Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum

Abstract

The life cycle of the parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, requires specialized protein expression for survival in the mammalian host and insect vector. To identify components of processes controlling gene expression during its life cycle, the malarial genome--along with seven crown eukaryote group genomes--was queried with a reference set of transcription-associated proteins (TAPs). Following clustering on the basis of sequence similarity of the TAPs with their homologs, and together with hidden Markov model profile searches, 156 P. falciparum TAPs were identified. This represents about a third of the number of TAPs usually found in the genome of a free-living eukaryote. Furthermore, the P. falciparum genome appears to contain a low number of sequences, which are highly conserved and abundant within the kingdoms of free-living eukaryotes, that contribute to gene-specific transcriptional regulation. However, in comparison with these other eukaryotic genomes, the CCCH-type zinc finger (common in proteins modulating mRNA decay and translation rates) was found to be the most abundant in the P. falciparum genome. This observation, together with the paucity of malarial transcriptional regulators identified, suggests Plasmodium protein levels are primarily determined by posttranscriptional mechanisms.

Figure 1

Phylogenetic distribution of genes matching TRANSFAC-linked HMMs. The first column shows the Pfam accession numbers of the HMMs used in the genome searches (Table 1). If the HMM matches any malaria sequences, it is shown in purple, along with the number of P. falciparum sequences matching it (also in purple). The length of the strips in the next column (color-coded by species, see the key), indicates the proportion of sequences in a particular species, of the eight genomes that are matched by the HMM. The total number of sequences matching the HMM is indicated on the right of these strips. The bar graphs show the number of sequences that match the HMM, normalized by genome size and expressed as number of sequences per 10,000 genes. The two numbers above each other, and immediately to the right of the bar graphs, show the maximum and minimum normalized number of matches observed when the genomes were searched with the particular HMM. In the following column, if an HMM matches P. falciparum sequences, the normalized number of matching malaria sequences is displayed in the purple rounded box. HMMs matching only crown eukaryote group sequences are indicated by dashes. The penultimate column shows the average, normalized number of matches to the HMM in the seven crown eukaryote group genomes, along with the standard deviation. The final column shows the Pfam description of the HMM — this is in italics if the HMM matches malarial sequences.

Figure 2

Malarial TAP homologs and their expression patterns. The left column lists the 95 P. falciparum sequences identified by the TRIBE-MCL clustering and annotation procedure. Sequence identifiers are shown in brown. Next to each sequence identifier is shown a functional annotation of the protein. If the annotation contains a double colon (::), then the complex of which the sequence is a component is listed to the left of the double colon. Annotations containing {PFnnnnn} indicate the Pfam accession number(s) of the HMM(s) that match(es) the sequence. (Bottom) The right column (between the two parallel lines) shows the Pfam accession number of a HMM and the identifiers of the malarial sequences that match the HMM. (Top) The right-hand column represents as pie charts, the proportion of the malarial TAPs expressed in the sporozoite (S), merozoite (M), trophozoite (T), and gametocyte (G) stages. The expression profiles were obtained from the multidimensional protein identification technology (MudPIT) dataset. The blue and green sectors of the piecharts indicate the number of proteins not associated with transcription (also shown as percentage of total number expressed in the stage), whose expression is either specific to or unrestricted to a stage, respectively. The number of TAPs that are only expressed in the stage is indicated in the red box, and the number in the rounded orange box indicates the number that are also expressed in other stages. The percentage of these TAPs, of the total number of proteins expressed in the stage, is also indicated. In the square orange box, each of the three sectors of the pie chart shows the percentage of the nonstage-specific TAPs expressed in the other three stages.