Unraveling 14-3-3 Proteins in C4 Panicoids with Emphasis on Model Plant Setaria italica Reveals Phosphorylation-Dependent Subcellular Localization of RS Splicing Factor

Abstract

14-3-3 proteins are a large multigenic family of regulatory proteins ubiquitously found in eukaryotes. In plants, 14-3-3 proteins are reported to play significant role in both development and response to stress stimuli. Therefore, considering their importance, genome-wide analyses have been performed in many plants including Arabidopsis, rice and soybean. But, till date, no comprehensive investigation has been conducted in any C4 panicoid crops. In view of this, the present study was performed to identify 8, 5 and 26 potential 14-3-3 gene family members in foxtail millet (Si14-3-3), sorghum (Sb14-3-3) and maize (Zm14-3-3), respectively. In silico characterization revealed large variations in their gene structures; segmental and tandem duplications have played a major role in expansion of these genes in foxtail millet and maize. Gene ontology annotation showed the participation of 14-3-3 proteins in diverse biological processes and molecular functions, and in silico expression profiling indicated their higher expression in all the investigated tissues. Comparative mapping was performed to derive the orthologous relationships between 14-3-3 genes of foxtail millet and other Poaceae members, which showed a higher, as well as similar percentage of orthology among these crops. Expression profiling of Si14-3-3 genes during different time-points of abiotic stress and hormonal treatments showed a differential expression pattern of these genes, and sub-cellular localization studies revealed the site of action of Si14-3-3 proteins within the cells. Further downstream characterization indicated the interaction of Si14-3-3 with a nucleocytoplasmic shuttling phosphoprotein (SiRSZ21A) in a phosphorylation-dependent manner, and this demonstrates that Si14-3-3 might regulate the splicing events by binding with phosphorylated SiRSZ21A. Taken together, the present study is a comprehensive analysis of 14-3-3 gene family members in foxtail millet, sorghum and maize, which provides interesting information on their gene structure, protein domains, phylogenetic and evolutionary relationships, and expression patterns during abiotic stresses and hormonal treatments, which could be useful in choosing candidate members for further functional characterization. In addition, demonstration of interaction between Si14-3-3 and SiRSZ21A provides novel clues on the involvement of 14-3-3 proteins in the splicing events.

Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance

“…The decrease in synteny with increase in phylogenetic distance between the Poaceae members demonstrates the degree of genetic-relatedness of the corresponding genomes. This is in agreement to previous genome-wide analyses performed for NAC 34, WD40 35, AP2/ERF 36, C 2 H 2 zinc finger and MYB transcription factors3738, DCL, AGO and RDR 39, 14-3-3  40, secondary cell wall genes and WRKY transcription factors4142, and ADP-ribosylation factor43 in foxtail millet. The effect of Darwinian selection in divergence of these genes is examined by investigating the ratio of rate of non-synonymous substitution (Ka) to synonymous substitution (Ks) for all the orthologous gene pairs.…”

“…The average Ka/Ks ratios of foxtail millet-sorghum, -maize, -rice and - Brachypodium were 0.8, 0.2, 0.6 and 0.5, respectively (Supplementary Table 3). The Ka/Ks ratio below 1 for all the orthologous gene-pairs demonstrated that the genes were under intense positive purifying selection, which accorded well with evolutionary analysis of NAC , WD40 , AP2/ERF , C 2 H 2 zinc finger and MYB transcription factors, DCL, AGO and RDR , 14-3-3 , secondary cell wall genes and WRKY transcription factors, and ADP-ribosylation factor gene families in foxtail millet34353637383940414243. The study also revealed the period of divergence of foxtail millet-sorghum, -maize, -rice and - Brachypodium as 25.8, 28, 36.5 and 50.7 million years ago, respectively.…”

Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress

“…Further, decrease in number of orthologous genes between foxtail millet-sorghum (~98%), -maize (~88%), -rice (~75.5%) and - Brachypodium (~54.6%) reveals the close-evolutionary relationship of foxtail millet with sorghum and maize, followed by rice and Brachypodium. This is in agreement with the comparative maps developed using NAC 15, WD40 16, AP2/ERF 17, C 2 H 2 zinc finger and MYB transcription factors1819, DCL, AGO and RDR 20, 14-3-3 21, secondary cell wall genes and WRKY transcription factors2223, and ADP-ribosylation factor24 gene families of foxtail millet.…”

Global Transcriptome Analysis of Combined Abiotic Stress Signaling Genes Unravels Key Players in Oryza sativa L.: An In silico Approach

“…Rice AbS responsive genes were found to be more homologous to maize and foxtail millet highlights its close evolutionary relationships while the decrease in synteny with sorghum due to the increase in genetic distance across the phylogeny (Bennetzen et al, 2012; Zhang et al, 2012). This pattern of decreasing synteny was also observed in the comparative mapping of NAC TFs (Puranik et al, 2013), WD40 genes (Mishra et al, 2014), C 2 H 2 zinc fingers (Muthamilarasan et al, 2014a), MYB TFs (Muthamilarasan et al, 2014b), AP2/ERFs (Lata et al, 2014) and 14-3-3 proteins (Kumar et al, 2015). This comparative map data would assist in understanding the evolutionary process of AbS responsive genes among the Poaceae members.…”