Genome-wide occurrences of candidate motifs. Most of the candidate motifs with verified biological function are over-represented within upstream regions. Motif density is plotted as number of motifs per 10 kb for each data set - upstream sequences (red) and coding sequences (blue) (Table 2) - on the y-axis for each candidate motif on the x-axis.

Candidate motifs identified upstream of the ribosomal protein genes, upstream location, site-directed mutagenesis and results of reporter assays. Motif RPA (TRP-1) does not influence reporter activity, and motif RPB (TRP-2) acts as an enhancer of gene-expression from the RPL9 promoter. (a) Sequence logos represent the consensus sequence for each candidate motif. The y-axis represents information content at each position. (b) Occurrences and positions of the motifs in the promoter region relative to the translational start site of each gene. The gene names are abbreviated as shown in Table 1. The underlined gene name indicates the representative promoter used in the reporter assays. (c) The WT motifs and their mutagenized (MUT) versions in the representative promoter are represented. (d) The graphs depict luciferase activity as ratios of firefly:renilla activity in relative luciferase units (RLU) from the different constructs containing either WT or mutagenized versions of RPA, RPB, both motifs or both copies of motif RPB. All luciferase readings are relative to an internal control (α-tubulin-renilla). Error bars represent standard error calculated across the means of three independent electroporations. p-values describe the probability that the difference in expression between the WT and mutagenized promoters may be due to chance.

Candidate motifs identified upstream of the micronemal protein-encoding genes, upstream location, site-directed mutagenesis and results of reporter assays. Motifs MICA and MICB display an additive effect in the regulation of the gene encoding microneme 8. (a) Sequence logos represent the consensus sequence for each candidate motif. The y-axis represents information content at each position. (b) Occurrences and positions of the motifs in the promoter region relative to the translational start site of each gene. The gene names are abbreviated as shown in Table 1. The underlined gene name indicates the representative promoter used in reporter assays. Motif MICA, found in both E. tenella and T. gondii, is denoted by a circle and motif MICB, exclusive to T. gondii, is denoted by a square. (c) The WT motifs and their mutagenized (MUT) versions in the representative promoter are represented. (d) The graphs depict luciferase activity as ratios of firefly:renilla activity in relative luciferase units (RLU) from the different constructs containing either WT or mutagenized versions of MICA, MICB, or both motifs. All luciferase readings are relative to an internal control (α-tubulin-renilla). Error bars represent standard error calculated across the means of three independent electroporations. p-values describe the probability that the difference in expression between the WT and mutagenized promoters may be due to chance.

Candidate motifs identified upstream of the nucleotide biosynthetic genes, upstream location, site-directed mutagenesis and results of reporter assays. Motifs NTBA and NTBB show redundancy in function by negatively affecting gene expression from the UPRT promoter among the nucleotide metabolism genes. (a) Sequence logos represent the consensus sequence for each candidate motif. The y-axis represents information content at each position. (b) Occurrences and positions of the motifs in the promoter region relative to the translational start site of each gene. The gene names are abbreviated as shown in Table 1. The underlined gene name indicates the representative promoter used in reporter assays. Motif NTBA, found in both E. tenella and T. gondii, is denoted by a circle and motif NTBB, exclusive to T. gondii, is denoted by a square. (c) The WT motifs and their mutagenized (MUT) versions in the representative promoter are represented. (d) The graphs depict luciferase activity as ratios of firefly:renilla activity in relative luciferase units (RLU) from the different constructs containing either WT or mutagenized versions of NTBA, NTBB, or both motifs. All luciferase readings are relative to an internal control (α-tubulin-renilla). Error bars represent standard error calculated across the means of three independent electroporations. p-values describe the probability that the difference in expression between the WT and mutagenized promoters may be due to chance.

Candidate motifs identified upstream of glycolytic genes, upstream location, site-directed mutagenesis and results of reporter assays. Motifs GLYCA and GLYCB act in concert to influence gene-expression from the Eno2 promoter. (a) Sequence logos represent the consensus sequence for each candidate motif. The y-axis represents information content at each position. (b) Occurrences and positions of the motifs in the promoter region relative to the translational start site of each gene. The gene names are abbreviated as shown in Table 1. The underlined gene name indicates the representative promoter used in reporter assays. Motif GLYCA, found in both E. tenella and T. gondii, is denoted by a circle and motif GLYCB, exclusive to T. gondii, is denoted by a square. Solid shapes denote motifs on the opposite strand. (c) The wild-type (WT) motifs and their mutagenized (MUT) versions in the representative promoter are represented. (d) The graphs depict luciferase activity as ratios of firefly:renilla activity in relative luciferase units (RLU) from the different constructs containing either WT or mutagenized versions of GLYCA, GLYCB, or both motifs. All luciferase readings are relative to an internal control (α-tubulin-renilla). Error bars represent standard error calculated across the means of three independent electroporations. p-values describe the probability that the difference in expression between the WT and mutagenized promoters may be due to chance.