In Silico Identification of Potentially Functional Conserved Motifs in Two Components of the 5’ to 3’ mRNA Decay Pathway of Plants

Abstract

Pathways of mRNA degradation influence the remodeling of the transcriptomes. The 5’ to 3’ mRNA decay pathway consist on three subsequently acting mechanisms: deadenylation, decapping and 5’ to 3’ exonucleolytic decay. Specific physical interactions between the components of this pathway are essential to generate functional complexes that properly destroy unnecessary transcripts in eukaryotes. Most of the information about the structure of the components of this pathway comes from studies in yeast and animals, but little is known about the conservation of protein-protein interaction domains and motifs in the homolog decay factors of plants. The decapping subunit DCP1 and the 5’ to 3’ exoribonuclease XRN4 are critical components of this pathway. To get an overview of the structure and conservation of these proteins in plants, the sequences of the corresponding homologs of angiosperms, bryophytes and the gymnosperm Picea abies were retrieved, aligned and subjected to search of conserved sequences. Comparisons revealed conserved domains and structural motifs in plants and metazoans, which implies shared physical interactions that might arise during the early evolution of eukaryotes, for example, the trimerization of DCP1 and the recognition of proline-rich sequences (PRS) by β-sheets of the Dcp1/EVH1-like domain. However, the in silico analysis revealed that plant decay factors contain specific motifs, such as the PRS in DCP1 itself, that could have emerged to confer specialized functions in plants. Furthermore, this analysis revealed that XRN4 homologs of angiosperms acquired a sequence reminiscent to the homolog 5’ to 3’ exoribonuclease of fruit fly that allow the interaction with DCP1.