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Open Access Research article

Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes

Luís Korrodi-Gregório1, Joana Abrantes23, Thorsten Muller4, José Melo-Ferreira2, Katrin Marcus4, Odete AB da Cruz e Silva5, Margarida Fardilha1 and Pedro J Esteves26*

Author Affiliations

1 Signal Transduction Laboratory, Centre for Cell Biology, Biology and Health Science Department, University of Aveiro, Aveiro, Portugal

2 CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal

3 INSERM, U892, Université de Nantes, Nantes, France

4 Functional Proteomics, Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany

5 Neuroscience Laboratory, Centre for Cell Biology, Biology Department and Health Science Department, University of Aveiro, Aveiro, Portugal

6 CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra, Portugal

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BMC Evolutionary Biology 2013, 13:242  doi:10.1186/1471-2148-13-242

Published: 6 November 2013

Abstract

Background

Pseudogenes are traditionally considered “dead” genes, therefore lacking biological functions. This view has however been challenged during the last decade. This is the case of the Protein phosphatase 1 regulatory subunit 2 (PPP1R2) or inhibitor-2 gene family, for which several incomplete copies exist scattered throughout the genome.

Results

In this study, the pseudogenization process of PPP1R2 was analyzed. Ten PPP1R2-related pseudogenes (PPP1R2P1-P10), highly similar to PPP1R2, were retrieved from the human genome assembly present in the databases. The phylogenetic analysis of mammalian PPP1R2 and related pseudogenes suggested that PPP1R2P7 and PPP1R2P9 retroposons appeared before the great mammalian radiation, while the remaining pseudogenes are primate-specific and retroposed at different times during Primate evolution. Although considered inactive, four of these pseudogenes seem to be transcribed and possibly possess biological functions. Given the role of PPP1R2 in sperm motility, the presence of these proteins was assessed in human sperm, and two PPP1R2-related proteins were detected, PPP1R2P3 and PPP1R2P9. Signatures of negative and positive selection were also detected in PPP1R2P9, further suggesting a role as a functional protein.

Conclusions

The results show that contrary to initial observations PPP1R2-related pseudogenes are not simple bystanders of the evolutionary process but may rather be at the origin of genes with novel functions.

Keywords:
PPP1; PPP1R2; Retroposons; Pseudogenization; Evolution; Vertebrates