One RNA polymerase serving two genomes.

The land plant Arabidopsis thaliana contains three closely related nuclear genes encoding phage-type RNA polymerases (RpoT;1, RpoT;2 and RpoT;3). The gene products of RpoT;1 and RpoT;3 have previously been shown to be imported into mitochondria and chloroplasts, respectively. Here we show that the transit peptide of RpoT;2 possesses dual targeting properties. Transient expression assays in tobacco protoplasts as well as stable transformation of Arabidopsis plants demonstrate efficient targeting of fusion peptides consisting of the N-terminus of RpoT;2 joined to green fluorescent protein to both organelles. Thus, RpoT;2 might be the first RNA polymerase shown to transcribe genes in two different genomes. RNA polymerase activity of recombinant RpoT;2 is uneffected by the inhibitor tagetin, qualifying the gene product of RpoT;2 as a phage-type polymerase.

Green fluorescent protein as a marker to investigate targeting of organellar RNA polymerases of higher plants in vivo.

The recent identification of phage-type RNA polymerases encoded in the nuclear genome of higher plants has provided circumstantial evidence for functioning of these polymerases in the transcription of the mitochondrial and plastid genomes, as demonstrated by sequence analysis and in vitro import experiments. To determine the subcellular localization of the phage-type organellar RNA polymerases in plants, the putative transit peptides of the RNA polymerases RpoT;1 and RpoT;3 from Arabidopsis thaliana and RpoT from Chenopodium album were fused to the coding sequence of a green fluorescent protein (GFP). The constructs were used to stably transform A. thaliana. Transgenic plants were examined for green fluorescence with epifluorescence and confocal laser scanning microscopy. Plants expressing the GFP fusions under control of the CaMV35S promoter exhibited a distinct subcellular localization of the GFP fluorescence for each of the fusion constructs. In plants expressing GFP fusions with the putative transit peptides of ARAth;RpoT;1 and CHEal;RpoT, fluorescence was found exclusively in mitochondria, both in root and leaf cells. In contrast, GFP fluorescence in plants expressing the ARAth;RpoT;3-GFP construct accumulated in chloroplasts of leaf cells and nongreen plastids (leucoplasts) of root cells. By demonstrating targeting in plants, the data add substantial evidence for the phage-type RNA polymerases from C. album and A. thaliana to function in the transcriptional machinery of mitochondria and plastids.

Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis.

In addition to the RNA polymerases (RNAPs) transcribing the nuclear genes, eukaryotic cells also require RNAPs to transcribe the genes of the mitochondrial genome and, in plants, of the chloroplast genome. The plant Arabidopsis thaliana was found to contain two nuclear genes similar to genes encoding the mitochondrial RNAP from yeast and RNAPs of bacteriophages T7, T3, and SP6. The putative transit peptides of the two polymerases were capable of targeting fusion proteins to mitochondria and chloroplasts, respectively, in vitro. The results indicate that the mitochondrial RNAP in plants is a bacteriophage-type enzyme. A gene duplication event may have generated the second RNAP, which along with the plastid-encoded eubacteria-like RNAP could transcribe the chloroplast genome.

Cloning and characterization of a cDNA encoding a bacteriophage-type RNA polymerase from the higher plant Chenopodium album.

We have cloned a full-length cDNA from the higher plant Chenopodium album coding for a single subunit bacteriophage-type RNA polymerase. The cDNA isolated from an actively growing cell suspension culture recognized a 3.8 kb transcript on Northern blots. The open reading frame comprises 987 amino acids with a predicted molecular mass of 112 kDa. A comparison of the protein sequence with those of the two known fungal mitochondrial RNA polymerases, from Saccharomyces cerevisiae and Neurospora crassa , reveals extensive homology between the three enzymes. with complete conservation of all catalytically essential amino acids. The putative mitochondrial RNA polymerase from C.album , as well as homologous sequences from rice and barley, which have been partially cloned, lack two catalytically non-essential regions of up to 176 amino acids near the C-terminus present in the two fungal mitochondrial RNA polymerases. The extreme N-terminus of the cloned C.album RNA polymerase displays features of a potential mitochondrial transit sequence. In phylogenetic trees constructed to compare the evolutionary relationships between the different single subunit RNA polymerases the C.album sequence forms a subgroup together with the S.cerevisiae and the N.crassa mitochondrial RNA polymerases, well separating from both bacteriophage enzymes and plasmid-encoded RNA polymerases found in mitochondria of many fungi and some higher plants.

Characterization of the single psbA gene of Prochlorococcus marinus CCMP 1375 (Prochlorophyta).

