A comparative proteomic analysis of the simple amino acid repeat distributions in Plasmodia reveals lineage specific amino acid selection

Dalby, A.R. 2009. A comparative proteomic analysis of the simple amino acid repeat distributions in Plasmodia reveals lineage specific amino acid selection. PLoS ONE. 4 (7), p. e6231.

TitleA comparative proteomic analysis of the simple amino acid repeat distributions in Plasmodia reveals lineage specific amino acid selection
AuthorsDalby, A.R.
Abstract

Background: Microsatellites have been used extensively in the field of comparative genomics. By studying microsatellites in coding regions we have a simple model of how genotypic changes undergo selection as they are directly expressed in the phenotype as altered proteins. The simplest of these tandem repeats in coding regions are the tri-nucleotide repeats which produce a repeat of a single amino acid when translated into proteins. Tri-nucleotide repeats are often disease associated, and are also known to be unstable to both expansion and contraction. This makes them sensitive markers for studying proteome evolution, in closely related species.

Results: The evolutionary history of the family of malarial causing parasites Plasmodia is complex because of the life-cycle of the organism, where it interacts with a number of different hosts and goes through a series of tissue specific stages. This study shows that the divergence between the primate and rodent malarial parasites has resulted in a lineage specific change in the simple amino acid repeat distribution that is correlated to A–T content. The paper also shows that this altered use of amino acids in SAARs is consistent with the repeat distributions being under selective pressure. Conclusions: The study shows that simple amino acid repeat distributions can be used to group related species and to examine their phylogenetic relationships. This study also shows that an outgroup species with a similar A–T content can be distinguished based only on the amino acid usage in repeats, and suggest that this might be a useful feature for proteome clustering. The lineage specific use of amino acids in repeat regions suggests that comparative studies of SAAR distributions between proteomes gives an insight into the mechanisms of expansion and the selective pressures acting on the organism.

JournalPLoS ONE
Journal citation4 (7), p. e6231
ISSN1932-6203
Year2009
PublisherPublic Library of Science
FileDalby_2009_as_published.pdf
Digital Object Identifier (DOI)doi:10.1371/journal.pone.0006231
Publication dates
Published2009

Related outputs

Complete analysis of the H5 hemagglutinin and N8 neuraminidase phylogenetic trees reveals that the H5N8 subtype has been produced by multiple reassortment events
Dalby, A.R. 2016. Complete analysis of the H5 hemagglutinin and N8 neuraminidase phylogenetic trees reveals that the H5N8 subtype has been produced by multiple reassortment events. F1000Research . 5, p. 2463.

Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation
Dalby, A.R. and Shamsir, M. 2015. Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation. F1000Research. 4 (589).

The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways
Dalby, A.R. and Iqbal, M. 2015. The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways. PeerJ. 3.

A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin
Dalby, A.R. and Iqbal, M. 2014. A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin. PeerJ. 2.

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Dalby, A.R. and Bailey, I. 2014. The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma. Microarrays. 3 (4), pp. 212-225.

Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level
Dalby, A.R., Emam, I. and Franke, R. 2012. Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level. PLoS ONE. 7 (11), p. e50253.

Identification of Schistosoma mansoni microRNAs
Simões, M.C., Lee, J., Djikeng, A., Cerqueira, G.C., Zerlotini, A., da Silva-Pereira, R.A., Dalby, A.R., LoVerde, P., El-Sayed, N.M. and Oliveira, G. 2011. Identification of Schistosoma mansoni microRNAs. BMC Genomics. 12 (47), pp. 1-17.

Developing stochastic models for spatial inference: bacterial chemotaxis
Yu, Y.D., Choi, Y., Teo, Y.Y. and Dalby, A.R. 2010. Developing stochastic models for spatial inference: bacterial chemotaxis. PLoS ONE. 5 (5), p. e10464.

Permalink - https://westminsterresearch.westminster.ac.uk/item/90wq6/a-comparative-proteomic-analysis-of-the-simple-amino-acid-repeat-distributions-in-plasmodia-reveals-lineage-specific-amino-acid-selection


Share this
Tweet
Email