Recombination within the inverted repeat sequences of the Chlamydomonas reinhardii chloroplast genome produces two orientation isomers

Abstract

Two orientations of the Chlamydomonas reinhardii chloroplast (ct) genome are shown to be produced by recombination within the inverted repeat (IR) sequences that separate the two single copy (SC) regions. SC region 1 is bounded on its two ends by EeoRI restriction endonuclease fragments of 3.2 and 4.7 kilobase pairs (kb) (Rochaix 1978). The 3.2 kb EeoRI fragment overlaps a 51.3 kb BglII fragment spanning one of the 19.7 kb IR sequences, and the 4.7 kb EcoRI fragment overlaps a 42.1 kb BglII fragment spanning the other 19.7 kb IR sequence. We have shown by hybridization analysis that the 3.2 kb fragment also overlaps a BgIII fragment with a predicted size of 52.3 kb, and that the 4.7 kb fragment also overlaps a BglII fragment of a predicted size of 41.1 kb. The second set of BglII fragments are isomers produced by recombination localized to the IR region. The two isomers are present in approximately equimolar ratio. Knowledge of the isomeric composition of the C. reinhardii ctDNA is essential for establishing a correlation between genetic and physical maps of the ct genome.

Characterization of Satellite DNA from Three Marine Dinoflagellates (Dinophyceae): Glenodinium sp. and Two Members of the Toxic Genus, Protogonyaulax

“…The occurrence of ribosomal DNA in A-T rich satellites contrasts with observations that nuclear ribosomal DNA in terrestrial plants has been localized to guaninecytosine rich satellites, whose densities are heavier than that of nDNA (17,25). However, Chlamydomonas reinhardtii ribosomal DNA is found in Hoechst-CsCl gradients at a relatively A-T rich region (2).…”

Genetic Engineering for Microalgae Strain Improvement in Relation to Biocrude Production Systems

“…Though absent in present-day cyanobacteria and not essential for the general chloroplast genome function, the inverted repeat sequences show properties which suggest their involvement in gene maintenance and increased genome stability (Goulding et al 1996). Chloroplast genomes can undergo homologous recombination between the inverted repeat sequences as several studies have shown two populations of plastomes in the same organism differing only in the single-copy sequence orientation (Aldrich et al 1985;Palmer 1983;Stein et al 1986). Furthermore, it has been observed that the inverted repeat regions accumulate nucleotide substitution mutations 2.3 times more slowly than the single-copy regions (Perry and Wolfe 2002;Ravi et al 2008;Shaw et al 2007).…”

Replication, Recombination, and Repair in the Chloroplast Genetic System of Chlamydomonas

“…Moreover, Woefle et al (1993) have noted that recombination could act to initiate DNA replication and thus yield a cpDNA having a mosaicism of incorporated label. As described in more detail in later sections, other studies with mitotically growing cells have demonstrated frequent intramolecular recombination between the inverted repeats (Aldrich et al, 1985) and intra-or intermolecular recombination between duplications created through biolistic transformation (Cerutti et al, 1995), indicating that the enzymes for recombination are indeed present in vegetative cells.…”

“…As has been observed in higher plants, homologous intramolecular recombination occurs between the two copies of the large inverted repeat, resulting in two isomers of cpDNA that have the two single copy regions in opposite orientations (Aldrich et al, 1985;Palmer et al, 1985). To determine if 'flip-flop' recombination is a frequent event, Aldrich et al (1985) assessed the arrangement of the cpDNA isolated from three liquid cultures that had been derived from single vegetative cells.…”

“…To determine if 'flip-flop' recombination is a frequent event, Aldrich et al (1985) assessed the arrangement of the cpDNA isolated from three liquid cultures that had been derived from single vegetative cells. They reasoned that if flip-flop recombination of the cpDNA is infrequent, a single cell and the clonal line derived from it would have predominantly a single isomer.…”