The rubber tree kinome: Genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Abstract

The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, with the aim of providing novel inferences about the mechanisms associated with the stress response developed by PKs and retained throughout evolution, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species Manihot esculenta and Ricinus communis. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.

TheCucumis sativuskinome: Identification, annotation, and expression patterns in response to powdery mildew infection

“…Simultaneously, within the nucleus, PKs contribute significantly to the intricate machinery of gene regulation, influencing transcriptional processes that ultimately shape the plant’s responses to environmental challenges (Carbonnel et al, 2010). A pattern of specialized functions localized predominantly in the plasma membrane and nucleus emerges, aligning with observations in cucumber, common beans (Aono et al, 2023), Hevea brasiliensis and Manihot esculenta (Santos et al, 2023). This consistency across diverse plant species suggests a fundamental role for PKs in essential cellular processes and stress responses.…”

“…However, the observed diversity in subcellular locations among PKs also hints at their involvement in specific signaling pathways, highlighting the versatile and intricate nature of their functions. Similar results were also observed in common beans (Aono et al, 2023), Hevea brasiliensis , and Manihot esculenta (Santos et al, 2023). However, other genes can be found in various subcellular locations, suggesting their involvement in specific cellular processes, and signaling pathways in various cellular biological processes together with the stress responses.…”

“…The Csa kinome is a set of 831 protein kinases, that were retrieved from Csa proteome (CuGenDBv2: Gy14). The first plant kinome was defined in Arabidopsis in 2004 (Champion et al, 2004;Zulawski et al, 2014a), after that many others plant kinomes have been investigated in several plant species, such as, in rice (Dardick et al, 2007), maize (Wei et al, 2014a), tomato (Singh et al, 2014a), soybean (J Liu et al, 2015), wheat (Yan et al, 2017a), Brassica napus (Gill et al, 2017), Gossypium (Yan et al, 2018a), grapevine (Zhu et al, 2018c), pineapple (Zhu et al, 2018a), strawberry (Liu et al, 2020a), pecan (Zhu et al, 2021a), sugarcane and sorgum (Aono et al, 2021a), cowpea (Ferreira-Neto et al, 2021a), common bean (Aono et al, 2023), rubber tree (Santos et al, 2023). Some genome-wide analyses have been done in some sub-families of protein kinases (Wei et al, 2019) and dirigent gene family (Yadav et al, 2021) in the cucurbits species, there is no evidence of of comparative studies comprising all the protein kinase loci of Csa.…”

Genome-wide association reveals novel insights into the molecular mechanisms regulating stem volume inPinus taeda

“…Similarly, our analysis identified the transcription factor SCREAM2, which is known for its influence on the successive initiation, proliferation, and terminal differentiation of stomatal cell lineages [107]. Additionally, the LRR receptor-like serine/threonine-protein kinase RPK2 was found (which is also associated with ML results) to be clearly associated with stress response signaling [108]. All of these genes play pivotal roles in cellular regulation, emphasizing their importance within the coexpressed module.…”

Identifying Critical Regulators in the Viral Stress Response of Wheat (Triticum aestivum L.) Using Large-Scale Transcriptomics Data

“…Ubiquitin-26S proteasome system (UPS) has been considered a key mechanism for protein degradation [72], plant defense [73][74][75], and viral infection [73,[76][77][78]. The highest number of genes activated during all infection patterns belonged to the RLK-Pelle_DLSV PK family, which has been shown to play a role in stress signaling [79][80][81]. Three motifs were identified to be induced in wheat plants under bi-partite infections by BMV&BSMV, which are involved in CUL4 RING ubiquitin ligase.…”