Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs

Abstract

The function of most proteins is not determined experimentally, but is extrapolated from homologs. According to the "ortholog conjecture", or standard model of phylogenomics, protein function changes rapidly after duplication, leading to paralogs with different functions, while orthologs retain the ancestral function. We report here that a comparison of experimentally supported functional annotations among homologs from 13 genomes mostly supports this model. We show that to analyze GO annotation effectively, several confounding factors need to be controlled: authorship bias, variation of GO term frequency among species, variation of background similarity among species pairs, and propagated annotation bias. After controlling for these biases, we observe that orthologs have generally more similar functional annotations than paralogs. This is especially strong for sub-cellular localization. We observe only a weak decrease in functional similarity with increasing sequence divergence. These findings hold over a large diversity of species; notably orthologs from model organisms such as E. coli, yeast or mouse have conserved function with human proteins.

Figure 1. Potential confounding factors in GO analyses.

(A) Authorship bias: average GO Similarity of homologs pairs partitioned according to their provenance. (B) Variation of frequencies of GO terms among the 13 analyzed genomes (50 most common terms on average depicted). (C) Average background frequency for the different subtypes of gene pairs, obtained by computing the average similarity of random pairs from sequences involved in the respective categories. (D) Average GO similarity between homologous gene pairs partitioned according to their GO annotation evidence tags (Experimental: evidence code EXP and children; Uncurated: evidence code IEA; Curated: all other evidence codes). To compute the average similarity for each category, annotations from the other 2 categories are filtered out.

Figure 2. Function similarity of the different types of homologs, in yeasts.

Only pairs of annotations derived from different publications, which do not share any common author, were used. (A) over all Gene Ontology annotations; (B) restricted to the Cellular Component ontology; (C) restricted to the Biological Process ontology; (D) restricted to the Molecular Function ontology. Histograms represent sample density partitioned for each homology type, and error bars represent the 95% confidence interval around the mean.

Figure 3. Function similarity of the different types of homologs, for all 13 genomes.

Only pairs of annotations derived from different publications, which do not share any common author, were used. (A) over all Gene Ontology annotations; (B) restricted to the Cellular Component ontology; (C) restricted to the Biological Process ontology; (D) restricted to the Molecular Function ontology. Histograms represent sample density partitioned for each homology type, and error bars represent the 95% confidence interval around the mean.

Figure 4. Function similarity (all ontologies combined) of corresponding 1∶1 orthologs among human, mouse, and an outgroup.

The outgroups are (A) D. melanogaster, (B) S. cervisiae, and (C) E. coli. Strikingly, function is maintained among 1∶1 orthologs over all evolutionary ranges considered here. Histograms represent sample density partitioned for each homology type, and error bars represent the 95% confidence interval around the mean.