Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS)

dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
dc.contributor.authorLawton, Jennifer
dc.contributor.authorBrugat, Thibaut
dc.contributor.authorYan, Yam Xue
dc.contributor.authorReid, Adam James
dc.contributor.authorBöhme, Ulrike
dc.contributor.authorOtto, Thomas Dan
dc.contributor.authorPain, Arnab
dc.contributor.authorJackson, Andrew
dc.contributor.authorBerriman, Matthew
dc.contributor.authorCunningham, Deirdre
dc.contributor.authorPreiser, Peter
dc.contributor.authorLanghorne, Jean
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentPathogen Genomics Laboratory
dc.contributor.institutionDivision of Parasitology, MRC National Institute for Medical Research, London, United Kingdom
dc.contributor.institutionDivision of Genomics and Genetics, Nanyang Technological University Singapore, Singapore
dc.contributor.institutionParasite Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
dc.date.accessioned2014-08-27T09:41:51Z
dc.date.available2014-08-27T09:41:51Z
dc.date.issued2012-03-29
dc.date.published-online2012-03-29
dc.date.published-print2012
dc.description.abstractBackground: The pir genes comprise the largest multi-gene family in Plasmodium, with members found in P. vivax, P. knowlesi and the rodent malaria species. Despite comprising up to 5% of the genome, little is known about the functions of the proteins encoded by pir genes. P. chabaudi causes chronic infection in mice, which may be due to antigenic variation. In this model, pir genes are called cirs and may be involved in this mechanism, allowing evasion of host immune responses. In order to fully understand the role(s) of CIR proteins during P. chabaudi infection, a detailed characterization of the cir gene family was required.Results: The cir repertoire was annotated and a detailed bioinformatic characterization of the encoded CIR proteins was performed. Two major sub-families were identified, which have been named A and B. Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional divergence. In addition, the expression of the entire cir repertoire was analyzed via RNA sequencing and microarray. Up to 40% of the cir gene repertoire was expressed in the parasite population during infection, and dominant cir transcripts could be identified. In addition, some differences were observed in the pattern of expression between the cir subgroups at the peak of P. chabaudi infection. Finally, specific cir genes were expressed at different time points during asexual blood stages.Conclusions: In conclusion, the large number of cir genes and their expression throughout the intraerythrocytic cycle of development indicates that CIR proteins are likely to be important for parasite survival. In particular, the detection of dominant cir transcripts at the peak of P. chabaudi infection supports the idea that CIR proteins are expressed, and could perform important functions in the biology of this parasite. Further application of the methodologies described here may allow the elucidation of CIR sub-family A and B protein functions, including their contribution to antigenic variation and immune evasion. 2012 Lawton et al; licensee BioMed Central Ltd.
dc.eprint.versionPublisher's Version/PDF
dc.identifier.citationLawton J, Brugat T, Yan Y, Reid A, Böhme U, et al. (2012) Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS). BMC Genomics 13: 125. doi:10.1186/1471-2164-13-125.
dc.identifier.doi10.1186/1471-2164-13-125
dc.identifier.issn14712164
dc.identifier.journalBMC Genomics
dc.identifier.pmcidPMC3384456
dc.identifier.pmid22458863
dc.identifier.urihttp://hdl.handle.net/10754/325241
dc.language.isoen
dc.publisherSpringer Nature
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/2.0
dc.subjectamino acid
dc.subjectCIR protein
dc.subjectprotein
dc.subjectRNA
dc.subjectunclassified drug
dc.subjectmessenger RNA
dc.subjectprotozoal protein
dc.subjectprotozoal RNA
dc.subjectantigenic variation
dc.subjectbacterial genetics
dc.subjectCIR gene
dc.subjectcontrolled study
dc.subjectgene
dc.subjectgene expression
dc.subjectgenetic analysis
dc.subjectgenetic variability
dc.subjectimmune evasion
dc.subjectmicroarray analysis
dc.subjectmouse
dc.subjectmultigene family
dc.subjectnucleotide sequence
dc.subjectparasite survival
dc.subjectPlasmodium chabaudi
dc.subjectprotein analysis
dc.subjectprotein expression
dc.subjectprotein function
dc.subjectprotein motif
dc.subjectRNA sequence
dc.subjectamino acid sequence
dc.subjectbiology
dc.subjectchemistry
dc.subjectDNA microarray
dc.subjectgene
dc.subjectgene expression profiling
dc.subjectgenetics
dc.subjectgrowth, development and aging
dc.subjecthost pathogen interaction
dc.subjectlife cycle stage
dc.subjectmetabolism
dc.subjectmethodology
dc.subjectpathogenicity
dc.subjectphysiology
dc.subjectsequence analysis
dc.subjectsequence homology
dc.subjectMus
dc.subjectPlasmodium chabaudi
dc.subjectPlasmodium chabaudi chabaudi
dc.subjectPlasmodium knowlesi
dc.subjectPlasmodium vivax
dc.subjectRodentia
dc.subjectAmino Acid Motifs
dc.subjectAmino Acid Sequence
dc.subjectComputational Biology
dc.subjectConserved Sequence
dc.subjectGene Expression Profiling
dc.subjectGenes, Protozoan
dc.subjectHost-Pathogen Interactions
dc.subjectLife Cycle Stages
dc.subjectMice
dc.subjectMultigene Family
dc.subjectOligonucleotide Array Sequence Analysis
dc.subjectPlasmodium chabaudi
dc.subjectProtozoan Proteins
dc.subjectRNA, Messenger
dc.subjectRNA, Protozoan
dc.subjectSequence Analysis, RNA
dc.subjectSequence Homology, Amino Acid
dc.titleCharacterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS)
