Genes encoding pentatricopeptide repeat (PPR) proteins are not conserved in location in plant genomes and may be subject to diversifying selection

Rachel Geddy,Gregory G Brown

doi:10.1186/1471-2164-8-130

Rachel Geddy, Gregory G Brown

Open Access

https://doi.org/10.1186/1471-2164-8-130

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Abstract

BackgroundThe pentatricopeptide repeat (PPR) is a degenerate 35 amino acid motif that occurs in multiple tandem copies in members of a recently recognized eukaryotic gene family. Most analyzed eukaryotic genomes contain only a small number of PPR genes, but in plants the family is greatly expanded. The factors that underlie the expansion of this gene family in plants are not as yet understood.ResultsWe show that the location of PPR genes is highly variable in comparisons between orthologous, closely related, and otherwise co-linear chromosomal regions of the Brassica rapa or radish and Arabidopsis thaliana. This observation also pertains to paralogous duplicated segments of the genomes of Arabidopsis thaliana and Brassica rapa. In addition, we show that PPR genes that seem closely linearly aligned in these comparisons are not generally found to be closely related to one another at the nucleotide and amino acid sequence level. We observe a relatively high level of non-synonomous vs synonomous changes among a group tandemly repeated radish PPR genes, suggesting that these, and possibly other PPR genes, are subject to diversifying selection. We also show that a duplicated region of the Arabidopsis genome possesses a relatively high density of PPR genes showing high similarity to restorers of fertility of cytoplasmic male sterile (CMS) systems of petunia, radish and rice. The PPR genes in these regions, together with the restorer genes, are more highly similar to one another, in sequence as well as in structure, than to other PPR genes, even within the same sub-family.ConclusionOur results suggest are consistent with a model in which at least some PPR genes undergo a "birth and death" process that involves transposition to unrelated chromosomal sites. PPR genes hold certain features in common with disease resistance genes (R genes), and their "nomadic" character suggests that their evolutionary expansion in plants may have involved novel molecular processes and selective pressures.

Highlights

The pentatricopeptide repeat (PPR) is a degenerate 35 amino acid motif that occurs in multiple tandem copies in members of a recently recognized eukaryotic gene family
We show that PPR gene family members share characteristics with plant disease resistance genes (R genes); in particular we present evidence that at least some PPR genes, as per R genes, are subject to diversifying selection, i.e. an evolutionary process that selects for, rather than against, mutations that lead to amino acid replacements in the encoded proteins
We show here that PPR genes, at least those in the P subfamily, possess a novel, "nomadic" character in that their positions are highly variable in otherwise co-linear segments of closely related genomes

Summary

Introduction

The pentatricopeptide repeat (PPR) is a degenerate 35 amino acid motif that occurs in multiple tandem copies in members of a recently recognized eukaryotic gene family. Most analyzed eukaryotic genomes contain only a small number of PPR genes, but in plants the family is greatly expanded. The pentatricopeptide repeat (PPR) peptide motif, first described by Small and Peeters [1], is a degenerate 35 amino acid sequence, closely related to the 34 amino acid tetratricopeptide repeat (TPR) motif. TPRs occur as tandem repeats in a widespread protein family of both prokaryotes and eukaryotes. PPRs occur in multiple tandem repeats, but have far been found to be exclusively eukaryotic in their distribution. In PPR proteins, tandem repeats of these alpha-helical pairs are predicted to form a superhelix that encloses a central spiral groove with a positively charged ligandbinding surface [1]. PPR proteins are known to mediate specific RNA processing events including RNA editing [3], transcript processing [4], and translation initiation [5], and are thought to be capable of specific binding to both protein and RNA molecules

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