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Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats.

Fankhauser N, Nguyen-Ha TM, Adler J, Mäser P - Proteome Sci (2007)

Bottom Line: They find immunological applications in serodiagnostics and vaccine development.Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites.Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Bern, Institute of Cell Biology, Baltzerstrasse 4, CH-3012 Bern, Switzerland. pascal.maeser@izb.unibe.ch.

ABSTRACT

Background: Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms.

Results: We have developed Reptile http://reptile.unibe.ch, a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites.

Conclusion: Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at http://genomics.unibe.ch/dora.

No MeSH data available.


Related in: MedlinePlus

Potential N-glycosylation sites in the repeats. The percentage of asparagines that are in glycosylation consensus (Asn-not Pro-Ser/Thr) is plotted for repeats of P < 10-10 and for the remainders of the respective proteomes. Bars indicate the median. The organism with 30% of asparagines in the repeats in N-glycosylation consensus is T. brucei.
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Figure 3: Potential N-glycosylation sites in the repeats. The percentage of asparagines that are in glycosylation consensus (Asn-not Pro-Ser/Thr) is plotted for repeats of P < 10-10 and for the remainders of the respective proteomes. Bars indicate the median. The organism with 30% of asparagines in the repeats in N-glycosylation consensus is T. brucei.

Mentions: To further characterize the repeats, we investigated which amino acids are over- or underrepresented in repeats of P < 10-10 compared to the rest of the respective proteome. Overall, the amino acid composition of the repeats was more biased in eukaryotes than in bacteria (Figure 2). Small amino acids occurred more frequently in the repeats than large ones in both eukaryotes and prokaryotes. Hydrophobic residues were underrepresented in the repeats, with the exception of leucine, which in bacterial repeats was even overrepresented (p < 0.0001, two-tailed Wilcoxon signed rank test). Strongly overrepresented in the repeats were alanine (p < 0.0001) in bacteria and serine (p = 0.0001) in eukaryotes (Figure 2). Thus "cheap" amino acids seem to be preferred over energetically expensive ones. Interestingly, asparagine was overrepresented in the repeats from eukaryotes (p = 0.057) but not from bacteria (Figure 2), suggesting that asparagines might be preferentially glycosylated in repeats. Contrary to expectation though, the probability of an asparagine to be in N-glycosylation consensus was significantly lower in repeats than in non-repetitive sequences (Figure 3). This was the case for free-living eukaryotes (p = 0.004) as well as for parasites (p = 0.027). The only exception was T. brucei, where the likelihood of an asparagine to be in N-glycosylation consensus was three-fold higher in repetitive than in non-repetitive sequences (Figure 3).


Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats.

Fankhauser N, Nguyen-Ha TM, Adler J, Mäser P - Proteome Sci (2007)

Potential N-glycosylation sites in the repeats. The percentage of asparagines that are in glycosylation consensus (Asn-not Pro-Ser/Thr) is plotted for repeats of P < 10-10 and for the remainders of the respective proteomes. Bars indicate the median. The organism with 30% of asparagines in the repeats in N-glycosylation consensus is T. brucei.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2254594&req=5

Figure 3: Potential N-glycosylation sites in the repeats. The percentage of asparagines that are in glycosylation consensus (Asn-not Pro-Ser/Thr) is plotted for repeats of P < 10-10 and for the remainders of the respective proteomes. Bars indicate the median. The organism with 30% of asparagines in the repeats in N-glycosylation consensus is T. brucei.
Mentions: To further characterize the repeats, we investigated which amino acids are over- or underrepresented in repeats of P < 10-10 compared to the rest of the respective proteome. Overall, the amino acid composition of the repeats was more biased in eukaryotes than in bacteria (Figure 2). Small amino acids occurred more frequently in the repeats than large ones in both eukaryotes and prokaryotes. Hydrophobic residues were underrepresented in the repeats, with the exception of leucine, which in bacterial repeats was even overrepresented (p < 0.0001, two-tailed Wilcoxon signed rank test). Strongly overrepresented in the repeats were alanine (p < 0.0001) in bacteria and serine (p = 0.0001) in eukaryotes (Figure 2). Thus "cheap" amino acids seem to be preferred over energetically expensive ones. Interestingly, asparagine was overrepresented in the repeats from eukaryotes (p = 0.057) but not from bacteria (Figure 2), suggesting that asparagines might be preferentially glycosylated in repeats. Contrary to expectation though, the probability of an asparagine to be in N-glycosylation consensus was significantly lower in repeats than in non-repetitive sequences (Figure 3). This was the case for free-living eukaryotes (p = 0.004) as well as for parasites (p = 0.027). The only exception was T. brucei, where the likelihood of an asparagine to be in N-glycosylation consensus was three-fold higher in repetitive than in non-repetitive sequences (Figure 3).

Bottom Line: They find immunological applications in serodiagnostics and vaccine development.Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites.Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Bern, Institute of Cell Biology, Baltzerstrasse 4, CH-3012 Bern, Switzerland. pascal.maeser@izb.unibe.ch.

ABSTRACT

Background: Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms.

Results: We have developed Reptile http://reptile.unibe.ch, a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites.

Conclusion: Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at http://genomics.unibe.ch/dora.

No MeSH data available.


Related in: MedlinePlus