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. 2007 Oct;16(10):2251-9.
doi: 10.1110/ps.073067607.

Forbidden penta-peptides

Tamir Tuller  1 , Benny Chor, Nathan Nelson
Affiliations

Forbidden penta-peptides

Tamir Tuller et al. Protein Sci. 2007 Oct.

Abstract

There are 3,200,000 amino acid sequences of length 5 (penta-peptides). Statistically, we expect to see a distribution of penta-peptides that is determined by the frequency of the participating amino acids. We show, however, that not only are there thousands of such penta-peptides that are absent from all known proteomes, but many of them are coded for multiple times in the non-coding genomic regions. This suggests a strong selection process that prevents these peptides from being expressed. We also show that the characteristics of these forbidden penta-peptides vary among different phylogenetic groups (e.g., eukaryotes, prokaryotes, and archaea). Our analysis provides the first steps toward understanding the "grammar" of the forbidden penta-peptides.

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Figures

Figure 1.
Figure 1.
(A) Distributions of missing and forbidden penta-peptides with respect to phylogenetic groups. For each group we present the total number of organisms, the total length of the proteomes, the number of missing penta-peptides, the number of forbidden penta-peptides, and the number of forbidden penta-peptides that are present in a sibling phylogentic group. (B) Distributions of forbidden penta-peptides for each phylogenetic group, split according to three ranges of log P-values (nine major squares). The partition of each major square to nine subsquares (a subsquare for each of the phylogenetic groups) is according to the legend on the left. (C) A tree that describes the nine phylogenetic groups. Two phylogenetic groups with a common ancestor in the tree are called “sibling groups” (e.g., the Insects and the Vertebrates). The group “non-mammals” includes the organisms in our data set that are vertebrate but not mammals (two fish and a bird), so it is not monophyletic.
Figure 2.
Figure 2.
(A) Comparing the distribution of amino acids in forbidden penta-peptides and the background distributions in all proteomes in bacteria, archea, and eukaryotes. The square nodes denote the distributions of amino acids in the forbidden penta-peptides. The circular nodes denote the background distributions of amino acids in all proteins. The numbers on each edge denote the symmetric Kullback-Leibler distances (Cover and Thomas 1991) between the amino acid distributions across the edge. Chi-square test of all the distributions (background and in forbidden penta-peptides) gives very significant results, all log P-values >−16. This supports the hypothesis that all the distributions are different. (B) The distribution of amino acid in the penta-peptides that are forbidden with respect to bacteria, archaea, and eukaryotes.
Figure 3.
Figure 3.
Amino acid distribution in penta-peptides forbidden with respect to large phylogenetic subgroups. The numbers on the solid edges denote the symmetric Kullback-Leibler distances (Cover and Thomas 1991) between the amino acid distributions across the edge; the dashed lines denote the symmetric Kullback-Leibler distances between the background distribution of amino acids. Chi-square test of all the distributions (background and in forbidden penta-peptides) gives very significant results, all log P-values >−16. This supports the hypothesis that all the distributions are different. The estimated time from the divergence of each pair of sibling groups appears on the right.
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