Genome-Wide Identification and Expression Analysis of Two-Component System Genes in Tomato

Abstract

The two-component system (TCS), which comprises histidine kinases (HKs), phosphotransfers (HPs), and response regulator proteins (RRs), plays pivotal roles in regulating plant growth, development, and responses to biotic and abiotic stresses. TCS genes have been comprehensively identified and investigated in various crops but poorly characterized in tomato. In this work, a total of 65 TCS genes consisting of 20 HK(L)s, six HPs, and 39 RRs were identified from tomato genome. The classification, gene structures, conserved domains, chromosome distribution, phylogenetic relationship, gene duplication events, and subcellular localization of the TCS gene family were predicted and analyzed in detail. The amino acid sequences of tomato TCS family members, except those of type-B RRs, are highly conserved. The gene duplication events of the TCS family mainly occurred in the RR family. Furthermore, the expansion of RRs was attributed to both segment and tandem duplication. The subcellular localizations of the selected green fluorescent protein (GFP) fusion proteins exhibited a diverse subcellular targeting, thereby confirming their predicted divergent functionality. The majority of TCS family members showed distinct organ- or development-specific expression patterns. In addition, most of TCS genes were induced by abiotic stresses and exogenous phytohormones. The full elucidation of TCS elements will be helpful for comprehensive analysis of the molecular biology and physiological role of the TCS superfamily.

Comparative analysis of basic helix–loop–helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus

“…Only 12, 7, and 9 orthologous gene pairs had a Ka/Ks ratio of > 1 (Table S5, S6, S7), thereby suggesting that novel functions were likely to generate among these genes. Similar findings were observed in other gene families in plants, such as the TCS of tomato and PMEI of Brassica, of which most homolog pairs evolve through purifying selection, and a few or even no gene experiences positive selection [34,35]. Theoretically, after WGD and WGT events, the genome size of B. oleracea should be threefold larger than that of A. thaliana.…”

Genome-Wide Identification, Molecular Evolution, and Expression Profiling Analysis of Pectin Methylesterase Inhibitor Genes in Brassica campestris ssp. chinensis

“…Only one ortholog pair and one paralog pair have a ω ratio larger than 1 ( Figure 5 b,d), suggesting that novel functions were likely to generate among these genes. This is the same as some other gene families in plants, such as TCS of tomato, GRAS of Medicago truncatula , and NF-YB of Gossypium hirsutum , of which most homolog pairs evolve through purifying selection and few or even no gene experience positive selection [ 55 , 56 , 57 ].…”

Genome-Wide Identification of Two-Component Signal Transduction System Genes in Melon (<I>Cucumis melon</I> L.)

“…The TCS signaling is widely present in higher plant, including Arabidopsis tha-liana [8] [9], rice (Oryza sativa) [18], lotus (Lotus japonicus) [19], soybean (Glycine max) [14] [20], maize (Zea maize) [21], Physcomitrella patens [22] [23], and wheat (Triticum aestivum L.) [24], as well as horticultural crops such as Chinese cabbage (Brassica rapa) [20], tomato (Solanum lycopersicum) [25], cucumber (Cucumis sativus L.) [13] and watermelon (Citrullus lanatus) [13] ( Table 1). In Arabidopsis, there are 56 TCS genes and their functions have been extensively studied [8] [9].…”

“…c. Number of TM (transmembrane) from TMHMM Server v. 2.0 (http://www.cbs.dtu.dk/services/TMHMM/). d. The proteins belonged to Arabidopsis response regulator (ARR) or Arabidopsis pseudo-response regulator (APRR) family.participating in a negative feedback loop to reduce the plant sensitivity to cytokinins[28] [25].…”