Is transcription of higher plant chloroplast ribosomal operons regulated by premature termination?

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.

Characterization and properties of the spinach chloroplast transcriptionally active chromosome isolated at high ionic strength

The transcriptionally active chromosome (TAC) of spinach (Spinacia oleracea L.) chloroplasts has been isolated at a high ionic strength, with low mechanical shearing, by glycerol gradient centrifugation. The properties of the TAC differ from those previously reported for the TAC isolated either from Euglena chloroplasts or from spinach using a low-ionic-strength solubilization medium and gel filtration. The high-salt-isolated TAC is homogenous in density but not in size and contains fewer weakly bound proteins than its lowsalt-isolated homologue. In vitro, it promotes elongation of the RNA chains previously initiated in vivo. Transcription is not limited to the ribosomal DNA. The transcriptional pattern is not strongly affected by the high-salt preparation. Ribonuclease pretreatment of the TAC, prior to the in-vitro transcription, leads to a more than tenfold increase of the transcription activity. These properties are discussed in relation to the structure of the spinach chloroplast chromosome.

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.

Transcription of the chloroplast DNA: a review

The transcription systems of chloroplasts and bacteria share different properties. The genetic material of chloroplasts is organized in the same way as bacterial nucleoids. The regulatory DNA sequences for transcription have a strong homology with their E. coli counterparts and some regulatory mechanisms could be conserved. The RNA polymerase subunits and some transcription factors also share similarities with prokaryotes. However, the chloroplast core-enzyme seems to be synthesized in the cytoplasm from nuclear encoded messages.

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

The genes coding for rRNAs from mustard chloroplasts were mapped within the inverted repeat regions of intact ctDNA and on ctDNA fragments cloned in pBR322. R-loop analysis and restriction endonuclease mapping show that the genes for 16S rRNA map at distances of 17 kb from the junctions of the repeat regions with the large unique region. The genes for 23S rRNA are located at distances of 2.8 kb from the junctions with the small unique region. Genes for 4.5S and 5S rRNA are located in close proximity to the 23S rRNA genes towards the small unique region. DNA sequencing of portions of the 5' terminal third from the mustard 16S rRNA gene shows 96-99% homology with the corresponding regions of the maize, tobacco and spinach chloroplast genes. Sequencing of the region proximal to the 16S rRNA gene reveals the presence of a tRNA(Val) gene in nearly the same position and with identical sequence as in maize, tobacco and spinach. Somewhat less but still strong homology is also observed for the tDNA (Val)/16S rDNA intercistronic regions and for the regions upstream of the tRNA(Val) gene. However, due to many small and also a few larger deletions and insertions in the leader region, common reading frames coding for homologous peptides larger than 44 amino acids can not be detected; it is therefore unlikely that this region contains a protein coding gene.