Protein–protein interactions of the cytochrome c oxidase DNA barcoding region

Abstract

Enzymatic amplification of homologous regions of DNA using ‘universal’ polymerase chain reaction primers has provided insight into insect systematics, phylogeography, molecular evolution and species identification. One of the more commonly amplified and sequenced regions is a short region of the cytochrome c oxidase subunit I gene (COI), commonly called the barcoding region. COI is one of three mitochondrial‐encoded subunits of complex IV (Cox) of the electron transport chain. In addition to the mitochondrial subunits there are nine nuclear‐encoded subunits of the complex in Drosophila. Whereas a number of phylogenetic biases associated with this region have been examined and the quaternary structure of Cox has been modelled, the influence of protein–protein interactions on the observed patterns of evolution in this barcoding region of insects has never been examined critically. Using a well‐resolved independently derived phylogeny of 38 Diptera species, we examined the homogeneity of the substitution processes within the barcoding region. We show that, within Diptera, amino acid residues interacting with nuclear‐encoded subunits of Cox are evolving at elevated rates across the phylogeny. Furthermore, we show that codon position two is biased by protein–protein interactions. In contrast, third codon positions provide a less biased estimate of genetic variation in the region. This study highlights the need to examine the potential for systematic bias in DNA barcoding regions as part of the critical assessment of evidence in systematics and in biodiversity assessments.

Review and meta-analysis of natural selection in mitochondrial complex I in metazoans

“…; Puslednik et al. ; Zhang and Broughton ; Parmakelis et al. ), although this is likely to become an area of interest as more nuclear sequence becomes available.…”

“…However, interested readers are directed to general introductions to the field of protein co-evolution (Lovell and Robertson 2010;Fares et al 2011). To date, only a handful of co-evolutionary analyses have been applied to mitochondrial complexes (Goldberg et al 2003;Gershoni et al 2010;Garvin et al 2011;Puslednik et al 2012;Zhang and Broughton 2013;Parmakelis et al 2014), although this is likely to become an area of interest as more nuclear sequence becomes available. We performed a statistical coupling analysis (SCA) that identified several sites within the ND5 protein that appeared to strongly co-evolve with other sites that showed a signal for positive selection (Garvin et al 2011).…”

Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System

“…Amino acid substitution tables can be built from different structural environments, for example, solvent accessible and inaccessible regions within proteins of known tertiary structure, and be used for constructing refined and better supported evolutionary trees ( Overington et al 1990 ; Thorne et al 1996 ; Gong and Blundell 2008 ). In addition, if the tertiary structure is known for one of the sequences in an amino acid alignment it can be used to infer the structural environments for the other sequences (e.g., Mizuguchi et al 1998 ; Melvin et al 2008 ; Puslednik et al 2012 ).…”

Differential Expression of Genes that Control Respiration Contribute to Thermal Adaptation in Redband Trout ( Oncorhynchus mykiss gairdneri )

“…2015 ). More than 70 nuclear-encoded subunits of these complexes appear to coevolve with the mitochondrial-encoded subunits ( Gershoni et al 2010 ; Garvin et al 2011 , 2015 ; Puslednik et al 2012 ; Parmakelis et al 2013 ; Zhang and Broughton 2013 ) and it has also been recently shown that complexes I, III, and IV form higher order structures called “supercomplexes” ( Dudkina et al 2011 ; Lapuente-Brun et al 2013 ) that enhance respiration, possibly by decreasing the distances among active sites ( Kadenbach 2012 ) or improving the stability of complexes ( Blaza et al 2014 ).…”