Abstract
BackgroundProtein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Such domain fusion and recombination events are predicted to occur only once for a given multidomain architecture. However, other scenarios may be relevant in the evolution of specific proteins, such as convergent evolution of multidomain architectures. With this in mind, we study glutaredoxin (GRX) domains, because these domains of approximately one hundred amino acids are widespread in archaea, bacteria and eukaryotes and participate in fusion proteins. GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear.ResultsIn this work we analyze the distribution and evolution of GRX proteins in archaea, bacteria and eukaryotes. We study over one thousand GRX proteins, each containing at least one GRX domain, from hundreds of different organisms and trace the origin and evolution of the GRX domain within the tree of life.ConclusionOur results suggest that single domain GRX proteins of the CGFS and CPYC classes have, each, evolved through duplication and divergence from one initial gene that was present in the last common ancestor of all organisms. Remarkably, we identify a case of convergent evolution in domain architecture that involves the GRX domain. Two independent recombination events of a TRX domain to a GRX domain are likely to have occurred, which is an exception to the dominant mechanism of domain architecture evolution.
Highlights
Protein domains represent the basic units in the evolution of proteins
Because archaea only have a small number of GRX proteins of the CGFS class, we show the results for archaea GRXs of the CPYC class only
Because GRXs are present in archaea, bacteria and eukaryotes, our results suggest that both the CPYC class and the CGFS class of GRXs were already present in the last common ancestor (LCA)
Summary
Protein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Statistical analysis of known multidomain proteins has shown that a) there is a strong bias for individual domains involved in recombination and fusion events to be short [2], and b) some specific sets of recombined domains (supra domains) participate in further recombination and fusion events [3] This provides a model for the dominant (page number not for citation purposes). A recent theory proposes that, during major evolutionary transitions, evolution is biphasic, further complicating the model of protein evolution [7] According to this view, in an initial post-transition phase, large scale horizontal gene transfer (HGT) would occur. In an initial post-transition phase, large scale horizontal gene transfer (HGT) would occur This would be followed by a second phase where the more common mechanisms for protein evolution become dominant. It is of interest to analyze the evolution of a specific type of protein domain in order to assess the importance of the evolutionary mechanisms described above in the evolution of that domain
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