Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato

Abstract

The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses.

Tomato plant response to heat stress: a focus on candidate genes for yield-related traits

“…Another family, the GDSL esterase/lipase class, contains many functional genes playing a key role in the regulation of plant growth, response to stress and the morphogenesis of tissues and organs. In addition, these genes can respond to biotic and abiotic stresses ( Sun et al., 2022 ). GDSLs are also involved in pollen fertility in A. thaliana .…”

“…A knockout of GELP77 in this species caused male sterility and failure of pollen separation ( Tsugama et al., 2020 ). Sun et al. (2022) identified through a bioinformatic approach 80 GDSL esterase/lipase family genes in tomato, coded from SlGELP1 to SlGELP81.…”

“…A knockout of GELP77 in this species caused male sterility and failure of pollen separation (Tsugama et al, 2020). Sun et al (2022) identified through a bioinformatic approach 80 GDSL esterase/ lipase family genes in tomato, coded from SlGELP1 to SlGELP81. Finally, it was demonstrated that ethylene, a gaseous plant hormone, plays a key role in tomato pollen thermotolerance.…”