The plastome of Acetabularia mediterranea and Batophora oerstedii: inter-and intraspecific variability and physical properties

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.

Evolution and mechanism of translation in chloroplasts

The entire sequence (120-190 kb) of chloroplast genomes has been determined from a dozen plant species. The genome contains from 87 to 183 known genes, of which half encode components involved in translation. These include a complete set of rRNAs and about 30 tRNAs, which are likely to be sufficient to support translation in chloroplasts. RNA editing (mostly C to U base changes) occurs in some chloroplast transcripts, creating start and stop codons and changing codons to retain conserved amino acids. Many components that constitute the chloroplast translational machinery are similar to those of Escherichia coli, whereas only one third of the chloroplast mRNAs contain Shine-Dalgarno-like sequences at the correct positions. Analyses conducted in vivo and in vitro have revealed the existence of multiple mechanisms for translational initiation in chloroplasts.

Strong homology between the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase of two species of Acetabularia and the occurrence of unusual codon usage

Amino acid sequences of the small subunit of ribulose-1,5-bisphosphate carboxylase (SSU) of Acetabularia cliftonii and A. mediterranea were derived from five cDNA sequences of each of the two species of algae and by direct amino acid sequence determination of the isolated protein. An homology of more than 96% between the proteins indicates the close relationship between the two algae. All ten cDNAs in the reading frame display the termination codons TAA and/or TAG at various positions, which seem to code for the amino acid glutamine when compared with the amino acid sequence from the mature protein. This is reminiscent of proteins from ciliates where TAA and TAG also code for glutamine.