ParSeq: searching motifs with structural and biochemical properties

Schmollinger, Martin; Fischer, Igor; Nerz, Christiane; Pinkenburg, Simon; Götz, F.; Kaufmann, Michael; Lange, Klaus-Jörn; Reuter, Rolf; Zell, Andreas

doi:10.1093/bioinformatics/bth083

Cited by 10 publications

(5 citation statements)

References 2 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genome of S. aureus N315 was screened for genes encoding putative lipoproteins by using the ParSeq program (58). The search criteria were as follows: methionine at position 1, followed by 2 to 9 amino acids with at least one positive charge, followed by a hydrophobic stretch of 7 to 36 More than 70 putative lipoproteins were identified, 55 of which contained a signal peptide of typical length.…”

Section: Resultsmentioning

confidence: 99%

Staphylococcus aureusDeficient in Lipidation of Prelipoproteins Is Attenuated in Growth and Immune Activation

et al. 2005

View full text Add to dashboard Cite

A lipoprotein diacylglyceryl transferase (lgt) deletion mutant of Staphylococcus aureus SA113 was constructed. The lipoprotein and prelipoprotein expression, the growth behavior, and the ability of the mutant to elicit an immune response in various host cells were studied. In the wild type, the majority of [ 14 C]palmitate-labeled lipoproteins were located in the membrane fraction, although some lipoproteins were also present on the cell surface and in the culture supernatant. The lgt mutant completely lacked palmitate-labeled lipoproteins and released high amounts of some unmodified prelipoproteins, e.g., the oligopeptide-binding protein OppA, the peptidyl-prolyl cis-trans isomerase PrsA, and the staphylococcal iron transporter SitC, into the culture supernatant. The growth of the lgt mutant was hardly affected in rich medium but was retarded under nutrient limitation. The lgt mutant and its crude lysate induced much fewer proinflammatory cytokines and chemokines in human monocytic (MonoMac6), epithelial (pulmonary A549), and endothelial (human umbilical vein endothelial) cells than the wild type. However, in whole blood samples, the culture supernatant of the lgt mutant was equal or even superior to the wild-type supernatant in tumor necrosis factor alpha induction. Lipoprotein fractionation experiments provided evidence that a small proportion of the mature lipoproteins are released by the S. aureus wild type despite the lipid anchor and are trapped in part by the cell wall, thereby exposing the immune-activating lipid structure on the cell surface. Bacterial lipoproteins appear to be essential for a complete immune stimulation by gram-positive bacteria.

show abstract

Section: Resultsmentioning

confidence: 99%

Staphylococcus aureusDeficient in Lipidation of Prelipoproteins Is Attenuated in Growth and Immune Activation

et al. 2005

View full text Add to dashboard Cite

show abstract

“…On average, the number of Lpp in Staphylococcus aureus is between 55 and 70. For example, the genome of S. aureus N315 encodes about 55 putative Lpp (11,12), while in S. aureus USA300 there are roughly 63 Lpp identified by the PRED-LIPO program. Approximately 50% of the Lpp were annotated as transporters for amino acids, peptides, iron, zinc, or molybdenum or as chaperones.…”

mentioning

confidence: 99%

Lipoproteins of Gram-Positive Bacteria: Key Players in the Immune Response and Virulence

Nguyen

Götz

2016

Microbiol Mol Biol Rev

152

170

View full text Add to dashboard Cite

SUMMARYSince the discovery in 1973 of the first of the bacterial lipoproteins (Lpp) inEscherichia coli, Braun's lipoprotein, the ever-increasing number of publications indicates the importance of these proteins. Bacterial Lpp belong to the class of lipid-anchored proteins that in Gram-negative bacteria are anchored in both the cytoplasmic and outer membranes and in Gram-positive bacteria are anchored only in the cytoplasmic membrane. In contrast to the case for Gram-negative bacteria, in Gram-positive bacteria lipoprotein maturation and processing are not vital. Physiologically, Lpp play an important role in nutrient and ion acquisition, allowing particularly pathogenic species to better survive in the host. Bacterial Lpp are recognized by Toll-like receptor 2 (TLR2) of the innate immune system. The important role of Lpp in Gram-positive bacteria, particularly in the phylumFirmicutes, as key players in the immune response and pathogenicity has emerged only in recent years. In this review, we address the role of Lpp in signaling and modulating the immune response, in inflammation, and in pathogenicity. We also address the potential of Lpp as promising vaccine candidates.

