The ribosomal RNA genes from chloroplasts of mustard (Sinapis alba L.): mapping and sequencing of the leader region

Chloroplast rRNA transcription from structurally different tandem promoters: an additional novel-type promoter

Identification of transcription initiation sites in the promoter region of the tobacco chloroplast rRNA operon has been carried out by ribonuclease protection of in vitro capped RNAs and primer extension experiments. A promoter with typical chloroplast -10 and -35 motifs (P1) drives initiation of transcription from position -116 relative to the mature 16s rRNA sequence. In addition, we have found that a second primary transcript starts at position -64. This proximal promoter (P2) lacks any elements similar to those reported so far in chloroplast promoter regions, and hence P2 represents a novel-type promoter. Both transcripts are present in chloroplasts from green leaves and in non-photosynthetic proplastids from heterotrophically cultured cells (BY2), but their relative amounts appear to differ. The steady state level of the P2 transcript, with respect to P1, is higher in BY2 proplastids than in leaf chloroplasts.

Evidence for a translation-mediated attenuation of a spinach chloroplast rDNA operon

The presence of potential hairpin structures H1, H2, H3 in the leader region of a spinach rDNA operon led us to postulate that this operon is regulated by premature termination. The mechanism would be controlled by the presence or absence of ribosomes translating a leader peptide. In vitro synchronized transcription by E. coli RNA polymerase shows that pauses do occur in the leader region. By their sizes, the transient transcripts could correspond to pauses on H1 and H2 as predicted by the model in the absence of ribosomes. The complete leader sequence (pKOPH) and the leader sequence with the hairpin structures deleted (pKOP) have been used to the GalK gene in the pK01 plasmid. The resulting plasmids have been used to transform a GalK- E. coli strain. Measurements of GalK expression show that the promoter region of spinach chloroplast rDNA is neither subjected to the growth rate nor to the stringent control. However, under growth conditions leading to an excess of free ribosomes, the expression of GalK gene appears systematically to be reduced in pKOPH when compared with that of pKOP. These results are consistent with a role of the leader region in a translation-mediated attenuation of the chloroplast rDNA expression.

Functional in vivo verification in E. coli of promoter activities from the rDNA/tDNA(Val)(GAC) leader region of Zea mays chloroplasts

Restriction fragments containing upstream sequences of the rRNA operon from Zea mays chloroplasts were tested for promoter activity in vivo by insertion into an E. coli promoter-probe vector. The expression of this vector's reporter gene, which codes for alkaline phosphatase, was stimulated more than 1,500-fold upon linkage with the chloroplast rRNA promoter. Site specific mutagenesis of the invariant T of the -10 sequence of this promoter reduced the expression of the reporter gene to 2% of the wild type. This indicates that the chloroplast rRNA promoter, which directs transcriptional initiation 117 bp upstream of the 16S rRNA gene, is also active in the bacterial system. A restriction fragment further upstream containing the gene for tRNA(Val) (GAC) also showed strong promoter activity (29% as compared with the rRNA promoter). This promoter activity probably reflects the chloroplast promoter directing the synthesis of the tRNA(Val) (GAC) primary transcript. Surprisingly, this restriction fragment also displayed promoter activity (13% compared with the rRNA promoter) in reverse orientation.

The chloroplast tRNALys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide

The trnK gene endocing the tRNALys(UUU) has been located on mustard (Sinapis alba) chloroplast DNA, 263 bp upstream of the psbA gene on the same strand. The nucleotide sequence of the trnK gene and its flanking regions as well as the putative transcription start and termination sites are shown. The 5' end of the transcript lies 121 bp upstream of the 5' tRNA coding region and is preceded by procaryotic-type "-10" and "-35" sequence elements, while the 3' end maps 2.77 kb downstream to a DNA region with possible stemloop secondary structure. The anticodon loop of the tRNALys is interrupted by a 2,574 bp intron containing a long open reading frame, which codes for 524 amino acids. Based on conserved stem and loop structures, this intron has characteristic features of a class II intron. A region near the carboxyl terminus of the derived polypeptide appears structurally related to maturases.

