Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray

Zbynek Bozdech¹, Jingchun Zhu¹, Marcin P Joachimiak², Fred E Cohen², Brian Pulliam¹ and Joseph L DeRisi¹

¹Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA

²Department of Molecular and Cellular Pharmacology, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA

author email corresponding author email

Genome Biology 2003, 4:R9doi:10.1186/gb-2003-4-2-r9


Published:	31 January 2003

Subject areas: Microbiology and parasitology, Genome studies, Bioinformatics, Methods

Abstract

Background

The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development.

Results

We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3' end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes specific to these two stages.

Conclusions

DNA microarrays based on long oligonucleotides are powerful tools for the functional annotation and exploration of the P. falciparum genome. Expression profiling of trophozoites and schizonts revealed genes associated with stage-specific processes and may serve as the basis for future drug targets and vaccine development.