Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco (Nicotiana tabacum L.)

Abstract

Nicotine is a unique alkaloid present in tobacco that is widely used in cigarettes and in the agricultural, chemical, and pharmaceutical industries. However, the research on nicotine is mostly limited to its synthesis pathways, and only a few studies have explored the effects of other metabolic pathways on nicotine precursors. Regulating the nicotine content in tobacco can greatly promoting the application of nicotine in other fields. In this study, we performed global data-independent acquisition proteomics analysis of four tobacco varieties. Of the four varieties, one had high nicotine content and three had a low nicotine content. A total of 31,259 distinct peptides and 6,018 proteins across two samples were identified. A total of 45 differentially expressed proteins (DEPs) co-existed in the three comparison groups and were mainly involved in the transport and metallic processes of the substances. Most DEPs were enriched in the biosynthesis of secondary metals, glutathione metabolism, carbon metabolism, and glycolysis/gluconeogenesis. In addition, the weighted gene co-expression network analysis identified an expression module closely related to the nicotine content (Brown, r = 0.74, P = 0.006). Gene Ontology annotation and Kyoto Encyclopaedia of Genes and Genomes enrichment analysis showed that the module proteins were mainly involved in the synthesis and metabolism of nicotine precursors such as arginine, ornithine aspartate, proline, and glutathione. The increased levels of these precursors lead to the synthesis and accumulation of nicotine in plants. More importantly, these proteins regulate nicotine synthesis by affecting the formation of putrescine, which is the core intermediate product in nicotine anabolism. Our results provide a reference for tobacco variety selection with a suitable nicotine content and regulation of the nicotine content. Additionally, the results highlight the importance of other precursor metabolism in nicotine synthesis.

From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology

“…This gene was rapidly regulated by light and through additional studies, such as overexpression in pear peel and calli and Y2H, confirming its role in anthocyanin biosynthesis and also clarifying its mechanism of action [112]. Nicotine biosynthesis in tobacco was also investigated with WGCNA using different varieties with high and low metabolite content [105]. In this work, coexpressed modules were correlated with nicotine accumulation as an external trait, and genes associated to this module were related to metabolism of nicotine precursors such as Arg, Orn, Asp, Pro and GSH.…”

“…The most straightforward application of co-expression network analysis is the study of metabolic pathways and their regulation [104][105][106][107], including plant stress responses [108][109][110] and, more importantly, the identification of potential candidates for the biotechnological improvement of crops [51]. This is of special relevance, as it makes it possible to directly transfer all knowledge gained in model species over the years to species of agronomic interest, such as soybean [108].…”

Unravelling the Functional Role of GthGAPC2 in Cotton's Defense Against Verticillium dahliae through Proteome

“…Currently, seven distinct modules possessing candidate proteins linked to V. dahliae resistance have been identified (Figure 3b). Previous studies have also highlighted the significance of coexpression network analysis in identifying hub genes/proteins (Mo et al, 2022; Proost & Mutwil, 2017). RT‐qPCR was used to study the expression dynamics of identified candidates as described previously (Ju et al, 2023; Wu et al, 2022; Xiong et al, 2021).…”

Current Status and De Novo Synthesis of Anti-Tumor Alkaloids in Nicotiana

“…Nicotine is the major (0.6~3.0% of the dry weight) alkaloid present in Nicotiana spp. [ 44 , 45 ]. Nicotine does not initiate cancer but can affect cancer development through activation and binding with the acetylcholine receptors to synthase tobacco-specific N-nitrosamines or inhibition of immune response by affecting dendritic cells [ 46 ].…”