Genome‐wide analysis and phosphorylation sites identification of the 14‐3‐3 gene family and functional characterization of MeGRF3 in cassava

Abstract

The biological functionality of many members of the 14‐3‐3 gene family is regulated via phosphorylation at multiple amino acid residues. The specific phosphorylation‐mediated regulation of these proteins during cassava root tuberization, however, is not well understood. In this study, 15 different 14‐3‐3 genes (designated MeGRF1 – 15) were identified within the cassava genome. Based upon evolutionary conservation and structural analyses, these cassava 14‐3‐3 proteins were grouped into ε and non‐ε clusters. We found these 15 MeGRF genes to be unevenly distributed across the eight cassava chromosomes. When comparing the expression of these genes during different developmental stages, we found that three of these genes (MeGRF9, 12 and 15) were overexpressed at all developmental stages at 75, 104, 135, 182 and 267 days post‐planting relative to the fibrous root stage, whereas two (MeGRF5 and 7) were downregulated during these same points. In addition, the expression of most MeGRF genes changed significantly in the early and middle stages of root tuberization. This suggests that these different MeGRF genes likely play distinct regulatory roles during cassava root tuberization. Subsequently, 18 phosphorylated amino acid residues were detected on nine of these MeGRF proteins. A phosphomimetic mutation at serine‐65 in MeGRF3 in Arabidopsis thaliana (Arabidopsis) slightly influenced starch metabolism in these plants, and significantly affected the role of MeGRF3 in salt stress responses. Together these results indicate that 14‐3‐3 genes play key roles in responses to abiotic stress and the regulation of starch metabolism, offering valuable insights into the functions of these genes in cassava.

Genome-wide identification and characterization of 14-3-3 gene family related to negative regulation of starch accumulation in storage root of Manihot esculenta

“…In the present study, the prediction of the structure and function of cassava 14-3-3 proteins by bioinformatics shows that 16 cassava 14-3-3 proteins are structurally unstable and evolutionarily highly conserved hydrophilic protein families, in which the secondary structure of Me14-3-3 protein isomers is very similar. Compared with both sequences between MeGRF1-15 from Chang et al (2020) and Me14-3-3I-XVI in the present study, we found 13 sequences that showed 100% similarity, while Me14-3-3IV and MeGRF15 displayed 90% similarity, and Me14-3-3XIV and MeGRF8 showed 99% similarity. However, Me14-3-3II did not have any similarity with the MeGRF family (Supplementary Table S3).…”

“…A previous study showed that 15 different 14-3-3 genes (designated MeGRF1-15) were identified within the cassava genome. Based on evolutionary conservation and structural analyses, these cassava 14-3-3 proteins were grouped into the ϵ and non-ϵ clusters ( Chang et al., 2020 ). In the present study, the prediction of the structure and function of cassava 14-3-3 proteins by bioinformatics shows that 16 cassava 14-3-3 proteins are structurally unstable and evolutionarily highly conserved hydrophilic protein families, in which the secondary structure of Me14-3-3 protein isomers is very similar.…”

Multi-dimensional demarcation of phylogenetic groups of plant 14-3-3 isoforms using biochemical signatures

“…G . WebLogo (Crooks et al ., 2004) diagrams showing the amino acids found in positions P1 (residue 27 in omega) and P2 (residue 51 in omega) in 161 isoforms of 14-3-3 from 13 sequenced Eudicot species ( A. thaliana, Glycine max, Nicotiana tabacum, Malus domestica, Solanum lycopersicum, Camellia sinensis, Manihot esculenta, Hevea brasiliensis, Theobroma cacao, Coffea arabica, Populus trichocarpa, Vitis vinifera, Medicago truncatula ) (Mikhaylova et al ., 2021; Jia et al ., 2022; Zhang et al ., 2022; Zuo et al ., 2021; Chang et al ., 2020; Tian et al ., 2015). Note the wide co-occurrence of the Phe (position P1) and Ala (position P2) in non-epsilon groups, suggesting usefulness of a FA criterion for the epsilon/non-epsilon demarcation.…”

Genome-wide identification and gene expression analysis of the 14–3-3 gene family in potato (Solanum tuberosum L.)

“…14–3-3 proteins play important roles in plant growth, development, and stress responses. The completion of genome sequencing of model plants and various crops has allowed a large number of 14–3-3 genes to be identified in several plants, including Arabidopsis (15) [ 12 ], tomato (12) [ 30 ], Vitis vinifera (grape) (11) [ 31 ], peanut (14) [ 32 ], mango (16) [ 33 ], soybean (22) [ 34 ], rice (17) [ 25 , 35 ], Hevea brasiliensis (10) [ 36 ], cucumber (10) [ 37 ], Medicago truncatula (10) [ 38 ], apple (18) [ 39 ], and cassava (15) [ 40 ]. The genome sequence of potatoes was released in 2011 (PGSC, 2011).…”

“…There is increasing evidence that plant 14–3-3 genes act as signal mediators in hormone signal transduction pathways regulating plant development and tolerance to various abiotic stresses [ 13 , 20 , 23 , 40 , 42 ]. For example, studies on barley Hv14–3-3 have shown that 14–3-3 proteins are induced by ABA and participate in ABA signaling pathways [ 50 ].…”