Mapping the Chloroplast DNA of Vicia faba

Transfer RNAs and tRNA genes of Vicia faba chloroplasts

Isolated chloroplasts from broad bean and common bean were found to contain a minimum of 31 and 32 tRNA species, respectively. These individual chloroplast tRNAs were (32)P-labeled in vitro and hybridized to DNA fragments obtained upon digestion of broad bean and common bean chloroplast DNAs with various restriction endonucleases. At least 30 tRNA genes were localized on the physical maps of the two chloroplast genomes. Comparison of the broad bean tRNA gene map to that of common bean revealed DNA sequence rearrangements, such as inversions, insertions/ deletions and duplications, within these two members of the Legu minosae family.

The localization and orientation of specific genes in the chloroplast chromosome of Vicia faba

The genes for six chloroplast polypeptides have been localized on the map of Vicia faba chloroplast DNA using heterologous probes. These include the three subunits (α, β, ε) of CF1 of ATP synthase, subunit III of CF0 from ATP synthase, the 32 kilodalton thylakoidal membrane protein of photosystem II and cytochrome f of the electron transport chain. The direction of transcription has been determined for the three subunits of CF1 and the 32 kilodalton thylakoidal protein. The physical map of the chloroplast DNA has also been expanded to include Sma1 sites in addition to previously mapped restriction enzyme sites. Finally, the genetic arrangement of Vicia faba chloroplast DNA was compared to other known genetic maps.

Chloroplast DNA diversity in Vicia faba and its close wild relatives: implications for reassessment

To obtain new information on phylogenetic relationships between wild and cultivated broad bean, restriction fragment length polymorphism (RFLP) analysis of chloroplast (cp) DNAs from Vicia faba and eight subspecies/species of its close wild relatives grouped together in the Narbonensis complex was carried out using 14 restriction endonucleases. The molecular sizes of the cpDNAs obtained were similar (122.6-123.4 kbp), indicating that they had all lost one of inverted repeats. Among the more than 300 sites surveyed, the three subspecies within V. narbonensis, which exhibit just as many types of karyotypes, were shown to have identical cp fragment patterns. Genetic distances between all of the pairs of species were calculated from RFLP data. The cpDNA diversity within the Narbonensis complex was found to be more extensive than expected, except for the genetic relationship between V. hyaeniscyamus and V. johannis in which a total of three mutations were detected among the 300 sites sampled, thereby showing their close relatedness. The cpDNA of V. faba vis-a-vis its wild relatives also exhibited startling differences, indicating a clear division of Vicia species into two distinct lineages. This analysis unambiguously provides new evidence that the wild species grouped in the complex did not contribute their plastomes to the evolution of V. faba, and hence none of the species can be considered to be putative allies of broad bean. The present study also demonstrates profound cpDNA diversity among closely related species that have lost one of inverted repeats.

A model for the evolution of the Vicia faba chloroplast genome

The Vicia faba chloroplast genome lacks inverted repeat sequences and contains only one set of ribosomal RNA genes. The genetic organization has been altered by inversions, relative to the typical arrangement of most higher plant chloroplast genomes. The Vicia faba plastid genome thus represents one of the more interesting results of chloroplast genomic evolution. The present study employs small DNA probes and Southern blot hybridizations to investigate the steps involved in the evolution of the Vicia faba chloroplast genome. The data from heterologous hybridizations between chloroplast DNA of Brassica napus (a conserved genome) and of Vicia faba led to three observations: 1) The inverted repeat segment closest to the psbA gene was deleted prior to the rearrangements. 2) A quarter of the ancestral small single copy region was lost during the deletion. 3) The genetic organization observed in Vicia faba resulted from three inversions after the deletion event. Our findings, combined with previous observations, helped devise a stepwise model for the evolution of the Vicia faba chloroplast genome. The area of the small single copy region absent from the Vicia faba chloroplast chromosome lacks in vivo transcription activity in Brassica napus.

