Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants

Arthur G Hunt,Qingshun Q Li,Denghui Xing

doi:10.1186/1471-2164-13-641

Abstract

BackgroundPolyadenylation, an essential step in eukaryotic gene expression, requires both cis-elements and a plethora of trans-acting polyadenylation factors. The polyadenylation factors are largely conserved across mammals and fungi. The conservation seems also extended to plants based on the analyses of Arabidopsis polyadenylation factors. To extend this observation, we systemically identified the orthologs of yeast and human polyadenylation factors from 10 plant species chosen based on both the availability of their genome sequences and their positions in the evolutionary tree, which render them representatives of different plant lineages.ResultsThe evolutionary trajectories revealed several interesting features of plant polyadenylation factors. First, the number of genes encoding plant polyadenylation factors was clearly increased from “lower” to “higher” plants. Second, the gene expansion in higher plants was biased to some polyadenylation factors, particularly those involved in RNA binding. Finally, while there are clear commonalities, the differences in the polyadenylation apparatus were obvious across different species, suggesting an ongoing process of evolutionary change. These features lead to a model in which the plant polyadenylation complex consists of a conserved core, which is rather rigid in terms of evolutionary conservation, and a panoply of peripheral subunits, which are less conserved and associated with the core in various combinations, forming a collection of somewhat distinct complex assemblies.ConclusionsThe multiple forms of plant polyadenylation complex, together with the diversified polyA signals may explain the intensive alternative polyadenylation (APA) and its regulatory role in biological functions of higher plants.

Highlights

Polyadenylation, an essential step in eukaryotic gene expression, requires both cis-elements and a plethora of trans-acting polyadenylation factors
The sets of genes encoding polyadenylation factor subunits vary in different plant genomes Previously, we identified and characterized Arabidopsis thaliana proteins similar to subunits of yeast and human polyadenylation factors [3]
To better understand the nature of the polyadenylation apparatus in plants, we identified orthologs of yeast and human polyadenylation factors from several representative organisms of the plant lineage: Arabidopsis lyrata, Glycine max, Vitis vinifera, Populus trichocarpa, Oryza sativa subsp

Summary

Introduction

Polyadenylation, an essential step in eukaryotic gene expression, requires both cis-elements and a plethora of trans-acting polyadenylation factors. Messenger RNA 3’end polyadenylation is an essential step for most of eukaryotic mRNA biogenesis It requires both cis-elements within a pre-mRNA sequence and trans-acting factors consisting of dynamic and complicated polyadenylation complexes [1,2,3,4]. A recent study suggests that more than 80 proteins from different pathways of RNA biogenesis associate with active polyadenylation gene expression are largely unknown, there is evidence that both cis-elements and trans-acting factors are involved in APA [21,22,23]. These data support the notion that multiple complexes, which likely share the core factors of polyadenylation machinery, operate in the polyadenylation of subsets of genes in response to different developmental and environmental cues

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