Instability of a yellow mutation in Chlamydomonas reinhardtii is not due to TOC1 elements

Large arrays of tandemly repeated DNA sequences in the green alga Chlamydomonas reinhardtii

We describe the characterization of tandemly repeated DNA sequences, which resemble the satellite DNA sequences of multicellular eucaryotes, in the unicellular green alga Chlamydomonas reinhardtii. Restriction enzymes that cleave C. reinhardtii DNA relatively frequently produce a number of high molecular weight DNA fragments in addition to the bulk of low molecular weight DNA fragments. pTANC 1.5 contains a 1.5 kb Sau3A fragment cloned from one of these large bands. pTANC 1.5 hybridized to at least three large arrays (200 to 700 kb) of tandemly repeated DNA sequences in the cell-wall-deficient strain cw1.5. These arrays are composed of repeat units that are each cleaved once by BamHl into bands of 1.5, 1.9, 2.0 and 2.5 kb in size. The copy numbers of the 1.5, 1.9, 2.0 and 2.5 kb BamHl bands vary between different C. reinhardtii strains. Chlamydomonas smithii and a number of C. reinhardtii strains are deficient in all four BamHl bands. Genetic analysis of wild-type strain 137c, which is deficient in the 2.0 kb BamHl band, indicates that the 1.5, 1.9 and 2.5 kb BamHl bands derive from at least five loci. The 1.5, 1.9 and 2.5 kb repeat units are not extensively interspersed with each other in strain 137c. Pulsed-field gel electrophoresis of intact C. reinhardtii chromosomes indicates that TANC arrays are present on more than one chromosome.

Conservation in structure of TOC1 transposons from Chlamydomonas reinhardtii

TOC1 transposons from Chlamydomonas reinhardtii have an unusual arrangement of long terminal repeats. Polymorphic regions between TOC1 transposons were identified by restriction mapping on Southern blots. The variation in size of an internal MluI fragment defines two subclasses of TOC1 elements. Full-length cloned members of each subclass of TOC1 element were compared by electron microscope heteroduplex analysis. The cloned elements were co-linear over their entire length with no large sequence discontinuities. Base substitutions and small insertion/deletion events of less than 50 bp are responsible for forming the two subclasses of TOC1 elements.

Structure and inheritance of sense and anti-sense transcripts from a transposon in the green alga Chlamydomonas reinhardtii

We have studied the transcription pattern of a 5700 base-pair transposon (TOC1) in Chlamydomonas reinhardtii. Northern blotting and nuclease S1 protection experiments define three classes of major TOC1 RNAs that accumulate to different levels in a number of strains and segregate independently in the progeny of crosses: class 1 RNAs are unstable near full-length sense transcripts whose 5' end maps to the left 217 base-pair repeat of TOC1, class 2 and class 3 RNAs are large, discrete chimaeric transcripts containing full-length sense (class 2) and anti-sense (class 3) copies of TOC1. Sequence motifs common to the 5' non-transcribed regions of C. reinhardtii genes were found upstream from the putative initiation site of class 1 transcripts. A functional polyadenylation site was located in the far-right 237 base-pair repeat of TOC1. Class 1 TOC1 transcripts are initiated, and probably terminated, within the terminal repeats of TOC1 and may represent retrotransposition intermediates. Class 2 and 3 TOC1 transcripts co-segregate with specific TOC1 elements identified on Southern blots. The loci that control the production of high levels of class 1 transcripts could correspond to specific TOC1 elements, i.e. only a few TOC1 elements are transcribed, or to a regulatory locus. The accumulation of an 11,500 to 12,000 base sense transcript (class 2) is reduced two- to fourfold by the presence of a 9500 to 9700 base antisense transcript (class 3). In contrast, the accumulation of the 5' ends of class 1 transcripts are unaffected by the anti-sense TOC1 transcript.