Proteomic signatures: Amino acid and oligopeptide compositions differentiate among phyla

Abstract

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.

Counting sulfhydryls and disulfide bonds in peptides and proteins using mercurial ions as an MS-tag

“…PC 3 was prepared as described previously [14]. PC 3 (50 L, 15 M) in Tris-buffer (20 mM, pH 7) was mixed with 5 L CH 3 HgCl methanol solution (30 mM) and 5 L HOOCOC 6 H 4 OHgOH (30 mM in 1 mM NaOH solution) and then the mixture was incubated in the dark at room temperature for 20 min. Before derivatization, the disulfide bonds in lysozyme (50 L, 10 M) were reduced with TCEP (10ϫ in excess compared to the disulfide bonds) at room temperature for 20 min.…”

“…␤-Lactoglobulin (5 M) was directly mixed with a 2.5-fold excess amount of CH 3 HgCl to react with free sulfhydryl. Then the solution was heated in 8 M urea to denature the labeled ␤-lactoglobulin and treated in the same way as lysozyme to label disulfide bonds at room temperature for 1 h.…”

“…PC 3 , which has the structure (␥OGluOCys) 3 OGly, was chosen as a model peptide (Figure 2a). Although HOOCOC 6 H 4 OHg ϩ has been used to label OSHs, we always obtain incompletely derivatized PC 3 (data not shown) because of the steric hindrance arising from the close arrangement of OSHs in the molecule.…”

“…Although HOOCOC 6 H 4 OHg ϩ has been used to label OSHs, we always obtain incompletely derivatized PC 3 (data not shown) because of the steric hindrance arising from the close arrangement of OSHs in the molecule. Considering that the dissociation constant between CH 3 Hg ϩ and cysteine is as low as 10 Ϫ20.3 [15], that the ratio of the dissociation constants of [CH 3 …”

“…Therefore, identification of OSH and OSOSO can give valuable information concerning the relationship between the structure and function of a protein. On the other hand, frequency analysis of amino acids in the proteomes of fully sequenced genomes shows that cysteine is one of the most rarely used amino acids in proteins across all superkingdoms [3]. Because of their ubiquity but lower abundance, OSHs provide a greater opportunity for saturating the reactive sites, resulting in more reproducible quantitative labeling and less impact on the proteins.…”