show abstract

“…The Tat SP of peroxidase was identified in staphylococcal genomes by use of the software tool ParSeq, a program that combines the search for motifs with a search for certain structural properties (40). The search pattern used was X 1 RRX 2 X 3 X 4 , in which the amino acid at position X 1 had a hydrophobicity score of Ͻ0.26, X 2 had to be one of certain residues (ARKDEF), X 3 had a hydrophobicity score of Ͼ0.77 (positively charged residues were excluded from this position), and X 4 was one of certain residues (ILVMF).…”

Section: Identification Of Tat Substrates By Parseq a Modified Tatfimentioning

confidence: 99%

Role of the Twin-Arginine Translocation Pathway in Staphylococcus

Biswas

Nerz

et al. 2009

J Bacteriol

View full text Add to dashboard Cite

In Staphylococcus, the twin-arginine translocation (Tat) pathway is present only in some species and is composed of TatA and TatC. The tatAC operon is associated with the fepABC operon, which encodes homologs to an iron-binding lipoprotein, an iron-dependent peroxidase (FepB), and a high-affinity iron permease. The FepB protein has a typical twin-arginine (RR) signal peptide. The tat and fep operons constitute an entity that is not present in all staphylococcal species. Our analysis was focused on Staphylococcus aureus and S. carnosus strains. Tat deletion mutants (⌬tatAC) were unable to export active FepB, indicating that this enzyme is a Tat substrate. When the RR signal sequence from FepB was fused to prolipase and protein A, their export became Tat dependent. Since no other protein with a Tat signal could be detected, the fepABC-tatAC genes comprise not only a genetic but also a functional unit. We demonstrated that FepABC drives iron import, and in a mouse kidney abscess model, the bacterial loads of ⌬tatAC and ⌬tat-fep mutants were decreased. For the first time, we show that the Tat pathway in S. aureus is functional and serves to translocate the iron-dependent peroxidase FepB.The Sec pathway is the major secretion system that exports the majority of extracytosolic proteins in pro-and eukaryotes. Proteins are translocated through this pathway in a more or less unfolded state. A second protein export pathway was identified first in the chloroplast thylakoid membrane (8) and later in several bacteria (4,14,35). This pathway has been designated the twin-arginine translocation system (Tat), as the preproteins targeted to this pathway carry a characteristic amino acid motif, including two consecutive arginine residues, which are essential for the recognition by the Tat translocon. The Tat pathway operates independently of the Sec pathway and exports exoproteins across the bacterial cytoplasmic membrane, apparently in a fully folded conformation (3). Many of these proteins are complexed with cofactors.Studies of several bacterial species, including Escherichia coli (37), Bacillus subtilis (22, 23), Pseudomonas aeruginosa (31), Legionella pneumophila (10, 11), and Mycobacterium smegmatis (29), have demonstrated that they possess a functional Tat export pathway. In E. coli, the TatA, TatB, and TatC proteins have been demonstrated to be essential for Tat-dependent protein translocation (4). However, several bacterial and archaeal species lack a TatB-like protein. For example, the B. subtilis genome encodes three TatA-and two TatC-like proteins. Thus, at least one copy of the TatA homologue and one copy of the TatC homologue are required for a functional Tat pathway. In Bacillus subtilis, several proteins were predicted that could potentially use the Tat pathway, as their signal peptides (SPs) contain RR or KR motifs. However, proteomic analysis revealed that 13 proteins with potential RR/KR SPs were Tat independent, showing that the Tat machinery does not recognize their RR/KR motifs. In fact, only the phosphodiest...

show abstract

ParSeq: searching motifs with structural and biochemical properties

Abstract: http://www-pr.informatik.uni-tuebingen.de/parseq

Cited by 10 publications

References 2 publications

Staphylococcus aureusDeficient in Lipidation of Prelipoproteins Is Attenuated in Growth and Immune Activation

Staphylococcus aureusDeficient in Lipidation of Prelipoproteins Is Attenuated in Growth and Immune Activation

Lipoproteins of Gram-Positive Bacteria: Key Players in the Immune Response and Virulence

Role of the Twin-Arginine Translocation Pathway in Staphylococcus

Contact Info

Product

Resources

About