Figure 1.
The frequencies of PPP and PPG motifs in the complete proteomes of 35 organisms from six kingdoms of life and a phylogenetic analysis of EF-P/aIF5A/eIF5A.
(A) The complete proteomes of 35 species were retrieved from multiple databases as described under Materials and Methods. The PPP and PPG frequencies are indicated as numbers per 10,000 amino acids. The total numbers of PPP motif, PPG motif, ORFs and amino acids in the whole proteome of each organism as well as the frequencies of PPP and PPG motifs (calculated by the division of total PPP or PPG motifs by total amino acids) are listed in Table S1. An asterisk (*) indicates a unicellular eukaryote that can develop into a multicellular organism. (B) An evolutionary relationship of EF-P/aIF5A/eIF5A homologs among 35 different organisms is represented by a phylogenetic tree.
Figure 2.
Comparison of the number and percentage of proteins containing PPP or PPG motifs in M. cuprina, E. coli, G. lamblia, S. cerevisiae, A. thaliana, D. melanogaster, M. musculus, and H. sapiens.
Proteins containing ≥1, ≥2 and ≥3 PPP or PPG units were compiled as described under Materials and Methods and these groups are indicated by unit numbers, ≥1, ≥2 and ≥3 on the Y-axis along with the organism name. The number of proteins in these groups, or in the total pool, is indicated as bars with a value on the right side of each bar and the percent in brackets. The complete lists of genes (name, description, amino acid length and number of PPP or PPG units) encoding proteins with ≥1 PPP or PPG units for each species are provided as Supporting Information (Table S2–Table S17).
Table 1.
Number of consecutive proline repeats in the eight proteomes.
Figure 3.
The distribution of protein lengths and the frequencies of PPP, PPG and proline in proteomes of the five species.
(A) Protein length is expressed as the number of amino acid residues per protein. The distribution of protein lengths of total proteins and of those containing ≥1, ≥2, and ≥3 PPP or PPG units are represented by box and whisker plot. The boxes indicate the 25th and 75th percentile; horizontal line in the box is plotted at the median and the whiskers ranges from minimum length to maximum. The mean is shown by a black dot inside the boxes. Frequencies of (B) PPP, (C) PPG and (D) proline were calculated by division of total number of PPP or PPG units and of proline with total amino acid numbers in each proteome and the actual values are listed in Table 2.
Table 2.
Number and frequencies of PPP, PPG or proline in the five proteomes.
Figure 4.
Comparison of (A) average protein length, the frequency of (B) PPP and of (C) PPG in the total proteome and in orthologous protein pools.
The orthologous protein pools were generated from each species: pool 1, those shared by all five species; pool 2, those shared by four eukaryotes; pool 3, those shared by the fly, mouse and human; pool 4, those shared by mouse and human and the values of ortholog pools were compared with those of the total proteins pool in each species. For each species, pool numbers are indicated, and T denotes total pool. The distribution of protein lengths is shown by box and whisker plots and the frequencies of PPP and PPG were determined as in Fig. 3.
Figure 5.
Number and frequency of tandem repeats of 20 individual amino acids in five proteomes and orthologous protein pools.
(A) Amino acid repeats (≥3 amino acids) were estimated as triplet units. For repeats longer than 3 amino acids, the number of triplet units was assigned as the whole number from division of the consecutive amino acids with 3, as was done for PPP. (B) The frequency of each amino acid triplet unit was determined by division of the total number of triplet units with the total number of amino acids in each proteome listed in Table 2. (C) The frequencies of tandem repeats of Glu, Pro and Leu in four orthologous protein pools used in Fig. 4.
Figure 6.
Functional ontology diagrams of S. cerevisiae genes encoding ≥2 PPP units, or yeast orthologous genes and of human genes encoding PPP or PPG motifs at highest frequency (>0.01).
(A) 76 S. cerevisiae genes encoding highest level of polyproline (listed in Table S18) were classified based on the GO annotations available on SGD. (B) 257 S. cerevisiae orthologous genes (pool 1, genes common from E. coli to human, listed in Table S19) were classified as in (A). (C) 148 human genes encoding PPP at high frequency (>0.01) listed in Table S20 and (D) 79 human genes encoding PPG at the frequency (>0.01) listed in Table S21 were functionally classified.