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Evidence-based annotation of the malaria parasite's genome using comparative expression profiling.

Zhou Y, Ramachandran V, Kumar KA, Westenberger S, Refour P, Zhou B, Li F, Young JA, Chen K, Plouffe D, Henson K, Nussenzweig V, Carlton J, Vinetz JM, Duraisingh MT, Winzeler EA - PLoS ONE (2008)

Bottom Line: Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages.We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms.We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function.

View Article: PubMed Central - PubMed

Affiliation: Genomics Institute of the Novartis Research Foundation, San Diego, California, USA.

ABSTRACT
A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylum-specific. This problem is especially acute in pathogens, such as malaria parasites, where genetic and biochemical investigations are likely to be more difficult. Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages. We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms. We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function. These analyses, together with protein-protein interaction data, provide probabilistic models that predict the function of 926 uncharacterized malaria genes and also suggest that malaria parasites may provide a simple model system for the study of some human processes. These data also provide a foundation for further studies of transcriptional regulation in malaria parasites.

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Two-hybrid interaction networks among genes that are co-expressed.A. Invasion; B. Cellular carbohydrate catabolism; C. Cytosolic ribosome; D. RNA methyltransferase activity.
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pone-0001570-g005: Two-hybrid interaction networks among genes that are co-expressed.A. Invasion; B. Cellular carbohydrate catabolism; C. Cytosolic ribosome; D. RNA methyltransferase activity.

Mentions: Further support for expression-based function predictions were obtained from two-hybrid data from a large scale study of interactions between erythrocytic stage proteins [34]. It had previously been noted that there was enrichment for two-hybrid interactions amongst genes expressed late in the erythrocytic cycle [34]. Our new data and analysis method provided additional support for the likely significance of the two hybrid interactions in 57 clusters (p≤0.01) (Figure 1, Table S1). As expected, there was an abundance of interactions in the invasion cluster mentioned previously. Two hybrid interaction data were available for 35 of the 71 P. falciparum genes in the invasion cluster; 31 of these form 83 direct or indirect interactions pairs among themselves (Figure 5A). The probability of observing this enrichment by chance is <10−6. A group containing many of the genes in the cellular carbohydrate catabolism pathway (GO:0044275) also had more two-hybrid interactions than could be expected by chance alone (45 P. f. genes by expression, 29 proteins with two hybrid data, ten of which interact with other members of the group (p = 0.003)). This group included MAL8P1.17, a protein disulfide isomerase that interacts with enolase (PF10_0155), glyceraldehyde-3-phosphate dehydrogenase (PF14_0598) and phosphoglycerate kinase (PFI1105w) (Figure 5B). The cluster of 99 P. falciparum genes enriched for structural constituents of the ribosome had 54 genes with protein-protein interaction data within the group and 35 of these have interactions with other members of the group (p = 0.003) (Figure 5C). In a fourth example, we considered an expression cluster of 100 genes, several with RNA methyltransferase activity (Figure 5D). The combined two-hybrid and expression data indicated that most of the proteins in this group were very likely involved in RNA processing. For example, the uncharacterized gene PF07_0121 had a yeast ortholog factor required for a late assembly step of the 60S subunit; PF11_0305, another uncharacterized protein, had a yeast ortholog which is a constituent of the 66S pre-ribosome particle; and PF10_0200 has a yeast ortholog, YNL132w (See Table 2), which also interacts with many nucleolus ribosome assembly proteins (http://www.yeastgenome.org/, [35]). MAL13P1.14 encodes an ATP-dependent DEAD box helicase and interacts with four other members of the expression set, including PFL0815w (a DNA-binding chaperone), and two uncharacterized proteins, PF07_0106 and PFA0410w. The yeast orthologs of both MAL13P1.14 and PFL0815w are co-expressed along with other RNA modification enzymes and the yeast ortholog for MAL13P1.14 is the U3 snoRNP protein, a nucleolar protein involved in mRNA processing. Although many of the proteins were uncharacterized, this is probably because many of the genes were also uncharacterized in yeast or humans. These genes would be less likely to be good drug targets due to their cross-species conservation. The two-hybrid data includes few proteins that are expressed in the sexual or insect stages because the library was derived from blood stage material. Thus, little two-hybrid support was found for genes that have roles in sexual development, sporozoite function or other processes occurring in the non-erythrocytic stages (Figure 1). In all, protein-protein interaction analysis provided support for 970 OPI function assignments, 78% of which belong to 229 P. falciparum proteins not yet captured by existing manual annotations. Together with the previous cross-species co-expression evidence, we identified a total of 5,471 supported function predictions, including new functional characterizations for 926 malaria genes (Table S2).


Evidence-based annotation of the malaria parasite's genome using comparative expression profiling.

