Different sequence patterns in signal peptides from mycoplasmas, other gram-positive bacteria, andEscherichia coli: A multivariate data analysis

Abstract

Signal peptides are essential N-terminal extensions in export proteins, and have a positively charged N-terminus, a hydrophobic central core, and a C-terminal cleavage region. They interact in a consecutive manner with different accessory proteins during the secretion process. Potential patterns or periodicity in the amino acid (aa) sequence were searched, using multivariate techniques, for a large number of signal peptides from mollicutes (mycoplasmas), other Gram-positive bacteria, and Escherichia coli. Mollicutes signal peptides were significantly different from the E. coli and Gram-positive ones by their N-terminal charge, peptide length, and especially, unique periodicities of side chain hydrophobicity and volumes. Their lipoprotein signal peptides were longer than for any other bacteria. Significant differences were also recorded between the other bacterial peptide groups. Specific aa patterns were more related within the signal peptides from several groups of secreted bacillus enzymes, than for all signal peptides from one bacillus species. In E. coli, signal peptides from proteins routed for the various destinations revealed significant and compartment-specific sequence patterns not evident by other methods. This was substantiated from a large number of signal peptide secretion mutants for the E. coli periplasmic space. It is proposed that the differences in aa patterns and side-chain properties are related to the secondary structure sidedness and topology of the signal peptides, and important for specific interactions during the secretion process.

The Bacillus subtilis 168 csn gene encodes a chitosanase with similar properties to a Streptomyces enzyme

“…The N-terminal sequence analysis predicted a cleavage site between Ala-35 and Ala-36. The putative Csn signal peptide length (35 aa), hydrophobicity (0n7; Kyte & Doolittle ;1982) and number of positive charges (4) are closer to those of the streptomycetes group (mean peptide length, 35n5p7n9 ; mean hydrophobicity, 0n56p0n6, mean number of positive charges, 3n9p2n4; Edman et al, 1999) than to those of Bacillus (mean peptide length, 28n2p5n6 ; mean hydrophobicity, 0n93p0n4, mean number of positive charges, 2n0p0n9; Edman et al, 1999). The estimated molecular mass for the 242 amino acid mature Csn was 27n4 kDa.…”

Characterization of novel LPXTG-containing proteins of Staphylococcus aureus identified from genome sequences

“…SasA bears an unusually long signal peptide that probably targets this protein for secretion by the accessory SecA2/SecY2 system (Bensing & Sullam, 2002), although why this should require an accessory secretion system is also unclear. Specific amino acid patterns have previously been identified within signal peptides of proteins of similar function or of proteins destined for different cellular compartments (Edman et al, 1999). Expression of hybrid proteins with different signal peptide types within wild-type and SecA2 mutants could address the effects of the (F/Y)SIRK motif and of the SasA extended signal sequence on efficiency and mechanism of secretion.…”

Signal Peptidases

“…One of the most popular and accessible is the SignalP World Wide Web server (http:// www.cbs.dtu.dk/services/SignalP/), which is based on a combination of several artificial neural networks. , The signal peptides from Gram-positive bacteria are significantly longer than those from other organisms and have a much longer h-region . The average eukaryotic signal peptide is 22.6 amino acids in length, the average Gram-negative signal peptide is 25.1 amino acids in length, and the average Gram-positive signal peptide contains 32.0 amino acids. , The signal peptides from Gram-positive bacteria in general have an n-region containing more lysine and arginine residues than that seen in the signal peptides from Gram-negative bacteria or the eukaryotic ER …”