in ripening kiwifruit

J Adv Res. 2022 Sep:40:59-68. doi: 10.1016/j.jare.2021.11.019. Epub 2021 Dec 4.

Authors

Qiu-Yun Zhang¹, Jun Ge², Xin-Cheng Liu¹, Wen-Qiu Wang¹, Xiao-Fen Liu¹, Xue-Ren Yin³

Affiliations

¹ Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China.
² Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, China.
³ Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China. Electronic address: xuerenyin@zju.edu.cn.

Abstract

Introduction: Cell wall degradation and remodeling is the key factor causing fruit softening during ripening.

Objectives: To explore the mechanism underlying postharvest cell wall metabolism, a transcriptome analysis method for more precious prediction on functional genes was needed.

Methods: Kiwifruits treated by ethylene (a conventional and effective phytohormone to accelerate climacteric fruit ripening and softening as kiwifruits) or air were taken as materials. Here, Consensus Coexpression Network Analysis (CCNA), a procedure evolved from Weighted Gene Co-expression Network Analysis (WGCNA) package in R, was applied and generated 85 consensus clusters from twelve transcriptome libraries. Advanced and comprehensive modifications were achieved by combination of CCNA and WGCNA with introduction of physiological traits, including firmness, cell wall materials, cellulose, hemicellulose, water soluble pectin, covalent binding pectin and ionic soluble pectin.

Results: As a result, six cell wall metabolisms related structural genes AdGAL1, AdMAN1, AdPL1, AdPL5, Adβ-Gal5, AdPME1 and four transcription factors AdZAT5, AdDOF3, AdNAC083, AdMYBR4 were identified as hub candidate genes for pectin degradation. Dual-luciferase system and electrophoretic mobility shift assays validated that promoters of AdPL5 and Adβ-Gal5 were recognized and trans-activated by transcription factor AdZAT5. The relatively higher enzyme activities of PL and β-Gal were observed in ethylene treated kiwifruit, further emphasized the critical roles of these two pectin related genes for fruit softening. Moreover, stable transient overexpression AdZAT5 in kiwifruit significantly enhanced AdPL5 and Adβ-Gal5 expression, which confirmed the in vivo regulations between transcription factor and pectin related genes.

Conclusion: Thus, modification and application of CCNA would be powerful for the precious phishing the unknown regulators. It revealed that AdZAT5 is a key factor for pectin degradation by binding and regulating effector genes AdPL5 and Adβ-Gal5.

Keywords: AdPL5; AdZAT5; Adβ-Gal5; CCNA; Cell wall remodeling.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Actinidia* / genetics
Actinidia* / metabolism
Consensus
Ethylenes / metabolism
Fruit* / genetics
Fruit* / metabolism
Pectins / metabolism
Transcription Factors / genetics
Transcription Factors / metabolism

Substances

Ethylenes
Transcription Factors
Pectins
ethylene