Zhou Y, Ramachandran V, Kumar KA, Westenberger S, Refour P, Zhou B, Li F, Young JA, Chen K, Plouffe D, Henson K, Nussenzweig V, Carlton J, Vinetz JM, Duraisingh MT, Winzeler EA - PLoS ONE (2008)

Two-hybrid interaction networks among genes that are co-expressed.A. Invasion; B. Cellular carbohydrate catabolism; C. Cytosolic ribosome; D. RNA methyltransferase activity.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2215772&req=5

pone-0001570-g005: Two-hybrid interaction networks among genes that are co-expressed.A. Invasion; B. Cellular carbohydrate catabolism; C. Cytosolic ribosome; D. RNA methyltransferase activity.
Mentions: Further support for expression-based function predictions were obtained from two-hybrid data from a large scale study of interactions between erythrocytic stage proteins [34]. It had previously been noted that there was enrichment for two-hybrid interactions amongst genes expressed late in the erythrocytic cycle [34]. Our new data and analysis method provided additional support for the likely significance of the two hybrid interactions in 57 clusters (p≤0.01) (Figure 1, Table S1). As expected, there was an abundance of interactions in the invasion cluster mentioned previously. Two hybrid interaction data were available for 35 of the 71 P. falciparum genes in the invasion cluster; 31 of these form 83 direct or indirect interactions pairs among themselves (Figure 5A). The probability of observing this enrichment by chance is <10−6. A group containing many of the genes in the cellular carbohydrate catabolism pathway (GO:0044275) also had more two-hybrid interactions than could be expected by chance alone (45 P. f. genes by expression, 29 proteins with two hybrid data, ten of which interact with other members of the group (p = 0.003)). This group included MAL8P1.17, a protein disulfide isomerase that interacts with enolase (PF10_0155), glyceraldehyde-3-phosphate dehydrogenase (PF14_0598) and phosphoglycerate kinase (PFI1105w) (Figure 5B). The cluster of 99 P. falciparum genes enriched for structural constituents of the ribosome had 54 genes with protein-protein interaction data within the group and 35 of these have interactions with other members of the group (p = 0.003) (Figure 5C). In a fourth example, we considered an expression cluster of 100 genes, several with RNA methyltransferase activity (Figure 5D). The combined two-hybrid and expression data indicated that most of the proteins in this group were very likely involved in RNA processing. For example, the uncharacterized gene PF07_0121 had a yeast ortholog factor required for a late assembly step of the 60S subunit; PF11_0305, another uncharacterized protein, had a yeast ortholog which is a constituent of the 66S pre-ribosome particle; and PF10_0200 has a yeast ortholog, YNL132w (See Table 2), which also interacts with many nucleolus ribosome assembly proteins (http://www.yeastgenome.org/, [35]). MAL13P1.14 encodes an ATP-dependent DEAD box helicase and interacts with four other members of the expression set, including PFL0815w (a DNA-binding chaperone), and two uncharacterized proteins, PF07_0106 and PFA0410w. The yeast orthologs of both MAL13P1.14 and PFL0815w are co-expressed along with other RNA modification enzymes and the yeast ortholog for MAL13P1.14 is the U3 snoRNP protein, a nucleolar protein involved in mRNA processing. Although many of the proteins were uncharacterized, this is probably because many of the genes were also uncharacterized in yeast or humans. These genes would be less likely to be good drug targets due to their cross-species conservation. The two-hybrid data includes few proteins that are expressed in the sexual or insect stages because the library was derived from blood stage material. Thus, little two-hybrid support was found for genes that have roles in sexual development, sporozoite function or other processes occurring in the non-erythrocytic stages (Figure 1). In all, protein-protein interaction analysis provided support for 970 OPI function assignments, 78% of which belong to 229 P. falciparum proteins not yet captured by existing manual annotations. Together with the previous cross-species co-expression evidence, we identified a total of 5,471 supported function predictions, including new functional characterizations for 926 malaria genes (Table S2).

Bottom Line: Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages.We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms.We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function.

View Article: PubMed Central - PubMed

Affiliation: Genomics Institute of the Novartis Research Foundation, San Diego, California, USA.

ABSTRACT
A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across organisms of different phyla or are phylum-specific. This problem is especially acute in pathogens, such as malaria parasites, where genetic and biochemical investigations are likely to be more difficult. Here we perform comparative expression analysis on Plasmodium parasite life cycle data derived from P. falciparum blood, sporozoite, zygote and ookinete stages, and P. yoelii mosquito oocyst and salivary gland sporozoites, blood and liver stages and show that type II fatty acid biosynthesis genes are upregulated in liver and insect stages relative to asexual blood stages. We also show that some universally uncharacterized genes with orthologs in Plasmodium species, Saccharomyces cerevisiae and humans show coordinated transcription patterns in large collections of human and yeast expression data and that the function of the uncharacterized genes can sometimes be predicted based on the expression patterns across these diverse organisms. We also use a comprehensive and unbiased literature mining method to predict which uncharacterized parasite-specific genes are likely to have roles in processes such as gliding motility, host-cell interactions, sporozoite stage, or rhoptry function. These analyses, together with protein-protein interaction data, provide probabilistic models that predict the function of 926 uncharacterized malaria genes and also suggest that malaria parasites may provide a simple model system for the study of some human processes. These data also provide a foundation for further studies of transcriptional regulation in malaria parasites.

Show MeSH
Related in: MedlinePlus