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Open Access Research article

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Núria Radó-Trilla1 and MMar Albà12*

Author Affiliations

1 Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB) - IMIM (Hospital del Mar Research Institute), Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Spain

2 Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain

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BMC Evolutionary Biology 2012, 12:155  doi:10.1186/1471-2148-12-155

Published: 24 August 2012

Abstract

Background

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few amino acids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution.

Results

We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance.

Conclusion

We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

Keywords:
Low-complexity region; Simple sequence; Amino acid tandem repeat; Vertebrate protein; Slippage