Distribution of transfer RNA genes in thePisum sativum chloroplast DNA

Pea chloroplast DNA primase: characterization and role in initiation of replication

A DNA primase activity was isolated from pea chloroplasts and examined for its role in replication. The DNA primase activity was separated from the majority of the chloroplast RNA polymerase activity by linear salt gradient elution from a DEAE-cellulose column, and the two enzyme activities were separately purified through heparin-Sepharose columns. The primase activity was not inhibited by tagetitoxin, a specific inhibitor of chloroplast RNA polymerase, or by polyclonal antibodies prepared against purified pea chloroplast RNA polymerase, while the RNA polymerase activity was inhibited completely by either tagetitoxin or the polyclonal antibodies. The DNA primase activity was capable of priming DNA replication on single-stranded templates including poly(dT), poly(dC), M13mp19, and M13mp19 + 2.1, which contains the AT-rich pea chloroplast origin of replication. The RNA polymerase fraction was incapable of supporting incorporation of 3H-TTP in in vitro replication reactions using any of these single-stranded DNA templates. Glycerol gradient analysis indicated that the pea chloroplast DNA primase (115-120 kDa) separated from the pea chloroplast DNA polymerase (90 kDa), but is much smaller than chloroplast RNA polymerase. Because of these differences in size, template specificity, sensitivity to inhibitors, and elution characteristics, it is clear that the pea chloroplast DNA primase is an distinct enzyme form RNA polymerase. In vitro replication activity using the DNA primase fraction required all four rNTPs for optimum activity. The chloroplast DNA primase was capable of priming DNA replication activity on any single-stranded M13 template, but shows a strong preference for M13mp19 + 2.1. Primers synthesized using M13mp19 + 2.1 are resistant to DNase I, and range in size from 4 to about 60 nucleotides.

Pea chloroplast tRNA(Lys) (UUU) gene: transcription and analysis of an intron-containing gene

The pea chloroplast trnK gene which encodes tRNA(Lys) (UUU) was sequenced. TrnK is located 210 bp upstream from the promoter of psbA and immediately downstream from the 3'-end of rbcL. The gene is transcribed from the same DNA strand as psbA and rbcL. A 2447 bp intron with class II features is located in the trnK anticodon loop. The intron contains a 506 amino acid open reading frame which could encode an RNA maturase. The primary transcript of trnK is 2.9 kb long; its 5'-end was identified as a site of transcription initiation by in vitro transcription experiments. The 5'-terminus is adjacent to DNA sequences previously identified as transcription promoter elements. The most abundant trnK transcript is 2.5 kb long with termini corresponding to the 5' and 3' ends of the trnK exons. Intron specific RNAs were not detected. This suggests that RNA processing which produces tRNA(Lys) leads to rapid degradation of intron sequences.

Pea chloroplast topoisomerase I: purification, characterization, and role in replication

A DNA-relaxing enzyme was purified 5 000-fold to homogeneity from isolated chloroplasts of Pisum sativum. The enzyme consists of a single polypeptide of 112 kDa. The enzyme was able to relax negatively supercoiled DNA in the absence of ATP. It is resistant to nalidixic acid and novobiocin, and causes a unit change in the linkage number of supercoiled DNA. The enzyme shows optimum activity at 37°C with 50 mM KCl and 10 mM MgCl2. From these properties, the enzyme can be classified as a prokaryotic type I topoisomerase.Using a partiall purified pea chloroplast DNA polymerase fraction devoid of topoisomerase I activity for in vitro replication on clones containing the pea chloroplast DNA origins of replication, a 2-6-fold stimulation of replication activity was obtained when the purified topoisomerase I was added to the reaction at 70-100 mM KCl. However, when the same reaction was carried out at 125 mM KCl, which does not affect DNA polymerase activity on calf thymus DNA but is completely inhibitory for topoisomerase I activity, a 4-fold drop in activity resulted. Novobiocin, an inhibitor of topoisomerase II, was not found to inhibit the in vitro replication of chloroplast DNA.

