Isolation of DNA from eukaryotic algae

The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization

This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping mitochondrial DNA (mtDNA) of 34 119 bp contains 58 densely packed genes (all without introns) and five unique open reading frames (ORFs). Protein genes code for components of respiratory chain complexes, ATP synthase and the mitoribosome, as well as one product of unknown function, encoded in many other protist mtDNAs (YMF16). In addition to small and large subunit ribosomal RNAs, 23 tRNAs are mtDNA-encoded, permitting translation of all codons present in protein-coding genes except ACN (Thr) and CGN (Arg). The missing tRNAs are assumed to be imported from the cytosol. Comparison of the C.SYNUROIDEUS: mtDNA with that of other stramenopiles allowed us to draw conclusions about mitochondrial genome organization, expression and evolution. First, we provide evidence that mitochondrial ORFs code for highly derived, unrecognizable versions of ribosomal or respiratory genes otherwise 'missing' in a particular mtDNA. Secondly, the observed constraints in mitochondrial genome rearrangements suggest operon-based, co-ordinated expression of genes functioning in common biological processes. Finally, stramenopile mtDNAs reveal an unexpectedly low variability in genome size and gene complement, testifying to substantial differences in the tempo of mtDNA evolution between major eukaryotic lineages.

Chloroplast encoded thioredoxin genes in the red algae Porphyra yezoensis and Griffithsia pacifica: evolutionary implications

A gene encoding a thioredoxin protein was identified in the chloroplast genome of the rhodophyte Porphyra yezoensis. The P. yezoensis trxA gene contains 324 bp and is transcribed into a 0.7 kb messenger RNA. Analysis of the transcription start site demonstrates that canonical chloroplast -10 and -35 sequences are not present. The deduced amino acid sequence of the thioredoxin gene from the red algae has the greatest similarity to type m thioredoxins, providing strong support for the hypothesis that type m thioredoxins in photosynthetic eukaryotes originated from an engulfed bacterial endosymbiont. Hybridization analysis of nuclear and chloroplast DNAs from several members of the phyla Chromophyta and Rhodophyta using P. yezoensis DNA as a probe demonstrated strong hybridization to the chloroplast and nuclear genomes of Griffithsia pacifica and a weak cross-hybridization to the chromophyte P. foliaceum. The G. pacifica chloroplast gene has a 66% identity with the P. yezoensis DNA, contains conserved active site amino acid residues, but lacks a methionine start codon.