Phylogenetic Differences in Content and Intensity of Periodic Proteins

Abstract

(247 words): Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-square-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 species reveals striking differences in the proportion of periodic proteins and the intensity of the most significant periodicities. Eukaryotes tend to have a higher proportion of periodic proteins than eubacteria, which in turn tend to have more than archaea. The intensity of periodicity in the most periodic proteins is also greatest in eukaryotes. By contrast, the relatively small group of periodic proteins in archaea also tend to be weakly periodic compared to those of eukaryotes and eubacteria. Exceptions to this general rule are found in those prokaryotes with multicellular life-cycle phases, e.g. Methanosarcina sps. or Anabaena sps., which have more periodicities than prokaryotes in general, and in unicellular eukaryotes, which have fewer than multicellular eukaryotes. The distribution of significantly periodic proteins in eukaryotes is over a wide range of period lengths, whereas prokaryotic proteins typically have a more limited set of period lengths. This is further investigated by repeating the analysis on the NRL-3D database of proteins of solved structure. Some short range periodicities are explicable in terms of basic secondary structure, e.g. alpha helices, while middle range periodicities are frequently found to consist of known short Pfam domains, e.g. leucine-rich repeats, tetratricopeptides or armadillo domains. However, not all can be explained in this way.3 Introduction:

Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty?

“…A survey on internal repeats in protein sequence databases [33] indicated that eukaryotes have a 3-4 fold higher incidence of internal repeats, as compared to prokaryotes or archaea [34]. Furthermore, long proteins often resulted from the concatenation of internal TRs.…”

Distinctive amino acid residue periodicities in terminal sequences of type III and type I secreted proteins from proteobacteria

“…The use of alternative alphabetic representations, i.e., the predefined groups of residues, considerably assists in highlighting periodicities in structural and / or functional properties of proteins that may be obscured in the standard 20-letter alphabet [8,9]. The obtained sets of periodicities at fixed orders of Fourier transform [11,13] therefore represent a body of periodicity profiles where each terminal sequence of secreted proteins (Table 1) has one profile for each predefined group of residues.…”

“…Subset B represented: neutral and weakly hydrophobic (A, G, P, S, T), hydrophilic acid (D, E, N, Q), hydrophilic basic (H, K, R), hydrophobic (I, L, M, V) and hydrophobic aromatic (F, W, Y) residues from Dayhoff alternative alphabetic 6-letter representation [9,15] of amino acids (letters C, D, E, F, G, respectively). Cysteine as the remaining separate group (letter A in Dayhoff alphabet) was not considered due to its presence in very few terminal fragments of proteins under study (Table 1).…”

“…It is generally accepted that protein molecules often have repetitive amino acid sequences of regular or latent (cryptic) periodicity [8][9][10][11]. The study of protein sequence periodicity is one of many approaches to find structural peculiarities of amino acid sequences and their relations with the spatial organization and function of proteins [10].…”

XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences

“…Nucleotide repeats occurring in protein coding genes can result in protein sequences containing repetitive elements. Though less studied than DNA repeats, peptide repeats are likewise known to be widespread in nature [ 6 - 8 ]. Peptide TRs impart a modular architecture to proteins and are found in important structural proteins such as animal collagens and keratins, insect and spider silks, plant cell wall extensins, and the proteins that form adhesive plaques and byssal threads of bivalve mussels [ 9 - 13 ].…”