The synthesis and origin of chloroplast low-molecular-weight ribosomal ribonucleic acid in spinach

Transcription of ribosomal DNA in chloroplasts of Spirodela oligorhizaa

The genes for the two large ribosomal RNAs (16S and 23S) and for the 4.5S rRNA in Spirodela oligorhiza chloroplast DNA are transcribed as one large, 7,000 nucleotides long precursor rRNA.Using S1-nuclease mapping, we have determined that the transcript ends 135 nucleotides 3' distal of the 4.5S rRNA gene. 5S rRNA therefore, is most likely transcribed separately.Northern blotting of chloroplast RNA with distinct probes derived from the rDNA region reveals RNAs, which can be described as intermediates in the processing of the large precursor. With these findings a pathway for the maturation of this precursor is proposed.

Structure and evolution of the 4.5-5S ribosomal RNA intergenic region from Glycine max (soya bean)

The nucleotide sequence for the 4.5-5S ribosomal DNA region from the chloroplastids of soya beans was determined as the basis of further comparative studies on the structure and evolution of this intergenic region. Comparisons with other plant sequences as well as equivalent sequences in eubacteria suggest that the longer internal transcribed spacer regions of plants have evolved, at least in part, by DNA sequence duplications and that the presence of the 4.5S rRNA in chloroplast may result from the accidental acquisition of a RNA maturation site during the evolution of longer internal transcribed spacer regions. Estimates of the secondary structures also indicate only a very limited retention of structural features and suggest that the primary role of the intergenic sequences may be to bring processed sites into close proximity.

Structure and transcription of the 5S rRNA gene from spinach chloroplasts

The nucleotide sequence of the spinach chloroplast 5S rRNA gene and its flanking regions has been determined. A prokaryotic type promoter is to be found upstream of the 5S rRNA gene. Northern blot experiments with selected gene probes show that the 5S gene is co-transcribed with the other ribosomal genes of the operon. This result is confirmed by 5' S1 mapping of in vivo RNAs synthesised in chloroplasts or in an E. coli strain harboring a multicopy plasmid containing the 5S rRNA gene and its flanking regions. In vitro transcription experiments show that initiation of transcription does not occur at the level of the putative 5S rRNA gene promoter. Therefore, we conclude that the 5S rRNA is synthesized only be co-transcription of its gene with the other ribosomal genes of the operon. 3' S1 nuclease mapping in the spacer region between the 4.5S and the 5S rRNA genes reveals a set of protected fragments located in an A.T rich region downstream of a very stable hairpin and immediately upstream of the putative 5S promoter. This result is interpreted by the presence of preterminated transcripts or processing sites in this region.

Cotranscription and processing of 23S, 4.5S and 5S rRNA in chloroplasts from Zea mays

The termini of rRNA processing intermediates and of mature rRNA species encoded by the 3' terminal region of 23S rDNA, by 4.5S rDNA, by the 5' terminal region of 5S rDNA and by the 23S/4.5S/5S intergenic regions from Zea mays chloroplast DNA were determined by using total RNA isolated from maize chloroplasts and 32P-labelled rDNA restriction fragments of these regions for nuclease S1 and primer extension mapping. Several processing sites detectable by both 3' and 5' terminally labelled probes could be identified and correlated to the secondary structure for the 23S/4.5S intergenic region. The complete 4.5S/5S intergenic region can be reverse transcribed and a common processing site for maturation of 4.5S and 5S rRNA close to the 3' end of 4.5S rRNA was detected. It is therefore concluded that 23S, 4.5S and 5S rRNA are cotranscribed.

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.

The nucleotide sequence of the cytoplasmic 5S rRNA from the horsetail, Equisetum arvense

Using 3'- and 5'-end labelling sequencing techniques, the following sequence for the cytoplasmic 5S rRNA of the horsetail Equisetum arvense could be determined: (sequence in text). This sequence exhibits all features expected for higher plant cytoplasmic 5S rRNAs, and can be fitted to the secondary structure model for 5S rRNA proposed by De Wachter et al. (15).

