Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors

Abstract

In view of the fact that appearance of novel protein domain architectures (DA) is closely associated with biological innovations, there is a growing interest in the genome-scale reconstruction of the evolutionary history of the domain architectures of multidomain proteins. In such analyses, however, it is usually ignored that a significant proportion of Metazoan sequences analyzed is mispredicted and that this may seriously affect the validity of the conclusions. To estimate the contribution of errors in gene prediction to differences in DA of predicted proteins, we have used the high quality manually curated UniProtKB/Swiss-Prot database as a reference. For genome-scale analysis of domain architectures of predicted proteins we focused on RefSeq, EnsEMBL and NCBI's GNOMON predicted sequences of Metazoan species with completely sequenced genomes. Comparison of the DA of UniProtKB/Swiss-Prot sequences of worm, fly, zebrafish, frog, chick, mouse, rat and orangutan with those of human Swiss-Prot entries have identified relatively few cases where orthologs had different DA, although the percentage with different DA increased with evolutionary distance. In contrast with this, comparison of the DA of human, orangutan, rat, mouse, chicken, frog, zebrafish, worm and fly RefSeq, EnsEMBL and NCBI's GNOMON predicted protein sequences with those of the corresponding/orthologous human Swiss-Prot entries identified a significantly higher proportion of domain architecture differences than in the case of the comparison of Swiss-Prot entries. Analysis of RefSeq, EnsEMBL and NCBI's GNOMON predicted protein sequences with DAs different from those of their Swiss-Prot orthologs confirmed that the higher rate of domain architecture differences is due to errors in gene prediction, the majority of which could be corrected with our FixPred protocol. We have also demonstrated that contamination of databases with incomplete, abnormal or mispredicted sequences introduces a bias in DA differences in as much as it increases the proportion of terminal over internal DA differences. Here we have shown that in the case of RefSeq, EnsEMBL and NCBI's GNOMON predicted protein sequences of Metazoan species, the contribution of gene prediction errors to domain architecture differences of orthologs is comparable to or greater than those due to true gene rearrangements. We have also demonstrated that domain architecture comparison may serve as a useful tool for the quality control of gene predictions and may thus guide the correction of sequence errors. Our findings caution that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. A reassessment of the DA evolution of orthologous and paralogous proteins is presented in an accompanying paper [1].

MisPred: a resource for identification of erroneous protein sequences in public databases

“…Domain architecture deviation. Rationale: changes in domain architecture of proteins are relatively rare evolutionary events (whereas the error rate in gene prediction is relatively high); therefore, if we find a hypothetical protein with a ‘novel’ domain architecture, then this is more likely to reflect an error in gene prediction than true innovation (10). (It must be pointed out that MisPred tool 11 is not yet available in searches on the MisPred website and that data generated with this tool are not yet deposited in the MisPred database.…”

Evolution of Protein Domain Architectures

“…Moreover, they demonstrated that terminal domain loss seldom involves losing only part of a domain, or rather, that such partial losses quickly progress into loss of the entire domain. However, it is important to ensure such observations are not confounded by cases where errors in gene boundary recognition make domain detection less accurate [73].…”

“…A detailed case study was made recently of netrin domaincontaining proteins, where polyphyletic evolution in metazoa seems well-supported [88]; these authors further suggest the term merology for such polyphyletic evolution. A series of papers by Nagy and Patthy et al [73,89,90] further elaborates on challenges faced within this line of research; they report strong confounding influence of gene prediction errors. They further propose the term epaktology for gene similarity resulting from the independent acquisition of two proteins by the same additional domain.…”

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs

“…As pointed out in the accompanying paper [4], reliable reconstruction of the evolutionary history of DA of multidomain proteins requires that the protein sequences compared are valid, complete and correct and that the evolutionary relationship of the multidomain proteins compared is correctly defined.…”