Class-Specific Evolution and Transcriptional Differentiation of 14-3-3 Family Members in Mesohexaploid Brassica rapa

Abstract

14-3-3s are highly conserved, multigene family proteins that have been implicated in modulating various biological processes. The presence of inherent polyploidy and genome complexity has limited the identification and characterization of 14-3-3 proteins from globally important Brassica crops. Through data mining of Brassica rapa, the model Brassica genome, we identified 21 members encoding 14-3-3 proteins namely, BraA.GRF14.a to BraA.GRF14.u. Phylogenetic analysis indicated that B. rapa contains both ε (epsilon) and non-ε 14-3-3 isoforms, having distinct intron-exon structural organization patterns. The non-ε isoforms showed lower divergence rate (Ks < 0.45) compared to ε protein isoforms (Ks > 0.48), suggesting class-specific divergence pattern. Synteny analysis revealed that mesohexaploid B. rapa genome has retained 1–5 orthologs of each Arabidopsis 14-3-3 gene, interspersed across its three fragmented sub-genomes. qRT-PCR analysis showed that 14 of the 21 BraA.GRF14 were expressed, wherein a higher abundance of non-ε transcripts was observed compared to the ε genes, indicating class-specific transcriptional bias. The BraA.GRF14 genes showed distinct expression pattern during plant developmental stages and in response to abiotic stress, phytohormone treatments, and nutrient deprivation conditions. Together, the distinct expression pattern and differential regulation of BraA.GRF14 genes indicated the occurrence of functional divergence of B. rapa 14-3-3 proteins during plant development and stress responses.

Genome-Wide Identification, Phylogeny, and Expression Analyses of the 14-3-3 Family Reveal Their Involvement in the Development, Ripening, and Abiotic Stress Response in Banana

“…The finding indicated that the banana 14-3-3 gene family had expanded compared to that in Arabidopsis (Rosenquist et al, 2001 ; Chevalier et al, 2009 ) and rice (Chen et al, 2006 ; Yao et al, 2007 ). Based on phylogenetic analysis, they are classified as either the ε group or the non-ε group, which is in accordance with previous phylogenic classification of 14-3-3s in rice (Chen et al, 2006 ), Arabidopsis (Chevalier et al, 2009 ), soybean (Li and Dhaubhadel, 2011 ), cotton (Sun et al, 2011 ), common bean (Tian et al, 2015 ), Populus (Li et al, 2015 ), Medicago truncatula (Qin et al, 2016 ), and B. rapa (Chandna et al, 2016 ). Gene structure analysis indicated that the number of exons and introns of ε group 14-3-3 genes from banana is more than non-ε group genes (Figure 3 ) which was also found in Arabidopsis , rice, common bean (Tian et al, 2015 ), M. truncatula (Qin et al, 2016 ), and B. rapa (Chandna et al, 2016 ).…”

“…Since the first plant 14-3-3 isoform was isolated from maize (de Vetten et al, 1992 ), genome-wide analyses have identified 13 14-3-3s from Arabidopsis (DeLille et al, 2001 ; Rosenquist et al, 2001 ; Chevalier et al, 2009 ), 8 from rice (Chen et al, 2006 ; Yao et al, 2007 ), 31 from cotton (Sun et al, 2011 ), 9 from common bean (Tian et al, 2015 ), 18 from soybean (Li and Dhaubhadel, 2011 ), 14 from Populus trichocarpa (Li et al, 2015 ), 12 from tomato (Xu and Shi, 2006 ), and 21 from Brassica rapa (Chandna et al, 2016 ). Biochemical and genetic analyses have revealed that the function of 14-3-3 proteins is related to plant growth and development.…”

“…Overexpression of Gh14-3-3L in cotton promoted fiber elongation and maturation (Zhou et al, 2015 ). In addition, expression analyses of the 14-3-3 gene family in various species indicated that its expression is altered under various abiotic stress, such as drought, salt, or cold (Li and Dhaubhadel, 2011 ; Kumar et al, 2015 ; Li et al, 2015 ; Tian et al, 2015 ; Chandna et al, 2016 ). Further studies support that 14-3-3 genes play a role in plant response to abiotic stress.…”

Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics

“…14-3-3 proteins are also known as positive regulators of H + -ATPase activity to control the electrochemical gradient across the plasma membrane, which contributes to the initiation of stress responses and other signal transduction pathways [93]. It has been reported that drought stress can directly alter the abundance of 14-3-3 proteins [94,95,96]. In addition, overexpression or silencing of the 14-3-3 protein genes can modulate drought tolerance of transgenic plants (e.g., Gossypium hirsutum and Arabidopsis ) [97,98].…”

Validation of reference genes for normalization of gene expression by qRT-PCR in a resveratrol-producing entophytic fungus (Alternaria sp. MG1)

“…Validation of appropriate reference genes is a prerequisite for accurate analysis of gene expression using qRT-PCR (Li et al 2016). In the past research, the most traditional reference genes used in qRT-PCR assay were genes such as ACT , TUB , and 18S .…”