Chemical accessibility of the 4.5S RNA in spinach chloroplast ribosomes

We have examined the accessibility to diethylpyrocarbonate of spinach chloroplast 4.5S ribosomal RNA when free and when it is part of the ribosomal structure. The modifications in free 4.5S RNA were found mostly in single-stranded regions of the secondary structure model proposed in our previous paper (Kumagai, I. et al. (1982) J.B.C. 257, 12924-28): adenines at positions 17, 19, 33, 36, 54, 55, 60, 64, 68, 72, 77, 86 and 87 were identified as the reactive residues. On the other hand, in 4.5S RNA in 70S ribosomes or 50S subunits, adenine 33 was exclusively modified, and its reactivity was much higher than in free 4.5S RNA. This highly accessible A33 of spinach 4.5S RNA is located within a characteristic seven nucleotide sequence, which is found in the 4.5S rRNAs from spinach, tobacco and a fern but deleted in 4.5S RNAs from maize and wheat.

The complete nucleotide sequence of a 23-S rRNA gene from tobacco chloroplasts

The nucleotide sequence of a tobacco chloroplast 23-S rRNA gene, including the spacer between it and the 4.5-S rRNA gene, has been determined. The 23-S rRNA coding region is 2804-base-pairs long. A comparison with the 23-S rRNA sequence of Escherichia coli reveals strong homology and further shows a similarity between the chloroplast 4.5-S rRNA and the 3'-terminal region of E. coli 23-S rRNA. However, the 101-base-pair spacer sequence between the 23-S and 4.5-S rRNA genes has little homology with E. coli 23-S rRNA.

The nucleotide sequence of chloroplast 4.5S rRNA from a fern, Dryopteris acuminata

The 4.5S rRNA was isolated from the chloroplast ribosomes from Dryopteris acuminata. The complete nucleotide sequence was determined to be: OHUAAGGUCACGGCAAGACGAGCCGUUUAUCACCACGAUAGGUGCUAAGUGGAGGUGCAGUAAUGUAUGCAGCUGAGGC AUCCUAAUAGACCGAGAGGUUUGAACOH. The 4.5S rRNA is composed of 103 nucleotides and shows strong homology with those from flowering plants.

Restriction endonuclease cleavage site map of chloroplast DNA from Oenothera parviflora (Euoenothera plastome IV)

1) More than 50 cleavage sites produced by the restriction endonucleases Sal I, Pst I, Kpn I, Sma I and Eco RI have been physically mapped on the 47 μm circular DNA molecule of the Euoenothera plastome IV. This plastome (= plastid genome) is considered to be the phylogenetically oldest of the subsection. 2) The DNA molecule is segmentally organized into four regions represented by a large duplicated sequence in inverted orientation whose copies are separated by two single-copy segments. The single-copy regions comprise about 14 and 57 Md in size, respectively. 3) The size of the inverted repeat, about 15 Md, was determined by restriction site mapping, by mapping of genes for ribosomal RNAs and by hybridization of a cRNA transcribed from a homologous part of Spinacia oleracea chloroplast DNA which appears to be phylogenetically conserved. 4) Hybridization of radio-iodinated spinach 16S, 23S and 5S chloroplast rRNA species to Southern blots of restricted plastome IV DNA has localized the rDNA to the inverted repeat regions, in the order given. The genes for 16S and 23S rRNA are separated by a 2.4 kbp spacer. 5) The physical map of the plastome IV DNA serves as basis for comparison with the DNA from the four other, closely related Euoenothera plastomes.

The 3'-terminal region of bacterial 23S ribosomal RNA: structure and homology with the 3'-terminal region of eukaryotic 28S rRNA and with chloroplast 4.5s rRNA

The sequence of the 110 nucleotide fragment located at the 3'-end of E.coli, P.vulgaris and A.punctata 23S rRNAs has been determined. The homology between the E.coli and P.vulgaris fragments is 90%, whereas that between the E.coli and A.punctate fragments is only 60%. The three rRNA fragments have sequences compatible with a secondary structure consisting of two hairpins. Using chemical and enzymatic methods recently developed for the study of the secondary structure of RNA, we demonstrated that one of these hairpins and part of the other are actually present in the three 3'-terminal fragments in solution. This supports the existence of these two hairpins in the intact molecule. Indeed, results obtained upon limited digestion of intact 23S RNA with T1 RNase were in good agreement with the existence of these two hairpins. We observed that the primary structures of the 3'-terminal regions of yeast 26S rRNA and X.laevis 28S rRNA are both compatible with a secondary structure similar to that found at the 3'-end of bacterial 23S rRNAs. Furthermore, both tobacco and wheat chloroplast 4.5S rRNAs can also be folded in a similar way as the 3'-terminal region of bacterial 23S rRNA, the 3'-end of chloroplast 4.5S rRNAs being complementary to the 5'-end of chloroplast 23S rRNA. This strongly reinforces the hypothesis that chloroplast 4.5S rRNA originates from the 3'-end of bacterial 23S rRNA and suggests that this rRNA may be base-paired with the 5'-end of chloroplast 23S rRNA. Invariant oligonucleotides are present at identical positions in the homologous secondary structures of E.coli 23S, yeast 26S, X.laevis 28S and wheat and tobacco 4.5S rRNAs. Surprisingly, the sequences of these oligonucleotides are not all conserved in the 3'-terminal regions of A.punctata or even P.vulgaris 23S rRNAs. Results obtained upon mild methylation of E.coli 50S subunits with dimethylsulfate strongly suggest that these invariant oligonucleotides are involved in RNA tertiary structure or in RNA-protein interactions.

