Effects on mtDNA content and transcript levels caused by a knockout of MOC1 in the mutant stm6. (A) Map of the C. reinhardtii mitochondrial genome. Genes are presented as rectangles, and black arrows indicate the directions of transcription. Protein-coding genes are shown in black, ribosomal genes in dark grey and tRNA genes in light grey. nd4, nd5, nd2, nd6 and nd1 encode subunits of the Nicotinamide adenine dinucleotide dehydrogenase complex (complex I). cob is apocytochrome b belonging to complex III. cox1 represents subunit 1 of cytochrome c oxidase (complex IV) and rtl a reverse transcriptase-like protein. W, Q and M represent tRNA genes for tryptophan, glutamine and methionine codons. The genes L1–L7 encode large-subunit rRNA-coding modules and genes S1–S4 small-subunit modules. LTU comprises the genes cob, nd4 and nd5 encoded on the (−)-strand and RTU comprises all remaining genes on the (+)-strand. Structural elements of the left and right telomeres are indicated as IR (inverted repeat region) and rr (86-bp repeat) according to Vahrenholz et al. (4). The map is drawn to scale except for the telomere region (white rectangles; rr and IR). (B) Reverse transcription–quantitative-PCR analyses with all mitochondrial genes encoding OXPHOS complex subunits, the rtl gene encoding a reverse transcriptase-like protein (black bars) and selected ribosomal RNA genes (grey bars). Transcript levels in stm6 (MOC1 k.o. strain) are given in per cent and were calculated relative to the level in the MOC1-complemented strain (set to 100%). Error bars indicate the standard error derived from two biological replicates each including three technical replicates (n = 6). (C) Analysis of bicistronic transcript levels in the MOC1 knockout strain and the complemented strain by RT–Q-PCR. The relative transcript level (MOC1-complemented strain set to 100%) in the knockout strain is plotted on the y-axis, and error bars indicate the standard error (n = 6). (D) Relative expression level ratios of processed to unprocessed transcripts were determined in the MOC1 knockout (MOC1 k.o.) and complemented strain (MOC1 c.s.) by RT–Q-PCR. Ratios in the knockout mutant (y-axis) are given relative to those found in the complemented strain (set to 1), and analysed RNA species are indicated on the x-axis. Error bars (n = 6) are derived from two biological replicates each including three technical replicates.