In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens
Pentraxin-3 (PTX-3) protein is an evolutionary conserved protein that acts as a soluble pattern-recognition receptor for pathogens and plays important role in innate immune response. It recognizes various pathogens by interacting with extracellular moieties such as glactomannan of conidia (Aspergill...
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doaj-68d2428005414663b4dd3418558539ca2020-11-24T22:31:17ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2016-02-01710.3389/fmicb.2016.00192178160In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogensRaman eThakur0Jata eShankar1JUIT Waknaghat Himachal Pradesh IndiaJUIT Waknaghat Himachal Pradesh IndiaPentraxin-3 (PTX-3) protein is an evolutionary conserved protein that acts as a soluble pattern-recognition receptor for pathogens and plays important role in innate immune response. It recognizes various pathogens by interacting with extracellular moieties such as glactomannan of conidia (Aspergillus fumigatus), lipopolysaccharide of Pseudomonas aeruginosa, Streptococcus pneumonia and Salmonella typhimurium. Thus, PTX-3 protein helps to clear these pathogens by activating downstream innate immune process. In this study, computational methods were used to analyze various non-synonymous single nucleotide polymorphisms (nsSNPs) in PTX-3 gene. Three different databases were used to retrieve SNP data sets followed by seven different in silico algorithms to screen nsSNPs in PTX-3 gene. Sequence homology based approach was used to identify nsSNPs. Conservation profile of PTX-3 protein amino acid residues were predicted by ConSurf web server. In total, 10 high-risk nsSNPs were identified in pentraxin-domain of PTX-3 gene. Out of these 10 high-risk nsSNPs, 4 were present in the conserved structural and functional residues of the pentraxin-domain, hence, selected for structural analyses. The results showed alteration in the putative structure of pentraxin-domain. Prediction of protein–protein interactions analysis showed association of PTX-3 protein with C1q component of complement pathway. Different functional and structural residues along with various putative phosphorylation sites and evolutionary relationship were also predicted for PTX-3 protein. This is the first extensive computational analyses of pentraxin protein family with nsSNPs and will serve as a valuable resource for future population based studies.http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00192/fullAspergillus fumigatuslipopolysaccharideIn-silicoGalactomannannsSNPsPTX-3 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Raman eThakur Jata eShankar |
spellingShingle |
Raman eThakur Jata eShankar In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens Frontiers in Microbiology Aspergillus fumigatus lipopolysaccharide In-silico Galactomannan nsSNPs PTX-3 |
author_facet |
Raman eThakur Jata eShankar |
author_sort |
Raman eThakur |
title |
In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens |
title_short |
In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens |
title_full |
In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens |
title_fullStr |
In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens |
title_full_unstemmed |
In silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens |
title_sort |
in silico analysis revealed high-risk single nucleotide polymorphisms in human pentraxin-3 gene and their impact on innate immune response against microbial pathogens |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2016-02-01 |
description |
Pentraxin-3 (PTX-3) protein is an evolutionary conserved protein that acts as a soluble pattern-recognition receptor for pathogens and plays important role in innate immune response. It recognizes various pathogens by interacting with extracellular moieties such as glactomannan of conidia (Aspergillus fumigatus), lipopolysaccharide of Pseudomonas aeruginosa, Streptococcus pneumonia and Salmonella typhimurium. Thus, PTX-3 protein helps to clear these pathogens by activating downstream innate immune process. In this study, computational methods were used to analyze various non-synonymous single nucleotide polymorphisms (nsSNPs) in PTX-3 gene. Three different databases were used to retrieve SNP data sets followed by seven different in silico algorithms to screen nsSNPs in PTX-3 gene. Sequence homology based approach was used to identify nsSNPs. Conservation profile of PTX-3 protein amino acid residues were predicted by ConSurf web server. In total, 10 high-risk nsSNPs were identified in pentraxin-domain of PTX-3 gene. Out of these 10 high-risk nsSNPs, 4 were present in the conserved structural and functional residues of the pentraxin-domain, hence, selected for structural analyses. The results showed alteration in the putative structure of pentraxin-domain. Prediction of protein–protein interactions analysis showed association of PTX-3 protein with C1q component of complement pathway. Different functional and structural residues along with various putative phosphorylation sites and evolutionary relationship were also predicted for PTX-3 protein. This is the first extensive computational analyses of pentraxin protein family with nsSNPs and will serve as a valuable resource for future population based studies. |
topic |
Aspergillus fumigatus lipopolysaccharide In-silico Galactomannan nsSNPs PTX-3 |
url |
http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00192/full |
work_keys_str_mv |
AT ramanethakur insilicoanalysisrevealedhighrisksinglenucleotidepolymorphismsinhumanpentraxin3geneandtheirimpactoninnateimmuneresponseagainstmicrobialpathogens AT jataeshankar insilicoanalysisrevealedhighrisksinglenucleotidepolymorphismsinhumanpentraxin3geneandtheirimpactoninnateimmuneresponseagainstmicrobialpathogens |
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