The nucleotide sequence of 4.5S ribosomal RNA from tobacco chloroplasts

The nucleotide sequence of tobacco chloroplast 4.5S ribosomal RNA has been determined to be: OHG-A-A-G-G-U-C-A-C-G-G-C-G-A-G-A-C-G-A-G-C-C-G-U-U-U-A-U-C-A-U-U-A-C-G-A-U-A-G-G-U-G-U-C-A-A-G-U-G-G-A-A-G-U-G-C-A-G-U-G-A-U-G-U-A-U-G-C-(G-A)-C-U-G-A-G-G-C-A-U-C-C-U-A-A-C-A-G-A-C-C-G-G-U-A-G-A-C-U-U-G-A-A-COH. The 4.5S RNA is 103 nucleotides long and its 5'-terminus is not phosphorylated.

Cloning and characterization of 4.5S and 5S RNA genes in tobacco chloroplasts

Tobacco chloroplast 4.5S and 5S RNAs were shown to hybridize with a 0.9 . 10(6) dalton EcoRI fragment of tobacco chloroplast DNA. Recombinant plasmids were constructed from fragments produced by partial digestion of the chloroplast DNA with EcoRI and the pMB9 plasmid as a vector. Five recombinants containing the 4.5S and 5S genes were selected by the colony hybridization technique. One of these plasmids contained also the 16S and 23S RNA genes and was mapped using several restriction endonucleases as well as DNA-RNA hybridization. The order of rRNA genes is 16S-23S-4.5S-5S and the four rRNA genes are coded for by the same DNA strand.

4.5S ribonucleic acid, a novel ribosome component in the chloroplasts of flowering plants

A species of low-molecular-weight ribosomal RNA, referred to as '4.5S rRNA', was found in addition to 5S rRNA in the large subunit of chloroplast ribosomes of a wide range of flowering plants. It was shown by sequence analysis that several variants of this RNA may occur in a plant. Furthermore, although in most flowering plants the predominant variant contains about 100 nucleotides, in the broad bean it has less than 80. It seems, therefore, to be much more diverse in size and sequence than the other ribosomal RNA species. Like 5S rRNA , it does not contain modified nucleotides and it is also unusual in having an unphosphorylated 5'-end. It is apparently neither a homologue of cytosol 5.8S rRNA nor a fragment of 23S rRNA.

The synthesis of chloroplast high-molecular-weight ribosomal ribonucleic acid in spinach

Illuminated suspensions of chloroplasts isolated from young spinach leaves show incorporation of [3H]uridine into several species of RNA. One such RNA species of Mr 2.7 x 10(6) shows sequence homology with both the chloroplast 23-S rRNA (Mr = 1.05 x 10(6)) and 16-S rRNA (Mr = 0.56 x 10(6)), as judged by DNA/RNA competition hybridization. Leaves labelled in vivo with [32P]orthophosphate in the presence of chloramphenicol accumulate labelled RNAs of Mr 1.28 x 10(6), 0.71/0.75 x 10(6) and 0.47 x 10(6). The 1.28 x 10(6)-Mr RNA shows 80.5% sequence homology with the 1.05 x 10(6)-Mr rRNA and the 0.71/0.75 x 10(6)-Mr RNA mixture shows 76% sequence homology with the 0.56 x 10(6)-Mr rRNA. We conclude that the pathway of rRNA maturation in spinach chloroplasts is similar to that of Escherichia coli.