Genome-Wide Analyses and Functional Classification of Proline Repeat-Rich Proteins: Potential Role of eIF5A in Eukaryotic Evolution

Abstract

The eukaryotic translation factor, eIF5A has been recently reported as a sequence-specific elongation factor that facilitates peptide bond formation at consecutive prolines in Saccharomyces cerevisiae, as its ortholog elongation factor P (EF-P) does in bacteria. We have searched the genome databases of 35 representative organisms from six kingdoms of life for PPP (Pro-Pro-Pro) and/or PPG (Pro-Pro-Gly)-encoding genes whose expression is expected to depend on eIF5A. We have made detailed analyses of proteome data of 5 selected species, Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, Mus musculus and Homo sapiens. The PPP and PPG motifs are low in the prokaryotic proteomes. However, their frequencies markedly increase with the biological complexity of eukaryotic organisms, and are higher in newly derived proteins than in those orthologous proteins commonly shared in all species. Ontology classifications of S. cerevisiae and human genes encoding the highest level of polyprolines reveal their strong association with several specific biological processes, including actin/cytoskeletal associated functions, RNA splicing/turnover, DNA binding/transcription and cell signaling. Previously reported phenotypic defects in actin polarity and mRNA decay of eIF5A mutant strains are consistent with the proposed role for eIF5A in the translation of the polyproline-containing proteins. Of all the amino acid tandem repeats (≥3 amino acids), only the proline repeat frequency correlates with functional complexity of the five organisms examined. Taken together, these findings suggest the importance of proline repeat-rich proteins and a potential role for eIF5A and its hypusine modification pathway in the course of eukaryotic evolution.

Biological Relevance and Therapeutic Potential of the Hypusine Modification System

“…Construction and Analysis of Protein-Protein Interaction Networks-For the construction of protein-protein interaction (PPI) networks for PPP (Pro-Pro-Pro)-and PPG (Pro-Pro-Gly)-rich proteins, genes with Ͼ1 PPP unit and Ͼ1 PPG unit were extracted as described by Mandal et al (35). The number of PPP and PPG units were defined by the whole number of consecutive prolines divided by 3, as described recently (35).…”

“…The number of PPP and PPG units were defined by the whole number of consecutive prolines divided by 3, as described recently (35). That means that 3-5 consecutive prolines were all counted as 1 PPP unit and 6 -8 consecutive prolines as 2 PPP units and so on.…”

The translation factor eIF5A and human cancer

“…The frequency of such motifs appears greater in humans, where about 10,000 motifs are found in 18,000 proteins [45]. In a genome-wide search for proteins with Pro-Pro-Pro and Pro-Pro-Gly sequences, the frequency of such motifs was found to be progressively higher as the organisms increased in complexity, suggesting a role for eIF5A in eukaryotic evolution [46]. …”

Deoxyhypusine Modification of Eukaryotic Translation Initiation Factor 5A (eIF5A) Is Essential for Trypanosoma brucei Growth and for Expression of Polyprolyl-containing Proteins

“…The covalent modifications of eIF5A with hypusine and of elongation factor P by lysinylation were both necessary to the function of these proteins in alleviating the ribosome stalling that occurs at these motifs. Although eIF5A/elongation factor P function in the translation of only a subset of proteins, the percentage of proteins containing proline-stalling motifs is high, and it is greater in eukaryotes than in bacteria (33% (human) versus 5.8% (Escherichia coli)) (14,23). Although it is still yet to be determined whether poly(Pro) proteins are involved in the control of specific cellular processes, in yeast it was found that a high fraction of proteins involved in cytoskeleton organization and active polarization contains poly(Pro) tracts (24).…”