Specific in vitro transcription of 16S rRNA gene by pea chloroplast RNA polymerase

A highly purified RNA polymerase preparation from pea chloroplasts has been shown to specifically transcribe the 16S rRNA gene in vitro using the recombinant pCB2-8 DNA as a template. The RNA polymerase has been found to show maximum activity and specificity with pea supercoiled rDNA as a template. At low concentrations of ribonucleoside triphosphates, the RNA polymerase selectively initiates transcription on the 16S rRNA gene. A part of the 16S rRNA gene has been sequenced. The mature 16S rRNA has been found by S1 nuclease analysis to contain sequences starting from GAAGCT. The in vitro synthesized RNA has been found to protect the same nucleotides GAAGCT. In addition, the in vitro synthesized RNA was also found to strongly protect bases starting with TATG located at about 260 bases away from the start site of the mature 16S rRNA.

The region distal to the rRNA operon from chloroplasts of maize contains genes coding for tRNA(Arg)(ACG) and tRNA (Asn)(GUU)

The nucleotide sequence distal to the rRNA operon from maize chloroplasts has been analyzed. It contains genes coding for tRNA(Arg)(ACG) and tRNA(Asn)(GUU). The tRNA(Arg)(ACG) gene, which is separated from the last rRNA gene of the rRNA operon, the 5S rDNA, by an intergenic region of 252 bp, has the same orientation as the rRNA operon. By S1 and primer extension mapping, the existence of transcripts from the entire 5S rDNA/tDNA(Arg)(ACG) intergenic region can be demonstrated. It is, therefore, concluded that tRNA(Arg)(ACG) represents a trailer tRNA which is cotranscribed with 5S rRNA as part of the primary rRNA transcript. The tDNA(Asn)(GUU), which is separated from tDNA(Arg)(ACG) by an intergenic region of 253 bp, has the opposite orientation with respect to the rRNA operon; it, therefore, represents a separate transcriptional unit whose promoter remains to be located. It is proposed that the two tRNA genes possess a common terminator region, which functions in both directions of transcription.

Polymorphism and gene arrangement among plastomes of ten Epilobium species

Plastid DNAs of ten different Epilobium species from four continents have been analysed using the restriction endonucleases BamHI, BglI, BglII, EcoRI, PstI, PvuII and SalI. With respect to the position of cleavage sites of those enzymes, each species has a specific plastome. Fragment patterns of different species from the same continent show a higher degree of similarity than those from different continents. Physical maps of the circular plastid DNA molecule have been constructed for each of the ten species by localising the cleavage sites of the enzymes BglI, PvuII and SalI. As in most other higher plants, the plastid DNA of Epilobium is segmentally organized into two inverted repeats separated by a large and a small single copy region. In heterologous hybridization experiments using radioactively labelled gene probes, the positions of structural genes coding for the rRNAs and for seven polypeptides have been determined. In contrast to its closest relative, Oenothera, the gene arrangement of Epilobium plastomes has the same order as in spinach. This indicates that changes in gene arrangement may be genus-specific and not the result of one or several events affecting all members of a plant family.

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.

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.

Characterization of transcriptionally active DNA-protein complexes from chloroplasts and etioplasts of mustard (Sinapis alba L.)

DNA-protein complexes that are capable of RNA synthesis in vitro (transcriptionally active chromosomes) were isolated from both chloroplasts and etioplasts of mustard (Sinapis alba L.) seedlings. Analyses of the polypeptide pattern of these complexes indicate that they comprise a specific subset of plastid proteins, distinct from the overall pattern of either the soluble or membrane-bound plastic proteins. DNA-protein complexes from the two plastid types have polypeptides in common. However, at least several polypeptides are highly enriched in either the chloroplast or the etioplast DNA-protein complex. The EcoRI restriction endonuclease fragments of the DNA associated with the complexes from either plastid type are the same. They are identical with the fragments obtained from highly purified chloroplast DNA. The transcriptional activity of the chloroplast complex is more than ten times higher than the activity of the etioplast complex. However, the complexes from either plastid type are capable of transcribing DNA regions containing genes for both the plastid rRNAs and for plastid proteins. In vitro transcripts were found to hybridize not only to DNA regions for mature in vivo RNA but also to adjacent regions, indicating synthesis of precursor RNA sequences by the transcriptionally active chromosomes.