Genome-wide identification of the regulatory network of mitogen-activated protein kinase signaling cascades gene families in Hevea Brasiliensis

Abstract

Background: The mitogen-activated protein kinase (MPK) cascade pathway represents a highly conserved signal transduction mechanism in plants, playing a crucial role in growth, development, and stress response. Nevertheless, systematic analysis on the MPK cascade genes in rubber trees remains unexplored.

Results: We conducted a comprehensive identification of the MPK cascade gene family of Hevea brasiliensis, identifying a total of 20 HbMPKs, 13 HbMPKKs, and 167 HbMAPKKKs genes. Through phylogenetic analysis and compared to Arabidopsis MPK cascade genes, HbMPKs and HbMPKKs were categorized into categorized four subgroups with no significant expansion or contraction, while the notably expanded HbMAPKKKs were divided into three subgroups: Raf, ZIK, and MEKK. Conserved motifs, gene structure, and motif analysis further bolster the validity of phylogenetic classification. Furthermore, expression profiling analysis based on public transcriptomic data revealed that these genes were differentially expressed in various tissues and differentially regulated in response to different stresses. Among them, the genes highly expressed in latex or the upregulated genes after tapped including HbMPK8, HbMPK12, HbMPK19, HbMPKK6, HbMPKK9, HbMPKKK15, HbMPKKK21 might be related to latex development and natural rubber (NR) yield. Through yeast two-hybrid assays, we successfully pinpointed 34 pairs of HbMPKKK-HbMPKK-HbMPK interaction modules. Integrating the interaction network and gene expression patterns, 12 potential HbMPK cascade signaling modules including HbMPKKK6/41/79-HbMPKK1-HbMPK9/12/15 and HbMPKKK6/14/21/41/79-HbMPKK9-HbMPK9/15 might involve in NR production and stress responses.

Conclusions: Our study comprehensively unveils the multidimensional characteristics of the MPK cascade gene family in rubber trees and successfully identifies its core signaling cascade module, laying a crucial foundation for future in-depth exploration of the biological functions of the MPK cascade signaling module in rubber trees.

Keywords: Hevea brasiliensis; Gene family; Kinases; MPK cascade.

Fig. 1

Distribution of HbMPK cascade genes in H. brasiliensis genome. A The HbMPK genes were unevenly distributed on 11 chromosomes. B The HbMPKK genes were distributed on 10 chromosomes. C For HbMPKKK genes, 155 HbMPKKKs were unevenly distributed across 18 chromosomes, while 12 HbMPKKKs were located on 4 scaffolds. The values (Mb) on the left side of the chromosome indicated the gene positions on the chromosome

Fig. 2

Phylogenetic relationships of MPK cascade genes from H. brasiliensis and A. thaliana. A Phylogenetic tree of MPK genes in H. brasiliensis and A. thaliana. B Phylogenetic tree of MPKK genes in H. brasiliensis and A. thaliana. C Phylogenetic tree of MPKKK genes in H. brasiliensis and A. thaliana. Different groups are highlighted in distinct colors. The MPK cascade genes of H. brasiliensis in blue circles, and A. thaliana in red circles

Fig. 3

Intraspecific collinearity analysis of HbMPK cascade genes. A Collinearity analysis of HbMPKs. B Collinearity analysis of HbMPKKs. C Collinearity analysis of HbMPKKKs. Colored blocks represent different chromosomes, and gene names were labeled around the circular genome. Curved lines indicate collinear gene pairs within the genome

Fig. 4

Expression profiling of HbMPK cascade genes across different tissues. A Tissue-specific expression levels of HbMPKs. B Tissue-specific expression levels of HbMPKKs. C Tissue-specific expression levels of HbMPKKKs. The color scale represents expression levels, ranging from blue (low expression) to red (high expression)

Fig. 5

Expression analysis of HbMPK cascade genes in tapped and virgin latex, healthy and TPD-affected trees. A Expression patterns in tapped latex and virgin latex. B Expression patterns in healthy trees and TPD-affected trees. The color scale represents expression levels, ranging from blue (low expression) to red (high expression). Differentially expressed genes are marked with red (up-regulated) and blue (down-regulated) annotations

Fig. 6

Y2H interaction analysis of HbMPK cascade proteins. Interactions between selected HbMPKKs and HbMPKs, and HbMPKKs and HbMPKKKs. Yeast cells carrying specific plasmid combinations were plated on SD/-Leu/-Trp (SD/-LT) and SD/ -Ade/-His/-Leu/-Trp (SD/-AHLT) medium. Positive control (+ , pGBKT7-P53 + pGADT7-T) and negative control (-, pGBKT7-Lam + pGADT7-T)

Fig. 7

Interaction network of HbMPK cascade genes. The lines between HbMPK cascade genes represent their interactions. Different colors indicate induction under specific treatment conditions and potential biological responses: green lines represent induction by MeJA and cold treatment, red lines represent induction by tapped treatment, blue lines represent induction in TPD-affected trees, and orange lines represent potential involvement in the growth and development of rubber tree laticifers. Lines with two colors indicate involvement in multiple responses