With active studying of disordered regions and their function we focus our attention on manifold long repeats of one amino acid (homorepeats) (see Fig.1). Our database includes 122 proteomes, 97 eukaryotic and 25 bacterial ones that can be divided into 9 kingdoms and 5 phyla of bacteria. Considering these proteomes we have 1 449 561 protein sequences. The database includes 771 786 of proteins with GO annotations. It has been found that leucine repeats were especially abundant in the «Receptor and/or Membrane» group, glutamine and alanine repeats in Transcription factor and/or Development, and lysine repeats in Metabolism. HRaP can be used to analyze evolution differences between proteins from different proteomes and connections of these regions with some definite functions.

Figure 1. Dependence of the number of proteins that contain homorepeats of different lengths for 20 amino acids in four proteomes.

To see the occurrence of a homorepeat, at the first step the user should choose a proteome among 122 considered ones, and then at the second step choose the investigated homorepeat with the given length or pattern. After that the list of proteins with the given homorepeat or pattern appears with GO annotations (if such is determined). Usually, long proteins contain a homorepeat or several different homorepeats. If several homorepeats and patterns exist in a protein then all these regions will be marked by different colors in the sequence. In the section HomoRepeats or Patterns you can find the occurrence of homorepeats with different lengths (or patterns) for all 122 proteomes. The patterns and homorepeats assotiated with the functions are presented in section GO annotations. Figure 2 presents a comparative analysis of the number of proteins containing homorepeats of 6 residues long in 122 proteomes.

Figure 2. Occurrence of 20 homorepeats of 6 residues long in 122 proteomes.

We can suggest that homorepeats and patterns are responsible for common functions of nonhomologous, unrelated proteins from different organisms. To confirm this, we have done the following analysis. All possible GO annotations for proteins were taken for the set of 122 proteomes. The number of different kinds of all annotations is 11 313. Proteins without annotations were combined into the class «absent annotation». The number of proteins including at least one pattern from the last version of the library (171 patterns, [1]) was calculated, «N_pt». Also the number of proteins including homorepeats of length 6 or larger was calculated, «N_hm». The number of proteins with the given annotation was calculated as well and indicated in the column «N_go». For each pattern or homorepeat we can calculate the frequency of occurrence in all proteins:

Taking into account 171 patterns, 20 homorepetas, and 11 313 kinds of GO annotations, we have 11 313*(171+20) = 2 160 783 ≈ 2·10⁶ possible combinations. Therefore, we should not pay attention on the events the probability of which is higher than 10⁻⁷. Taking this into account the probabilities p_z were colored according to the following conditions: green color corresponds to p_z<10⁻¹⁵, light green color corresponds to 10⁻¹⁵ ≤ p_z < 10⁻¹⁰, and light yellow color corresponds to 10⁻¹⁰ ≤ p_z < 10⁻⁷.

We also calculated the probabilities:

The patterns and homorepeats are sorted by p₁ and p₂ using the following colors: green — p₁>0.5, light green — 0.3<p₁<0.5, and light yellow — 0.1<p₁<0.3.

Tables

For each proteome we calculated a set of 109 values reflecting the number of proteins containing at least one disordered pattern for each of the 109 patterns from the library (set 2010). Then considering all possible pairs of proteomes, the correlation coefficients between the 109 values have been calculated resulting in the matrix of correlation coefficients. The correlation coefficient was calculated for each pair of proteomes separately, and then averaging has been done inside each kingdom and phylum. Similar values have been calculated for a set of 141 disordered patterns (set 2011), 171 disordered patterns (set 2012) and 20 homorepeats. A comparative analysis of the number of proteins containing homorepeats of 6 and more residues long in 122 proteomes has demonstrated that the correlation coefficients between numbers of proteins, where at least once a homorepeat of six and more residues long for each of the 20 types of amino acid residues appears in 9 kingdoms of eukaryota and 5 phyla of bacteria, are higher inside the considered kingdom than between them. The same result is valid for the 109 disordered selected patterns (set 2010) [1], the 141 disordered selected patterns (set 2011) [2], and the 171 disordered selected patterns (set 2012) [3].

1. M.Yu. Lobanov, O.V. Galzitskaya, Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes. Molecular BioSystems, 8 (2012) 327—337.
2. L. Mularoni, A. Ledda, M. Toll-Riera, M.M. Alba, Natural selection drives the accumulation of amino acid tandem repeats in human proteins, Genome Res., 20 (2010) 745—754.
3. M.Yu. Lobanov, E.I. Furletova, N.S. Bogatyreva, M.A. Roytberg, O.V. Galzitskaya, Library of disordered patterns in 3D protein structures, PLoS Computational Biology, 6 (10), (2010) e1000958.