Genetic Characterization of RNA Recognition Motif (RRM)-Containing Genes in Coconut Palm

TL;DR

This study identifies and characterizes RNA recognition motif (RRM) genes in coconut palm, revealing their roles in gene regulation and plant growth.

Contribution

The first comprehensive genomic and functional analysis of RRM genes in coconut palm, focusing on the role of CnHRLP1 in gibberellin signaling.

Findings

326 RRM genes were identified in coconut palm and classified into 11 clades based on domain architecture.

CnHRLP1 overexpression in Arabidopsis caused dwarfism and altered gibberellin biosynthesis and catabolism genes.

CnHRLP1 is a nuclear-localized transcriptional regulator that modulates plant hormone signaling pathways.

Abstract

RNA recognition motif (RRM)-containing proteins are important regulators involved in diverse cellular processes, including splicing, stability, transport, and translation of transcripts. However, their comprehensive characterization remains limited in perennial tropical crops like Cocos nucifera. In this study, we performed a genome-wide analysis of RRM genes in coconut, identifying a total of 326 CnRRM genes. Phylogenetic classification based on complete RRM domain sequences grouped these proteins into eleven clades (I–XI), each exhibiting distinct variations in motif length and domain architecture. Transcriptome profiling revealed diverse expression patterns across coconut tissues, ranging from constitutive to highly tissue-specific. The CnHRLP1 gene, encoding an hnRNP-like multi-RRM protein, was selected for further functional analysis. Subcellular localization showed that the CnHRLP1 protein is predominantly nuclear, and its constitutive overexpression in Arabidopsis led to a severe dwarf phenotype. RNA-seq analysis demonstrated that CnHRLP1 overexpression broadly reshaped the transcriptome. KEGG pathway enrichment highlighted a significant impact on plant hormone signaling, particularly the gibberellin (GA) pathway. CnHRLP1 overexpression induced the coordinated downregulation of key GA biosynthetic genes (KO, KAO1/2, GA20ox, GA3ox) and the upregulation of GA catabolic genes (GA2ox2/6), suggesting its role in modulating GA homeostasis. In conclusion, this study provides a genomic and functional overview of the coconut RRM protein family and establishes that the hnRNP-like protein CnHRLP1 functions as a transcriptional regulator that inhibits vegetative growth, potentially through the suppression of gibberellin biosynthesis.

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