Nucleotide sequence of the chloroplast gene responsible for triazine resistance in canola

The nucleotide sequence for the psbA gene from a triazine resistant cultivar of B. napus (cv 'Triton') has been determined. This gene encodes an open reading frame of 353 amino acids that is highly homologous to other higher plant psbA genes at both the nucleotide and amino acid levels. As has been found for other triazine resistant psbA genes, the 'Triton' psbA contains an A to G nucleotide change which results in a serine to glycine amino acid substitution at position 264. The B. napus psbA gene also has a G insertion at position -9 resulting in a ribosome binding site sequence (AGGA) just before the initial methionine and suggesting that the entire open reading frame is translated. A large (72 bp) insertion is also found upstream of the B. napus psbA gene which resembles a similar insertion in the mustard psbA. The "uncloneable" nature of the entire gene is further investigated through reconstruction experiments and the implications discussed.

The localization of genes for ribosomal, cytochrome b6/f complex and photosystems I and II polypeptides on the chloroplast chromosome of Vicia faba

Detailed studies of rearranged chloroplast genomes such as Vicia faba should give insights into the constraints governing the positional organization of the various gene clusters on the chloroplast chromosome. Seven polypeptide genes have already been mapped on the Vicia faba chloroplast genome (21, 22). In this report, ten additional chloroplast DNA-coded polypeptide genes have been mapped by heterologous hybridization. These genes include cytochrome b6 and subunit 4 of the cytochrome b6/f complex, the two P700 chlorophyll a apoproteins of photosystem I, the two chlorophyll a-binding proteins of photosystem II, cytochrome b559, the D2 polypeptide and two ribosomal proteins. The direction of transcription for five of these gene sequences has been established by utilizing 5' and 3' end specific gene probes. The genetic organization of the Vicia faba chloroplast genome was compared with the chloroplast maps of the standard conserved genome of spinach and the more rearranged genome of pea.

Mapping the chloroplast genome of triazine resistant canola

The chloroplast of a triazine resistant weed biotype of Brassica campestris (bird's rape) has been transferred by repeated back-crossing into an agriculturally important strain, 'Tower', of Brassica napus to form a triazine resistant cultivar of canola, 'Triton', that is low in both erucic acid and thioglucosinolate. In this report, the B. campestris derived chloroplast chromosome of B. napus (cv 'Triton') has been cloned into bacterial plasmids and physically mapped for eight restriction enzymes: Apa I, Bam HI, BglI, Hind III, Pst I, Pvu II, Sac I and Xho I. The genes for rRNA, rbcL, cytF, atpA, atpB, atpE, atpH and the triazine resistance gene, psbA were located on the map by heterologous hybridization. The directions of transcription for most of these genes were determined by reverse heterologous hybridization.

The intergenic region between the Vicia faba chloroplast tRNA(CAALeu) and tRNA(UAALeu) genes contains a partial copy of the split tRNA(UAALeu) gene

A cluster of three tRNA genes located on fragment Bam6a from Vicia faba chloroplast DNA has been sequenced: it contains the genes for tRNA(CAALeu), tRNA(UAALeu) and tRNA(Phe). The two tRNA(Leu) genes are separated by 443 bp and are transcribed divergently from different DNA strands. The intergenic region contains a series of short repeats and a partial copy of the split tRNA(UAALeu) gene which includes 100 bp of the 5' flanking region, 35 bp of the 5'exon and the first 42 bp of the intron. It is possible that some of these duplications occurred upon the rearrangement of the two tRNA(Leu) genes in broad bean (and in pea) or upon the deletion of one copy of the inverted repeat, since in all other higher plant chloroplast genomes studied so far these two tRNA(Leu) genes are located far apart on the genome, one being in the inverted repeat region, the other one in the large single copy region. The tRNA(Phe) and tRNA(UAALeu) are encoded by the same DNA strand, and separated by 110 bp.

Intervening sequences in chloroplast genomes

Chloroplast DNAs from the green algae Euglena gracilis and from broad beans (Vicia faba) were hybridized with homologous chloroplast RNA. The hybrids were analyzed by electron microscopy. Almost all transcribed regions of the Euglena genome, except for the rRNA genes, contain intervening sequences. A minimum of 50 introns was observed amounting to about 32 kb of the 145 kb genome. Only four spliced transcripts with a total number of six introns (about 0.8 kb each) were detected in the bean chloroplast RNA. A complete transcription map of the Euglena chloroplast genome was established. Transcribed regions occur on the strand that codes for the rRNAs (plus strand) as well as on the complementary strand (minus strand). The polarity of transcription reverses at least six times.