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The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems.

Oberstaller J, Pumpalova Y, Schieler A, Llinás M, Kissinger JC - Nucleic Acids Res. (2014)

Bottom Line: C. hominis orthologs of putative C. parvum ApiAP2 proteins and target genes show greater than average variation.C. parvum AP2 domains display reduced binding diversity relative to P. falciparum, with multiple domains binding the 5'-TGCAT-3', 5'-CACACA-3' and G-box motifs (5'-G[T/C]GGGG-3').C. parvum may provide clues to the ancestral state of apicomplexan transcriptional regulation, pre-AP2 domination.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, GA 30602, USA Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.

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C. parvum and P. falciparum AP2 domain ortholog binding motifs as determined by PBM. C. parvum domains are color-coded according to evolutionary groups based on OrthoMCL clustering at 1e-6 as discussed in Materials and Methods. Data for core DNA motifs determined for P. falciparum AP2 domains obtained from (37).
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Figure 3: C. parvum and P. falciparum AP2 domain ortholog binding motifs as determined by PBM. C. parvum domains are color-coded according to evolutionary groups based on OrthoMCL clustering at 1e-6 as discussed in Materials and Methods. Data for core DNA motifs determined for P. falciparum AP2 domains obtained from (37).

Mentions: The 23 C. parvum AP2 domains were further classified as ancestral, pan-apicomplexan or lineage-specific based on their phyletic distribution with OrthoMCL clustering using an e-value cutoff of 1e-6 (Figure 3). Apicomplexan AP2 domains that clustered with a P. marinus AP2 domain were classified as ancestral; these domains likely predate the divergence between perkinsids and the Apicomplexa. Four C. parvum AP2 domains (cgd4_1110_D1, cgd4_1110_D3, cgd8_3130 and cgd8_3230) are ancestral (Figure 3). Domains are indicated by gene ID, and in the case of multidomain proteins, numbered D1–D4 starting from the N-terminus. Domains that span all or most apicomplexan lineages, but were absent in Perkinsus were classified as pan-apicomplexan (10 C. parvum domains are in this category). The remaining nine domains have no orthologs outside of Cryptosporidium and are classified as lineage-specific. It is necessarily true that some pan-apicomplexan domains may have been present in the perkinsid/apicomplexan ancestor as well, and were subsequently lost in Perkinsus. Because there is no extant evidence of these domains in Perkinsus and because there is ambiguity with respect to when these domains arose, we maintain separate ‘ancestral’ and ‘pan-apicomplexan’ designations. Lineage-specific domains have no identifiable orthologs outside their respective taxa, though again it is a formal possibility that these could also be true ‘ancestral’ domains that were lost in other lineages.


The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems.

Oberstaller J, Pumpalova Y, Schieler A, Llinás M, Kissinger JC - Nucleic Acids Res. (2014)

C. parvum and P. falciparum AP2 domain ortholog binding motifs as determined by PBM. C. parvum domains are color-coded according to evolutionary groups based on OrthoMCL clustering at 1e-6 as discussed in Materials and Methods. Data for core DNA motifs determined for P. falciparum AP2 domains obtained from (37).
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Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4117751&req=5

Figure 3: C. parvum and P. falciparum AP2 domain ortholog binding motifs as determined by PBM. C. parvum domains are color-coded according to evolutionary groups based on OrthoMCL clustering at 1e-6 as discussed in Materials and Methods. Data for core DNA motifs determined for P. falciparum AP2 domains obtained from (37).
Mentions: The 23 C. parvum AP2 domains were further classified as ancestral, pan-apicomplexan or lineage-specific based on their phyletic distribution with OrthoMCL clustering using an e-value cutoff of 1e-6 (Figure 3). Apicomplexan AP2 domains that clustered with a P. marinus AP2 domain were classified as ancestral; these domains likely predate the divergence between perkinsids and the Apicomplexa. Four C. parvum AP2 domains (cgd4_1110_D1, cgd4_1110_D3, cgd8_3130 and cgd8_3230) are ancestral (Figure 3). Domains are indicated by gene ID, and in the case of multidomain proteins, numbered D1–D4 starting from the N-terminus. Domains that span all or most apicomplexan lineages, but were absent in Perkinsus were classified as pan-apicomplexan (10 C. parvum domains are in this category). The remaining nine domains have no orthologs outside of Cryptosporidium and are classified as lineage-specific. It is necessarily true that some pan-apicomplexan domains may have been present in the perkinsid/apicomplexan ancestor as well, and were subsequently lost in Perkinsus. Because there is no extant evidence of these domains in Perkinsus and because there is ambiguity with respect to when these domains arose, we maintain separate ‘ancestral’ and ‘pan-apicomplexan’ designations. Lineage-specific domains have no identifiable orthologs outside their respective taxa, though again it is a formal possibility that these could also be true ‘ancestral’ domains that were lost in other lineages.

Bottom Line: C. hominis orthologs of putative C. parvum ApiAP2 proteins and target genes show greater than average variation.C. parvum AP2 domains display reduced binding diversity relative to P. falciparum, with multiple domains binding the 5'-TGCAT-3', 5'-CACACA-3' and G-box motifs (5'-G[T/C]GGGG-3').C. parvum may provide clues to the ancestral state of apicomplexan transcriptional regulation, pre-AP2 domination.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, GA 30602, USA Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.

Show MeSH
Related in: MedlinePlus