Flanking signal and mature peptide residues influence signal peptide cleavage

Abstract

Background: Signal peptides (SPs) mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical, food and beverage and biotechnology industries yet our understanding of these peptides remains limited. This paper examines the most common type of signal peptides cleavable by the endoprotease signal peptidase I (SPase I), and the residues flanking the cleavage sites of three groups of signal peptide sequences, namely (i) eukaryotes (Euk) (ii) Gram-positive (Gram+) bacteria, and (iii) Gram-negative (Gram-) bacteria.

Results: In this study, 2352 secretory peptide sequences from a variety of organisms with amino-terminal SPs are extracted from the manually curated SPdb database for analysis based on physicochemical properties such as pI, aliphatic index, GRAVY score, hydrophobicity, net charge and position-specific residue preferences. Our findings show that the three groups share several similarities in general, but they display distinctive features upon examination in terms of their amino acid compositions and frequencies, and various physico-chemical properties. Thus, analysis or prediction of their sequences should be separated and treated as distinct groups.

Conclusion: We conclude that the peptide segment recognized by SPase I extends to the start of the mature protein to a limited extent, upon our survey of the amino acid residues surrounding the cleavage processing site. These flanking residues possibly influence the cleavage processing and contribute to non-canonical cleavage sites. Our findings are applicable in defining more accurate prediction tools for recognition and identification of cleavage site of SPs.

Figure 1

Boxplot illustrating the SPs distribution found in selected organisms and groups (Eukaryotes, Gram-positive and Gram-negative bacteria). Mean length (■) and median (-, grey bar) values are indicated.

Figure 2

Signal peptides from the three organism groups measured based on their length. The Y-axis shows the frequency of occurrences for a specific length of signal peptide while the X-axis depicts the various lengths.

Figure 3

Sequencelogos 37 of eukaryotic and bacterial (Gram-positive and Gram-negative) signal and mature peptides starting from posistion -35 to +5.[] The interface between position -1/+1 represents the SPase I cleavage site. The amino-acid residues are grouped and coloured based on the R group of their side-chain. Red denotes polar acidic amino-acid residues (D, E); Blue denotes polar basic amino-acid residues (K, R, H); Green denotes polar uncharged amino-acid residues (C, G, N, Q, S, T, Y); Black denotes non-polar hydrophobic amino-acid residues (A, F, I, L, M, P, V, W).

Figure 4

Net charge calculations of signal and mature peptides for the three groups of organisms. The net charges are grouped into three classes: positive (>0), neutral (= 0) and negative (<0) charge. The numbers represent the frequencies of which the charges are observed.

Figure 5

Comparison of the isoelectric point (pI), aliphatic index, GRAVY value and mean charge among the three organism groups. Data are represented by squares which denote SP while triangles denote MP.