title: Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains.
abstract: BACKGROUND
  Toxoplasma gondii has a largely clonal population in North America and Europe, with types I, II and III clonal lineages accounting for the majority of strains isolated from patients. RH, a particular type I strain, is most frequently used to characterize Toxoplasma biology. However, compared to other type I strains, RH has unique characteristics such as faster growth, increased extracellular survival rate and inability to form orally infectious cysts. Thus, to identify candidate genes that could account for these parasite phenotypic differences, we determined genetic differences and differential parasite gene expression between RH and another type I strain, GT1. Moreover, as differences in host cell modulation could affect Toxoplasma replication in the host, we determined differentially modulated host processes among the type I strains through host transcriptional profiling.
  
  
  RESULTS
  Through whole genome sequencing, we identified 1,394 single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) between RH and GT1. These SNPs/indels together with parasite gene expression differences between RH and GT1 were used to identify candidate genes that could account for type I phenotypic differences. A polymorphism in dense granule protein, GRA2, determined RH and GT1 differences in the evasion of the interferon gamma response. In addition, host transcriptional profiling identified that genes regulated by NF-ĸB, such as interleukin (IL)-12p40, were differentially modulated by the different type I strains. We subsequently showed that this difference in NF-ĸB activation was due to polymorphisms in GRA15. Furthermore, we observed that RH, but not other type I strains, recruited phosphorylated IĸBα (a component of the NF-ĸB complex) to the parasitophorous vacuole membrane and this recruitment of p- IĸBα was partially dependent on GRA2.
  
  
  CONCLUSIONS
  We identified candidate parasite genes that could be responsible for phenotypic variation among the type I strains through comparative genomics and transcriptomics. We also identified differentially modulated host pathways among the type I strains, and these can serve as a guideline for future studies in examining the phenotypic differences among type I strains.
authors.affiliation: Biology Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, building 68-270, Cambridge, MA 02139, USA.
authors.forename: Ninghan
authors.initials: N
authors.lastname: Yang
authors.forename: Andrew
authors.initials: A
authors.lastname: Farrell
authors.forename: Wendy
authors.initials: W
authors.lastname: Niedelman
authors.forename: Mariane
authors.initials: M
authors.lastname: Melo
authors.forename: Diana
authors.initials: D
authors.lastname: Lu
authors.forename: Lindsay
authors.initials: L
authors.lastname: Julien
authors.forename: Gabor T
authors.initials: GT
authors.lastname: Marth
authors.forename: Marc-Jan
authors.initials: MJ
authors.lastname: Gubbels
authors.forename: Jeroen P J
authors.initials: JP
authors.lastname: Saeij
mesh_terms: D000818:Animals; D005347:Fibroblasts / Q000469:parasitology; D005786:Gene Expression Regulation; D017125:Genes, Protozoan / Q000235:genetics; D057809:HEK293 Cells; D006801:Humans; D053762:Interleukin-12 Subunit p40 / Q000378:metabolism; D007425:Intracellular Membranes / Q000378:metabolism / Q000469:parasitology; D008264:Macrophages / Q000378:metabolism / Q000469:parasitology; D051379:Mice; D016328:NF-kappa B / Q000378:metabolism; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D021381:Protein Transport; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D014122:Toxoplasma / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D014617:Vacuoles / Q000378:metabolism
chemical_list: D053762:Interleukin-12 Subunit p40; D016328:NF-kappa B; D015800:Protozoan Proteins