Natural History of Transposition in the Green Alga Chlamydomonas reinhardtii: Use of the AMT4 Locus as an Experimental System

Abstract

The AMT4 locus of the green alga Chlamydomonas reinhardtii, which we mapped to the long arm of chromosome 8, provides a good experimental system for the study of transposition. Most mutations that confer resistance to the toxic ammonium analog methylammonium are in AMT4 and a high proportion of spontaneous mutations are caused by transposon-related events. Among the 15 such events that we have characterized at the molecular level, 9 were associated with insertions of the retrotransposon TOC1, 2 with a small Gulliver-related transposon, and 1 with the Tcr1 transposon. We found that Tcr1 is apparently a foldback transposon with terminal inverted repeats that are much longer and more complex than previously realized. A duplication of Tcr1 yielded a configuration thought to be important for chromosomal evolution. Other mutations in AMT4 were caused by two mobile elements that have not been described before. The sequence of one, which we propose to call the Bill element, indicates that it probably transposes by way of a DNA intermediate and requires functions that it does not encode. The sequence of the other and bioinformatic analysis indicates that it derives from a miniature retrotransposon or TRIM, which we propose to call MRC1 (miniature retrotransposon of Chlamydomonas).T HE AMT4 gene of Chlamydomonas reinhardtii codes for an NH 3 gas channel that also transports the toxic analog methylamine (CH 3 NH 2 ) (Kim et al. 2005). Like other AMT genes, AMT4 is highly expressed under nitrogen-limiting conditions (González-Ballester et al. 2004) and appears to be the major methylamine transporter. We have shown previously that most spontaneous mutations to methylamine (methylammonium) resistance occur in AMT4 and have briefly described several transposon-induced lesions (Kim et al. 2005).Transposable elements can be classified by their replicative intermediates: class I transposons, the retrotransposons, replicate by means of an RNA intermediate, whereas class II transposons replicate through a DNA intermediate (Sabot et al. 2004). Members of both these major families have been described in C. reinhardtii. TOC1

Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

“…The TOC1 and GULLIVER transposons are present as dispersed repeats in the C. reinhardtii genome at 10-40 copies/haploid genome and appear to integrate preferentially in euchromatic regions (Day et al 1988;Ferris 1989;Hall and Luck 1995;Kim et al 2006;Merchant et al 2007). In fact, some of these transposable elements were first isolated due to the mutant phenotypes caused by their insertion into active genes (Day et al 1988;Schnell and Lefebvre 1993).…”

Molecular techniques to interrogate and edit the Chlamydomonas nuclear genome

“…Chlamydomonas genes can be mutated by transposons. Chlamydomonas contains several transposable elements, including class I retrotransposon TOC1 (Day et al ., ) and REM1 (Pérez‐Alegre et al ., ) and class II elements Gulliver (Ferris, ), Pioneer1 (Graham et al ., ), Tcr1 (Ferris et al ., ), Tcr3 (Wang et al ., ), and Bill (Kim et al ., ). Transposable elements that transpose during mitotic growth may randomly integrate throughout the genome.…”

“…and Bill (Kim et al, 2006). Transposable elements that transpose during mitotic growth may randomly integrate throughout the genome.…”

“…Transposable elements that transpose during mitotic growth may randomly integrate throughout the genome. One study of spontaneous mutants found signatures of five different transposable elements at the AMT4 locus (encoding an NH 3 channel) (Kim et al, 2006). To identify genes disrupted by a transposon, a DNA fragment containing the transposon is isolated and sequenced.…”

The MIA complex is a conserved and novel dynein regulator essential for normal ciliary motility

“…2, A and B). The original mia1 mutant (King and Dutcher, 1997) has the 560-bp "Bill" transposon (Kim et al, 2006) inserted in the first exon of FAP100, resulting in failure of expression of this protein ( Fig. 3 A).…”