Characterization of inverted repeat sequences and ribosomal RNA genes of chloroplast DNA from Chlorella ellipsoidea

Organization, generation and replication of amphimeric genomes: a review

Genomes comprising a pair of separated inverted repeats and called 'amphimers' are reviewed. Amphimeric genomes are observed in a large variety of different organisms, ranging from archaebacteria to mammals. The widespread existence of amphimeric genomes in nature could be due to their particular dynamic structure. Amphimeric genomes containing long inverted segments may provide the only form in which a duplicated segment is stably retained in genomes. Amphimers are often found in amplified subgenomes, indicating that they could promote a special mechanism of DNA replication and amplification. The possible mechanisms of generation, isomerization and replication/amplification of different types of amphimeric genomes are discussed. The study of amphimeric mitochondrial petite genomes of yeast could be a good model system for the study of the role of inverted repeat sequences in genome dynamics.

Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division

The complete nucleotide sequence of the chloroplast genome (150,613 bp) from the unicellular green alga Chlorella vulgaris C-27 has been determined. The genome contains no large inverted repeat and has one copy of rRNA gene cluster consisting of 16S, 23S, and 5S rRNA genes. It contains 31 tRNA genes, of which the tRNALeu(GAG) gene has not been found in land plant chloroplast DNAs analyzed so far. Sixty-nine protein genes and eight ORFs conserved with those found in land plant chloroplasts have also been found. The most striking is the existence of two adjacent genes homologous to bacterial genes involved in cell division, minD and minE, which are arranged in the same order in Escherichia coli. This finding suggests that the mechanism of chloroplast division is similar to bacterial division. Other than minD and minE homologues, genes encoding ribosomal proteins L5, L12, L19, and S9 (rpl5, rpl12, rpl19, and rps9); a chlorophyll biosynthesis Mg chelating subunit (chlI); and elongation factor EF-Tu (tufA), which have not been reported from land plant chloroplast DNAs, are present in this genome. However, many of the new chloroplast genes recently found in red and brown algae have not been found in C. vulgaris. Furthermore, this algal species possesses two long ORFs related to ycf1 and ycf2 that are exclusively found in land plants. These observations suggest that C. vulgaris is closer to land plants than to red and brown algae.

Repetitive sequence-mediated rearrangements in Chlorella ellipsoidea chloroplast DNA: completion of nucleotide sequence of the large inverted repeat

A 3454 base pair (bp) sequence of the large inverted repeat (IR) of chloroplast DNA (cpDNA) from the unicellular green alga Chlorella ellipsoidea has been determined. The sequence includes: (1) the boundaries between the IR and the large single copy (LSC) and the small single copy (SSC) regions, (2) the gene for psbA and (3) an approximately 1.0 kbp region between psbA and the rRNA genes which contains a variety of short dispersed repeats. The total size of the Chlorella IR was determined to be 15243 bp. The junction between the IR and the small single copy region is located close to the putative promoter of the rRNA operon (906 bp upstream of the -35 sequence on each IR). The junction between the IR and the large single copy region is also just upstream of the putative psbA promoter, 218 bp upstream from the ATG initiation codon. A few sets of unique sequences were found repeatedly around both junctions. Some of the sequences flanking the IR-LSC junction suggest a unidirectional and serial expansion of the IR within the genome. The psbA gene is located close to the LSC-side junction and codes for a protein of 352 amino acid residues. A highly conserved C-terminal Gly is absent Unlike the psbA of Chlamydomonas species, which contains 2-4 large introns, the gene of Chlorella has no introns.(ABSTRACT TRUNCATED AT 250 WORDS)

Unusual characteristics of Codium fragile chloroplast DNA revealed by physical and gene mapping

A complete physical map of the Codium fragile chloroplast genome was constructed and the locations of a number of chloroplast genes were determined. Several features of this circular genome are unusual. At 89 kb in size, it is the smallest chloroplast genome known. Unlike most chloroplast genomes it lacks any large repeat elements. The 8 kb spacer region between the 16S and 23S rRNA genes is the largest such spacer characterized to date in chloroplast DNA. This spacer region is also unusual in that it contains the rps12 gene or at least a portion thereof. Three regions polymorphic for size are present in the Codium chloroplast genome. The psbA and psbC genes map closely to one of these regions, another region is in the spacer between the 16S and 23S rRNA genes and the third is very close to or possibly within the 16S rRNA gene. The gene order in the Codium genome bears no marked resemblance to either the "consensus" vascular plant order or to that of any green algal or bryophyte genome.