Characterization of P. sativum chloroplast psbA transcripts produced in vivo, in vitro and in E. coli

We have analyzed the region of the chloroplast genome from P. sativum which encodes the 5'-end of psbA. S1 nuclease mapping and primer extension analysis of chloroplast RNA revealed psbA transcripts with 5'-termini 92, 93 and 68 nucleotides upstream from the psbA open reading frame. The psbA transcripts with 5'-ends 92-93 nucleotides upstream from the psbA open reading frame can be labeled with alpha-(32)P-GTP by guanylyltransferase. DNA sequences 10 and 35 bp upstream from the longest psbA transcript showed homology to -10 and -35 consensus promoter sequences in E. coli. Truncated psbA constructs which contain the putative psbA promoter sequences were shown to promote transcription in E. coli from a site similar to that used by chloroplast RNA polymerase in vivo. Accurate transcription of psbA constructs was also observed in a homologous in vitro transcription extract from chloroplasts. Sequence analysis of the region upstream from the psbA transcripts revealed a putative 3'-exon of a tRNA-Lys (240 bp upstream) and an unidentified open reading frame (URF, 485 bp upstream). The 3'-end of the URF mRNA was located approximately 240 bp from the 5'-end of the longest psbA transcript indicating that the URF and tRNA-Lys sequence are cotranscribed. Comparison of P. sativum and N. tabacum DNA sequences at the 5'-end of psbA revealed homology between sequences coding for psbA mRNA including 40 bp upstream from the longest psbA transcript. A second region of homology which includes the tRNA-Lys sequence was also located. In contrast the intergenic DNA exhibited extensive divergence in size and sequence. re]19850627 rv]19851211 ac]19851216.

Divergence of chloroplast gene organization in three legumes: Pisum sativum, Vicia faba and Phaseolus vulgaris

Isolated chloroplasts from Pisum sativum were found to contain at least 32 tRNA species. Hybridization of in vitro labeled, identified, chloroplast tRNAs to Pisum chloroplast DNA fragments revealed the locations of the tRNA genes on the circular chloroplast genome. Comparison of this gene map to the maps of Vicia faba and Phaseolus vulgaris showed that the chloroplast genomes of Pisum and Phaseolus are otherwise more closely related than either genome is to the chloroplast genome of Vicia. Furthermore, the results suggest how possible recombination events could be involved in the evolution of these three closely related, but divergent, chloroplast genomes.

Localization of the genes coding for the 51 kDa PSII chlorophyll apoprotein, apocytochrome b6, the 65-70 kDa PSI chlorophyll apoproteins and the 44 kDa PSII chlorophyll apoprotein in pea chloroplast DNA

DNA probes isolated from previously mapped spinach genes were used to locate 5 genes on pea ctDNA by heterologous hybridization. The genes mapped include psbC, psaA, psaB, psbB, and petB. PsbB and petB mapped to a 6.7 kbp XbaI DNA fragment adjacent to the petD gene. Northern probes from within the DNA which codes for psbB and petD hybridized to 6 RNAs ranging from 1.2 to 5.6 kbp. The psaA and psaB genes, which code for 65-70 kDa proteins of Photosystem I, were mapped to a 7.5 kbp. XbaI DNA fragment. A 5.8 kbp RNA is transcribed from the region which contains the psaA and psaB genes suggesting that these genes are co-transcribed. Finally the psbC gene which codes for a 44 kDa chlorophyll-protein of Photosystem II was mapped to a 12.3 kbp PstI DNA fragment. The pea psbC open reading frame overlaps the psbD coding sequence and this gene pair is within 3 kbp of the psaA-psaB genes. Overall, the organization of the 3 gene clusters analyzed in peas is similar to that reported for spinach.

Nucleotide sequences of transfer RNA genes in the Pisum sativum chloroplast DNA

Eight transfer RNA (tRNA) genes which were previously mapped to five regions of the Pisum sativum (pea) chloroplast DNA (ctDNA) have been sequenced. They have been identified as tRNA(Val)(GAC), tRNA(Asn)(GUU), tRNA(Arg)(ACG), tRNA(Leu)(CAA), tRNA(Tyr)(GUA), tRNA(Glu)(UUC), tRNA(His)(GUG), and tRNA(Arg)(UCU) by their anticodons and by their similarity to other previously identified tRNA genes from the chloroplast DNAs of higher plants or from E. gracilis. In addition,two other tRNA genes, tRNA(Gly) (UCC) and tRNA(Ile)(GAU), have been partially sequenced. The tRNA genes are compared to other known chloroplast tRNA genes from higher plants and are found to be 90-100% homologous. In addition there are similarities in the overall arrangement of the individual genes between different plants. The 5' flanking regions and the internal sequences of tRNA genes have been studied for conserved regions and consensus sequences. Two unusual features have been found: there is an apparent intron in the D-loop of the tRNA(Gly)(UCC), and the tRNA(Glu)(UUC) contains GATTC in its T-loop.