Evolution of Plant AIG1-like Proteins: Different Modes of Sequence Divergence and Their Contributions to Functional Diversification

TL;DR

This study explores how plant AIG1-like proteins evolved through different genetic mechanisms, leading to their diverse functions in chloroplast import and disease resistance.

Contribution

The study reveals a novel recombination-based mechanism for head-to-head tandem duplication in the IAN subfamily and establishes an evolutionary framework for functional diversification.

Findings

Plant AIG1-like proteins are divided into three subfamilies (Toc34, Toc159, IAN) with distinct evolutionary patterns.

The IAN subfamily uses inverted repeats to generate head-to-head tandem duplicates through recombination.

Functional diversification is driven by C-terminal domain acquisitions and differences in duplication modes and evolutionary rates.

Abstract

AIG1 (avrRpt2-induced gene 1)-like proteins are a class of GTPases that play crucial roles in plants, functioning both in chloroplast protein import and disease resistance. However, their evolutionary history and the mechanisms driving this functional diversification remain poorly understood. Here, we performed a comprehensive genomic and evolutionary analysis of this gene family across the plant kingdom. We identified 90 AIG1-like genes from 11 sequenced plant species, representing major lineages from green algae to angiosperms. Phylogenetic analysis revealed that plant AIG1-like proteins form three monophyletic lineages corresponding to the Toc34, Toc159, and IAN subfamilies, which originated via two ancient duplications predating the divergence of green algae and land plants. These lineages exhibit dramatically divergent evolutionary patterns. The Toc34 subfamily is evolutionarily conserved, maintaining stable copy numbers and gene structure, indicative of strong functional constraints in its core role in plastid import. In contrast, the Toc159 and IAN subfamilies have undergone dynamic expansion via lineage-specific duplication mechanisms, including segmental duplication and prolific tandem duplication, respectively. Notably, we uncovered a novel mechanism for generating head-to-head tandem duplicates in the IAN subfamily, mediated by recombination between inverted repeats. Our analysis of ancestral gene numbers and gene gain/loss dynamics further highlights that functional diversification was driven by both the acquisition of distinct C-terminal targeting domains (M and TM domains) and profound differences in evolutionary rates and duplication modes among subfamilies. This study provides the first full-scale evolutionary framework for plant AIG1-like genes, establishing that functional specialization is rooted in distinct modes of sequence and genomic evolution.

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