TMT-label comparative proteomics reveals the vernalization mechanism in Wucai (Brassica campestris L.)

Xueqing Liu; Na Liao; Xiaoyan Tang; Kang Wang; Wenjie Wang; Afrasyab Khan; Chenggang Wang; Lingyun Yuan; Guohu Chen

doi:10.1016/j.jprot.2025.105398

TMT-label comparative proteomics reveals the vernalization mechanism in Wucai (Brassica campestris L.)

J Proteomics. 2025 Apr 15:314:105398. doi: 10.1016/j.jprot.2025.105398. Epub 2025 Feb 6.

Authors

Xueqing Liu¹, Na Liao², Xiaoyan Tang³, Kang Wang², Wenjie Wang⁴, Afrasyab Khan², Chenggang Wang⁵, Lingyun Yuan⁶, Guohu Chen⁷

Affiliations

¹ Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China.
² Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China.
³ Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China. Electronic address: txy@ahau.edu.cn.
⁴ Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China. Electronic address: wenjie_wang@ahau.edu.cn.
⁵ Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China. Electronic address: cgwang@ahau.edu.cn.
⁶ Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China. Electronic address: yuanlingyun@ahau.edu.cn.
⁷ Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China. Electronic address: cgh@ahau.edu.cn.

PMID: 39922279
DOI: 10.1016/j.jprot.2025.105398

Abstract

To investigate the molecular basis of vernalization in Wucai [Brassica campestris L. (Syn. Brassica rapa L.) ssp. chinensis var. rosularis Tsen], we performed differential proteomic analysis using a tandem mass tags (TMT)-based approach. Proteins from shoot apices subjected to 0, 15, and 30 days of vernalization (V0, V15, and V30) were analyzed to identify differentially abundant proteins (DAPs). A total of 8066 proteins were obtained, and 507 shared DAPs were involved in both initiation and progression of vernalization. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed functional enrichment in cellular processes, metabolic pathways, and translation-related activities, including photosynthesis, glucosinolate biosynthesis, and flavonoid biosynthesis. Proteomic data showed reduced abundance of photosynthesis-related proteins and upregulation of flavonoid biosynthesis during vernalization. Transcriptional validation of 24 proteins across metabolic and regulatory pathways corroborated proteomic findings, with notable peaks in genes associated with flavonoid biosynthesis at 15 days of vernalization, such as VESR1,CH13, CHS1, FHT, and FLS1. The functions of these genes in vernalization will be further analyzed. SIGNIFICANCE: Wucai is prone to premature bolting and flowering under cold conditions, as vernalization plays a key role in controlling flowering time in Chinese cabbage crops. However, the proteomic basis of vernalization remains poorly understood. In this study, TMT-based proteomic analysis identified DAPs associated with vernalization. Pathway enrichment analysis highlighted key DAPs and their roles in significantly enriched pathways relevant to vernalization. Notably, genes in the flavonoid biosynthesis pathway genes, including VESR1, CH13, CHS1, FHT, and FLS1, respond to vernalization. These findings offer novel insights into the molecular mechanisms underlying flowering time regulation in Wucai.

Keywords: Flavonoids biosynthesis; Photosynthesis; Proteomic analysis; Vernalization; Wucai.

Publication types

Comparative Study

MeSH terms

Brassica* / genetics
Brassica* / metabolism
Brassica* / physiology
Flowers / metabolism
Gene Expression Regulation, Plant*
Plant Proteins* / genetics
Plant Proteins* / metabolism
Proteomics* / methods
Tandem Mass Spectrometry
Vernalization

Substances

Plant Proteins