Figure 1.1: Production: General tendency (rough trend)
Protein elongation can occur in many ways, such as domain duplication or insertion and as recruitment of a transposable element fragment into the coding region, and it is believed to be a general tendency in protein evolution. Indeed, a previous study showed that yeast proteins are, on average, longer than their orthologs in bacteria, and in this study, we found that proteins in yeast, nematode, Drosophila, human, and Arabidopsis are, on average, longer than their orthologs in Escherichia coli. Surprisingly, however, we found conservation of protein sequence length across eukaryotic kingdoms. We collected 1,252 orthologous proteins from yeast, nematode, Drosophila, human, and Arabidopsis and found that the total length of these proteins is very similar among the five species and that there is no general tendency for a protein to increase or decrease in length. Furthermore, although paralogous proteins tend to undergo more sequence-length changes, there is also no general tendency for length increase. However, proteins that are commonly shared by Drosophila and human but not by yeast are, on average, substantially longer than proteins that are shared by yeast, Drosophila, and human. This is a puzzle that begs for an answer.
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shows more detailed comparisons of the human proteins with the ancestral proteins of yeast, nematode, Drosophila, human, and Arabidopsis. The length differences between human and ancestral protein sequences are nearly normally distributed around 0, indicating that there is a nearly equal probability for a protein to increase or decrease in length. Note that 48.7% of the 1,252 human proteins have not changed or have changed less than ±10 amino acids since their separation from the ancestral proteins () and that 68.4% of these human proteins differ from their ancestral counterparts by less than ±5% of the ancestral sequence lengths (). The same patterns are found for the 1,252 proteins in yeast, nematode, Drosophila, and Arabidopsis (data not shown). These observations suggest that there is no general tendency for eukaryotic proteins to increase in sequence length.