Genes Involved in Host-parasite Interactions Can Be Revealed by Their Correlated Expression

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2013 Jan 1

PMID 23275547

Citations 12

Authors

Adam James Reid

Matthew Berriman

Affiliations

Soon will be listed here.

Abstract

Molecular interactions between a parasite and its host are key to the ability of the parasite to enter the host and persist. Our understanding of the genes and proteins involved in these interactions is limited. To better understand these processes it would be advantageous to have a range of methods to predict pairs of genes involved in such interactions. Correlated gene expression profiles can be used to identify molecular interactions within a species. Here we have extended the concept to different species, showing that genes with correlated expression are more likely to encode proteins, which directly or indirectly participate in host-parasite interaction. We go on to examine our predictions of molecular interactions between the malaria parasite and both its mammalian host and insect vector. Our approach could be applied to study any interaction between species, for example, between a host and its parasites or pathogens, but also symbiotic and commensal pairings.

Citing Articles

Comparative Transcriptomics in Atlantic Salmon Head Kidney and SHK-1 Cell Line Exposed to the Sea Louse Cr-Cathepsin.

Leal Y, Valenzuela-Munoz V, Casuso A, Benavente B, Gallardo-Escarate C Genes (Basel). 2023; 14(4).

PMID: 37107663 PMC: 10138087. DOI: 10.3390/genes14040905.

Dual RNA Sequencing Meta-analysis in Infection Identifies Host-Parasite Interactions.

Mukherjee P, Burgio G, Heitlinger E mSystems. 2021; 6(2).

PMID: 33879496 PMC: 8546971. DOI: 10.1128/mSystems.00182-21.

Transcriptomic Profiling of Mouse Brain During Acute and Chronic Infections by Oocysts.

Hu R, He J, Elsheikha H, Zou Y, Ehsan M, Ma Q Front Microbiol. 2020; 11:570903.

PMID: 33193165 PMC: 7604304. DOI: 10.3389/fmicb.2020.570903.

Inter-Species/Host-Parasite Protein Interaction Predictions Reviewed.

Soyemi J, Isewon I, Oyelade J, Adebiyi E Curr Bioinform. 2019; 13(4):396-406.

PMID: 31496926 PMC: 6691774. DOI: 10.2174/1574893613666180108155851.

Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism.

Cuesta-Astroz Y, Santos A, Oliveira G, Jensen L Front Immunol. 2019; 10:212.

PMID: 30815000 PMC: 6381214. DOI: 10.3389/fimmu.2019.00212.

References

Shea P, Virtaneva K, Kupko 3rd J, Porcella S, Barry W, Wright F . Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus. Proc Natl Acad Sci U S A. 2010; 107(10):4693-8. PMC: 2842040. DOI: 10.1073/pnas.0906384107. View

Oakley M, McCutchan T, Anantharaman V, Ward J, Faucette L, Erexson C . Host biomarkers and biological pathways that are associated with the expression of experimental cerebral malaria in mice. Infect Immun. 2008; 76(10):4518-29. PMC: 2546852. DOI: 10.1128/IAI.00525-08. View

Krishnadev O, Srinivasan N . A data integration approach to predict host-pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite. In Silico Biol. 2008; 8(3-4):235-50. View

Croft D, OKelly G, Wu G, Haw R, Gillespie M, Matthews L . Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2010; 39(Database issue):D691-7. PMC: 3013646. DOI: 10.1093/nar/gkq1018. View

Xu X, Dong Y, Abraham E, Kocan A, Srinivasan P, Ghosh A . Transcriptome analysis of Anopheles stephensi-Plasmodium berghei interactions. Mol Biochem Parasitol. 2005; 142(1):76-87. DOI: 10.1016/j.molbiopara.2005.02.013. View

Kabyemela E, Fried M, Kurtis J, Mutabingwa T, Duffy P . Fetal responses during placental malaria modify the risk of low birth weight. Infect Immun. 2008; 76(4):1527-34. PMC: 2292860. DOI: 10.1128/IAI.00964-07. View

Cui L, Miao J . Chromatin-mediated epigenetic regulation in the malaria parasite Plasmodium falciparum. Eukaryot Cell. 2010; 9(8):1138-49. PMC: 2918932. DOI: 10.1128/EC.00036-10. View

Hertz-Fowler C, Peacock C, Wood V, Aslett M, Kerhornou A, Mooney P . GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res. 2003; 32(Database issue):D339-43. PMC: 308742. DOI: 10.1093/nar/gkh007. View

Logan-Klumpler F, De Silva N, Boehme U, Rogers M, Velarde G, McQuillan J . GeneDB--an annotation database for pathogens. Nucleic Acids Res. 2011; 40(Database issue):D98-108. PMC: 3245030. DOI: 10.1093/nar/gkr1032. View

10.

Sprinzak E, Margalit H . Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol. 2001; 311(4):681-92. DOI: 10.1006/jmbi.2001.4920. View

11.

Tailleux L, Waddell S, Pelizzola M, Mortellaro A, Withers M, Tanne A . Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS One. 2008; 3(1):e1403. PMC: 2151136. DOI: 10.1371/journal.pone.0001403. View

12.

Pulido-Mendez M, Sanctis J, Rodriguez-Acosta A . Leptin and leptin receptors during malaria infection in mice. Folia Parasitol (Praha). 2003; 49(4):249-51. DOI: 10.14411/fp.2002.046. View

13.

Patil A, Nakamura H . Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics. 2005; 6:100. PMC: 1127019. DOI: 10.1186/1471-2105-6-100. View

14.

Kersey P, Staines D, Lawson D, Kulesha E, Derwent P, Humphrey J . Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 2011; 40(Database issue):D91-7. PMC: 3245118. DOI: 10.1093/nar/gkr895. View

15.

Jansen R, Greenbaum D, Gerstein M . Relating whole-genome expression data with protein-protein interactions. Genome Res. 2002; 12(1):37-46. PMC: 155252. DOI: 10.1101/gr.205602. View

16.

Grigoriev A . A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 2001; 29(17):3513-9. PMC: 55876. DOI: 10.1093/nar/29.17.3513. View

17.

Tierney L, Linde J, Muller S, Brunke S, Molina J, Hube B . An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. Front Microbiol. 2012; 3:85. PMC: 3299011. DOI: 10.3389/fmicb.2012.00085. View

18.

Niesporek S, Meyer C, Kremsner P, May J . Polymorphisms of transporter associated with antigen processing type 1 (TAP1), proteasome subunit beta type 9 (PSMB9) and their common promoter in African children with different manifestations of malaria. Int J Immunogenet. 2005; 32(1):7-11. DOI: 10.1111/j.1744-313X.2005.00484.x. View

19.

Alexa A, Rahnenfuhrer J, Lengauer T . Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006; 22(13):1600-7. DOI: 10.1093/bioinformatics/btl140. View

20.

Taraschi T, ODonnell M, Martinez S, Schneider T, Trelka D, Fowler V . Generation of an erythrocyte vesicle transport system by Plasmodium falciparum malaria parasites. Blood. 2003; 102(9):3420-6. DOI: 10.1182/blood-2003-05-1448. View