dc.typeArticle
display.details.left<span><h5>License</h5>http://creativecommons.org/licenses/by/2.0<br><br><h5>Type</h5>Article<br><br><h5>Authors</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Lawton, Jennifer,equals">Lawton, Jennifer</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Brugat, Thibaut,equals">Brugat, Thibaut</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Yan, Yam Xue,equals">Yan, Yam Xue</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Reid, Adam James,equals">Reid, Adam James</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Böhme, Ulrike,equals">Böhme, Ulrike</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Otto, Thomas Dan,equals">Otto, Thomas Dan</a><br><a href="https://repository.kaust.edu.sa/search?query=orcid.id:0000-0002-1755-2819&spc.sf=dc.date.issued&spc.sd=DESC">Pain, Arnab</a> <a href="https://orcid.org/0000-0002-1755-2819" target="_blank"><img src="https://repository.kaust.edu.sa/server/api/core/bitstreams/82a625b4-ed4b-40c8-865a-d6a5225a26a4/content" width="16" height="16"/></a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Jackson, Andrew,equals">Jackson, Andrew</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Berriman, Matthew,equals">Berriman, Matthew</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Cunningham, Deirdre,equals">Cunningham, Deirdre</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Preiser, Peter,equals">Preiser, Peter</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Langhorne, Jean,equals">Langhorne, Jean</a><br><br><h5>KAUST Department</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Biological and Environmental Sciences and Engineering (BESE) Division,equals">Biological and Environmental Sciences and Engineering (BESE) Division</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Bioscience Program,equals">Bioscience Program</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Computational Bioscience Research Center (CBRC),equals">Computational Bioscience Research Center (CBRC)</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Pathogen Genomics Laboratory,equals">Pathogen Genomics Laboratory</a><br><br><h5>Online Publication Date</h5>2012-03-29<br><br><h5>Print Publication Date</h5>2012<br><br><h5>Date</h5>2012-03-29</span>
display.details.right<span><h5>Abstract</h5>Background: The pir genes comprise the largest multi-gene family in Plasmodium, with members found in P. vivax, P. knowlesi and the rodent malaria species. Despite comprising up to 5% of the genome, little is known about the functions of the proteins encoded by pir genes. P. chabaudi causes chronic infection in mice, which may be due to antigenic variation. In this model, pir genes are called cirs and may be involved in this mechanism, allowing evasion of host immune responses. In order to fully understand the role(s) of CIR proteins during P. chabaudi infection, a detailed characterization of the cir gene family was required.Results: The cir repertoire was annotated and a detailed bioinformatic characterization of the encoded CIR proteins was performed. Two major sub-families were identified, which have been named A and B. Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional divergence. In addition, the expression of the entire cir repertoire was analyzed via RNA sequencing and microarray. Up to 40% of the cir gene repertoire was expressed in the parasite population during infection, and dominant cir transcripts could be identified. In addition, some differences were observed in the pattern of expression between the cir subgroups at the peak of P. chabaudi infection. Finally, specific cir genes were expressed at different time points during asexual blood stages.Conclusions: In conclusion, the large number of cir genes and their expression throughout the intraerythrocytic cycle of development indicates that CIR proteins are likely to be important for parasite survival. In particular, the detection of dominant cir transcripts at the peak of P. chabaudi infection supports the idea that CIR proteins are expressed, and could perform important functions in the biology of this parasite. Further application of the methodologies described here may allow the elucidation of CIR sub-family A and B protein functions, including their contribution to antigenic variation and immune evasion. 2012 Lawton et al; licensee BioMed Central Ltd.<br><br><h5>Citation</h5>Lawton J, Brugat T, Yan Y, Reid A, Böhme U, et al. (2012) Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS). BMC Genomics 13: 125. doi:10.1186/1471-2164-13-125.<br><br><h5>Publisher</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.publisher=Springer Nature,equals">Springer Nature</a><br><br><h5>Journal</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.journal=BMC Genomics,equals">BMC Genomics</a><br><br><h5>DOI</h5><a href="https://doi.org/10.1186/1471-2164-13-125">10.1186/1471-2164-13-125</a><br><br><h5>PubMed ID</h5><a href="https://www.ncbi.nlm.nih.gov/pubmed/22458863">22458863</a><br><br><h5>PubMed Central ID</h5><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384456">PMC3384456</a></span>
kaust.personPain, Arnab
orcid.authorLawton, Jennifer
orcid.authorBrugat, Thibaut
orcid.authorYan, Yam Xue
orcid.authorReid, Adam James
orcid.authorBöhme, Ulrike
orcid.authorOtto, Thomas Dan
orcid.authorPain, Arnab::0000-0002-1755-2819
orcid.authorJackson, Andrew
orcid.authorBerriman, Matthew
orcid.authorCunningham, Deirdre
orcid.authorPreiser, Peter
orcid.authorLanghorne, Jean
orcid.id0000-0002-1755-2819
refterms.dateFOA2018-06-13T14:35:53Z
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