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Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients.

Merino EF, Fernandez-Becerra C, Madeira AM, Machado AL, Durham A, Gruber A, Hall N, del Portillo HA - Malar. J. (2003)

Bottom Line: An E-value of <10(-30) was used to define a significant database match.Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them.These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Parasitologia, ICB, Universidade de São Paulo, São Paulo, Brazil. efmerino@yahoo.com

ABSTRACT

Background: Plasmodium vivax is the most widely distributed human malaria, responsible for 70-80 million clinical cases each year and large socio-economical burdens for countries such as Brazil where it is the most prevalent species. Unfortunately, due to the impossibility of growing this parasite in continuous in vitro culture, research on P. vivax remains largely neglected.

Methods: A pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of P. vivax was performed. To do so, 1,184 clones from a cDNA library constructed with parasites obtained from 10 different human patients in the Brazilian Amazon were sequenced. Sequences were automatedly processed to remove contaminants and low quality reads. A total of 806 sequences with an average length of 586 bp met such criteria and their clustering revealed 666 distinct events. The consensus sequence of each cluster and the unique sequences of the singlets were used in similarity searches against different databases that included P. vivax, Plasmodium falciparum, Plasmodium yoelii, Plasmodium knowlesi, Apicomplexa and the GenBank non-redundant database. An E-value of <10(-30) was used to define a significant database match. ESTs were manually assigned a gene ontology (GO) terminology

Results: A total of 769 ESTs could be assigned a putative identity based upon sequence similarity to known proteins in GenBank. Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them.

Conclusion: These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced. Moreover, since the GC-content of the P. vivax genome is strikingly different from that of P. falciparum, these ESTs will help in the validation of gene predictions for P. vivax and to create a gene index of this malaria parasite.

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Related in: MedlinePlus

Gene Ontology classification of the P. vivax ESTs Classification of P. vivax ESTs according to "Molecular Function" of the GO system [21]. Figures on "Biological Process" and "Cellular Component" can be obtained from .
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Figure 2: Gene Ontology classification of the P. vivax ESTs Classification of P. vivax ESTs according to "Molecular Function" of the GO system [21]. Figures on "Biological Process" and "Cellular Component" can be obtained from .

Mentions: The gene ontology terminology is a controlled vocabulary to describe each product in terms of its molecular function, biological process or cellular [23] and which has been expanded to include specialized and parasite-specific terms [24]. We assigned GO terms manually to 164 ESTs and these results were compared with the annotations from the P. falciparum genome project (Figure 2 and supplementary figures at ). The remaining ESTs did not have sufficient protein similarity to justify GO terminology. During the asexual blood stages, malaria parasites undergo several rounds of invasion, growth, differentiation and mitotic replication. Accordingly, biological processes were mostly related to metabolism such as glycolysis, haem digestion, and ubiquitin-dependent proteasome degradation. Furthermore, this data is in agreement with recent expression and proteome analyses of the asexual blood stages of P. falciparum [25-27]. Interestingly, ESTs representing molecules involved in cell adhesion and antigenic variation were absent in P. vivax. Unlike P. falciparum, P. vivax does not cytoadhere and thus the absence of cell adhesion molecules was not unexpected. In fact, absence of genes coding for cytoadherent molecules had been previously documented from the complete sequence of a 199,866 bp genome region of P. vivax [4]. In contrast, the lack of immune evasion molecules within the P. vivax ESTs was striking, since P. vivax contains the vir multi-gene family with circa 600–1000 copies per haploid genome likely involved in antigenic variation [3].


Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients.

Merino EF, Fernandez-Becerra C, Madeira AM, Machado AL, Durham A, Gruber A, Hall N, del Portillo HA - Malar. J. (2003)

Gene Ontology classification of the P. vivax ESTs Classification of P. vivax ESTs according to "Molecular Function" of the GO system [21]. Figures on "Biological Process" and "Cellular Component" can be obtained from .
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC183858&req=5

Figure 2: Gene Ontology classification of the P. vivax ESTs Classification of P. vivax ESTs according to "Molecular Function" of the GO system [21]. Figures on "Biological Process" and "Cellular Component" can be obtained from .
Mentions: The gene ontology terminology is a controlled vocabulary to describe each product in terms of its molecular function, biological process or cellular [23] and which has been expanded to include specialized and parasite-specific terms [24]. We assigned GO terms manually to 164 ESTs and these results were compared with the annotations from the P. falciparum genome project (Figure 2 and supplementary figures at ). The remaining ESTs did not have sufficient protein similarity to justify GO terminology. During the asexual blood stages, malaria parasites undergo several rounds of invasion, growth, differentiation and mitotic replication. Accordingly, biological processes were mostly related to metabolism such as glycolysis, haem digestion, and ubiquitin-dependent proteasome degradation. Furthermore, this data is in agreement with recent expression and proteome analyses of the asexual blood stages of P. falciparum [25-27]. Interestingly, ESTs representing molecules involved in cell adhesion and antigenic variation were absent in P. vivax. Unlike P. falciparum, P. vivax does not cytoadhere and thus the absence of cell adhesion molecules was not unexpected. In fact, absence of genes coding for cytoadherent molecules had been previously documented from the complete sequence of a 199,866 bp genome region of P. vivax [4]. In contrast, the lack of immune evasion molecules within the P. vivax ESTs was striking, since P. vivax contains the vir multi-gene family with circa 600–1000 copies per haploid genome likely involved in antigenic variation [3].

Bottom Line: An E-value of <10(-30) was used to define a significant database match.Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them.These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Parasitologia, ICB, Universidade de São Paulo, São Paulo, Brazil. efmerino@yahoo.com

ABSTRACT

Background: Plasmodium vivax is the most widely distributed human malaria, responsible for 70-80 million clinical cases each year and large socio-economical burdens for countries such as Brazil where it is the most prevalent species. Unfortunately, due to the impossibility of growing this parasite in continuous in vitro culture, research on P. vivax remains largely neglected.

Methods: A pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of P. vivax was performed. To do so, 1,184 clones from a cDNA library constructed with parasites obtained from 10 different human patients in the Brazilian Amazon were sequenced. Sequences were automatedly processed to remove contaminants and low quality reads. A total of 806 sequences with an average length of 586 bp met such criteria and their clustering revealed 666 distinct events. The consensus sequence of each cluster and the unique sequences of the singlets were used in similarity searches against different databases that included P. vivax, Plasmodium falciparum, Plasmodium yoelii, Plasmodium knowlesi, Apicomplexa and the GenBank non-redundant database. An E-value of <10(-30) was used to define a significant database match. ESTs were manually assigned a gene ontology (GO) terminology

Results: A total of 769 ESTs could be assigned a putative identity based upon sequence similarity to known proteins in GenBank. Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them.

Conclusion: These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced. Moreover, since the GC-content of the P. vivax genome is strikingly different from that of P. falciparum, these ESTs will help in the validation of gene predictions for P. vivax and to create a gene index of this malaria parasite.

Show MeSH
Related in: MedlinePlus