Journal Article

Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation

Jonathan Corbi, Julien Y. Dutheil, Catherine Damerval, Maud I. Tenaillon and Domenica Manicacci

in Annals of Botany

Published on behalf of The Annals of Botany Company

Volume 109, issue 4, pages 693-708
Published in print March 2012 | ISSN: 0305-7364
Published online February 2012 | e-ISSN: 1095-8290 | DOI: http://dx.doi.org/10.1093/aob/mcr303
Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation

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  • Ecology and Conservation
  • Evolutionary Biology
  • Plant Sciences and Forestry

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Background and Aims

ADP-glucose pyrophosphorylase (AGPase) is a key enzyme of starch biosynthesis. In the green plant lineage, it is composed of two large (LSU) and two small (SSU) sub-units encoded by paralogous genes, as a consequence of several rounds of duplication. First, our aim was to detect specific patterns of molecular evolution following duplication events and the divergence between monocotyledons and dicotyledons. Secondly, we investigated coevolution between amino acids both within and between sub-units.

Methods

A phylogeny of each AGPase sub-unit was built using all gymnosperm and angiosperm sequences available in databases. Accelerated evolution along specific branches was tested using the ratio of the non-synonymous to the synonymous substitution rate. Coevolution between amino acids was investigated taking into account compensatory changes between co-substitutions.

Key Results

We showed that SSU paralogues evolved under high functional constraints during angiosperm radiation, with a significant level of coevolution between amino acids that participate in SSU major functions. In contrast, in the LSU paralogues, we identified residues under positive selection (1) following the first LSU duplication that gave rise to two paralogues mainly expressed in angiosperm source and sink tissues, respectively; and (2) following the emergence of grass-specific paralogues expressed in the endosperm. Finally, we found coevolution between residues that belong to the interaction domains of both sub-units.

Conclusions

Our results support the view that coevolution among amino acid residues, especially those lying in the interaction domain of each sub-unit, played an important role in AGPase evolution. First, within SSU, coevolution allowed compensating mutations in a highly constrained context. Secondly, the LSU paralogues probably acquired tissue-specific expression and regulatory properties via the coevolution between sub-unit interacting domains. Finally, the pattern we observed during LSU evolution is consistent with repeated sub-functionalization under ‘Escape from Adaptive Conflict’, a model rarely illustrated in the literature.

Keywords: Angiosperms; monocotyledons; dicotyledons; paralogue genes; molecular evolution; coevolution; neofunctionalization; subfunctionalization; starch synthesis; AGPase

Journal Article.  10900 words.  Illustrated.

Subjects: Ecology and Conservation ; Evolutionary Biology ; Plant Sciences and Forestry

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