An intron in the 23S rRNA gene of the Chlorella chloroplasts: complete nucleotide sequence of the 23S rRNA gene

A 243 bp intron was found within the 23S rRNA gene of the unicellular green alga Chlorella ellipsoidea. This intron is A+T-rich (63.7%) compared with the 23S rRNA (50.5%) and is located in domain II of the 23S rRNA. In contrast to rRNA introns so far known, this intron is considerably small and does not possess features of group I introns in spite of its possible folded secondary structure; this is a new type rRNA intron. The complete nucleotide sequence of the 23S rRNA gene (2,965 bp) was also compared with that of tobacco chloroplasts and E. coli.

Characterization of a chloroplast DNA sequence from Chlorella ellipsoidea that promotes autonomous replication in yeast

An EcoRI 2.7 kbp fragment from Chlorella ellipsoidea chloroplast DNA (cpDNA) cloned in YIp5 was shown to promote autonomous replication in Saccharomyces cerevisiae. The fragment was localized in the small single copy region close to the inverted repeat. The ARS activity (autonomously replicating sequences in yeast) was found to be confined within a subclone of a ca. 300 bp HindIII fragment. Sequence analysis of this fragment revealed its high AT content and the presence of several direct and inverted repeats and a few elements that were related to the yeast ARS consensus sequence. Electron microscopic studies revealed that this sequence did not coincide with the primary replication origin of chloroplast DNA. The functioning of this sequence as a possible origin of plasmid replication in vivo is discussed. This is the first report on Chlorella cpDNA sequence. re]19850821 rv]19851211 ac]19851216.

The plastome of a brown alga,Dictyota dichotoma : I. Physical properties and the Bam HI/Sal I/Bgl II cleavage site map

Plastids of the brown algaDictyota dichotoma contain a single homogeneous DNA species which bands at a buoyant density of 1.693 g/cm(3) in neutral CsCl equilibrium density gradients. The corresponding nuclear DNA has a density of 1.715 g/cm(3). The molecular size of the plastid DNA is 123 kbp as calculated by both electron microscopy of spread intact circular molecules and gel electrophoresis following single and double digestions with various restriction enzymes. A restriction map has been constructed using the endonucleases Sal I, Bam HI, and Bgl II which cleave theDictyota plastome into 6, 12, and 17 fragments, respectively. No large repeated regions, as found in chlorophycean andEuglena plastid DNAs, were detected.Dictyota dichotoma is the first member from the chlorophyll c-line of the algal pedigree for which a physical map of plastid DNA has been established.

A 21 kilobase-pair deletion/addition difference in the inverted repeat sequence of chloroplast DNA from Chlamydomonas eugametos and C. moewusii

Our recent physical mapping of chloroplast DNA (cpDNA) from Chlamydomonas moewusii, a unicellular green alga which is interfertile with Chlamydomonas eugametos, has revealed a two-fold size difference between the inverted repeat sequences of these algae. With a size of 42 kbp, the inverted repeat of C. moewusii is the largest yet identified in any chloroplast genome. Here we have compared the arrangement of conserved sequences within the two algal inverted repeats by hybridizing cloned restriction fragments representing over 90% of these repeats to Southern blots of cpDNA digests from the two algae. We found that the size difference between the two algal inverted repeats is due to the presence of an extra DNA segment of 21 kilobase pairs (kbp) in C. moewusii. Except for this sequence, the C. moewusii inverted repeat is highly homologous to the entire C. eugametos repeat and the arrangement of conserved sequences in the two repeats is identical. Southern hybridizations with specific gene probes revealed that the conserved sequences include the rDNA region and the genes coding for the large subunit of ribulose 1,5 bisphosphate carboxylase-oxygenase (rbcL) and for the '32 kilodalton' thylakoid membrane protein (psbA). With respect to the conserved sequences, the extra 21 kbp DNA segment of C. moewusii lies in the region of psbA, most probably slightly downstream from this gene.