Academic journal article Genetics

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

Academic journal article Genetics

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

Article excerpt

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).

THE AMT4 gene of Chlamydomonas reinhardtii codes for an NH^sub 3^ gas channel that also transports the toxic analog methylamine (CH^sub 3^NH2) (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 (transposon of Chlamydomonas) and REM1 are retrotransposons (DAY et al. 1988; PÉREZ-ALEGRE et al. 2005) and Gulliver, Pioneer, and Tcr3 (transposon of C. reinhardtii) are class II elements (FERRIS 1989; GRAHAM et al. 1995; WANG et al. 1998). Transposable elements may be further classified according to their transposition mechanism (CURCIO and DERBYSHIRE 2003). TOC1 has recently been shown to belong to the DIRS-1 subclass of retrotransposons (GOODWIN and POULTER 2004), along with DIRS-1 from Dictyostelium discoideum (CAPPELLO et al. 1985), PAT from Panagrellus redivivus (DE CHASTONAY et al. 1992), and Kangaroo from Volvox carterei (DUNCAN et al. 2002). The replication of these retrotransposons involves a circular intermediate, which integrates by means of a tyrosine transposase. REM1 is related to the Ty3-gypsy long terminal repeat (LTR) retrotransposon class (PÉREZ-ALEGRE et al. 2005), which integrates by means of a DDE transposase (named for the acidic amino acid residues aspartate-aspartateglutamate, which coordinate the metal ions required for catalysis) (CURCIO and DERBYSHIRE 2003). The Gulliver and Pioneer transposons have been included in the Activator (Ac) and Dissociation (Ds) family, first described by MCCLINTOCK (1947, 1951). These, too, utilize a DDE transposase. The Tcr1 element, one of three named TCR transposons, was first encountered by SCHNELL and LEFEBVRE (1993) and later used by FERRIS et al. (1996) to clone the FUS1 gene. It has not been assigned with respect to class or transposition mechanism.

Previous studies have indicated that C. reinhardtii carries a wide variety of transposable elements (LEFEBVRE and SILFLOW 1999). Online access to the nearly complete genome (v3.0) of this organism at the Joint Genome Institute (JGI) has brought increased awareness of the diversity and abundance of these elements. …

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