DNA sequence, copy number, expression and phylogenetic relevance of the psbA gene from the abundant marine prokaryote P. marinus CCMP 1375 was analyzed. The 7 amino acids near the C-terminus missing in higher plant and in Prochlorothrix hollandica D1 proteins are present in the derived amino acid sequence. P. marinus contains only a single psbA gene. Thus, this organism lacks the ability to adapt its photosystem II by replacement of one type of D1 by another, as several cyanobacteria do. Phylogenetic trees suggested the D1-1 iso-form from Synechococcus PCC 7942 as the next related D1 protein and place P. marinus separately from Prochlorothrix hollandica among the cyanobacteria.

DNA fragments of organellar origin in random amplified polymorphic DNA (RAPD) patterns of sugar beet (Beta vulgaris L.).

The technique of random amplified polymorphic DNA (RAPD) offers a broad range of applications in the investigation of plant genomes. A promising prospect is the use of RAPD products as genetic markers. We have investigated a possible organellar source of fragments in RAPD patterns of total DNA. Two nearly-isogenic lines of cytoplasmic male-sterile and male-fertile sugar beet (Beta vulgaris L.) were subjected to RAPD analysis with six different primers. Total, nuclear, mitochondrial (mt), and chloroplast (cp), DNA from each line were investigated. Reproducible DNA fingerprints could be obtained from both organellar DNAs. Differences in band patterns of mtDNA between cytoplasmic male-sterile and -fertile lines were observed with five out of six primers, whereas different cpDNA patterns were generated by one of the primers. Consequently, the RAPD technique can be used to discriminate between different cytoplasms. Clear evidence is provided for the organellar origin of fragments in genomic (total DNA) RAPD patterns. The consequences of these results for the interpretation of RAPD analyses are discussed.

A new type of cytoplasmic male sterility in rye (Secale cereale L.): analysis of mitochondrial DNA.

Mitochondrial (mt) DNA of a new type of rye cytoplasm ('Gülzow', G) that induces cytoplasmic male sterility (CMS) was analyzed and compared with rye mtDNAs of different origins MtDNA of the G type was easily distinguishable from mtDNA of another CMS source, 'Pampa' (P) type, and from mtDNA of fertile lines with respect to restriction fragment patterns and hybridization with mitochondrial genes. The results of the molecular analyses indicate a close, but not identical relationship between the mtDNA of the G type cytoplasm and that of cv 'Pluto'.

Cloning and sequencing of mutantpsbB genes of the cyanobacteriumSynechocystis PCC 6803.

Ten strains from a collection of mutants ofSynechocystis 6803 defective in Photosystem II (PS II) function were transformed with chromosomal DNA of wild-type and mutant cells. Cross hybridization data allowed to identify four groups of PS II-mutants. Highly efficient transformation was observed between different mutant groups, but not within the groups. Restoration of photosynthetic activity of the mutant cells was also achieved by transformation with different parts of a 5.6 kbBam HI fragment of wild typeSynechocystis DNA containing thepsbB gene. Each group of mutants was transformed to photoautotrophic growth by specific subfragments of thepsbB gene. DNA fragments of four selected mutant strains hybridizing with thepsbB gene were isolated and sequenced. The mutations were identified as a single nucleotide insertion or substitution leading to stop codon formation in two of the mutants, as a deletion of 12 nucleotides, or as a nucleotide substitution resulting in an amino acid substitution in the other two mutants. Deletion of 12 nucleotides in mutant strain PMB1 and stop codon formation in strain NF16 affect membrane-spanning regions of the gene product, the CP 47 protein.

Fingerprinting plant genomes with oligonucleotide probes specific for simple repetitive DNA sequences.

Oligonucleotides hybridizing to simple repetitive DNA patterns are highly informative as probes for DNA fingerprinting in all investigated animal species, including man. Here we demonstrate the applicability of this technique in higher plants. The oligonucleotide probes (GTG)5 and (GATA)4 were used to investigate the differences in DNA fingerprint patterns of the following angiosperm species: Triticum aestivum, Secale cereale, Hordeum vulgare, Beta vulgaris, Petunia hybrida, Brassica oleracea, and Nicotiana tabacum. Two species, Hordeum vulgare as a monocot and Beta vulgaris as a dicot, were analyzed in more detail. Their genomes differ considerably in both amount and organization of the simple repetitive sequences (GATA)n, (GACA)n, (GTG)n, and (CT)n due to the evolutionary distance of these two species. Furthermore, several lines and cultivars of Beta vulgaris and Hordeum vulgare can clearly be distinguished on the basis of their highly polymorphic patterns of these repetitive sequences.

Molecular characterization of mitochondrial DNA of different subtypes of male-sterile cytoplasms of the sugar beet Beta vulgaris L.

Mitochondrial (mt) DNA from eight cytoplasmic male-sterile (cms) lines of sugar beet from different breeding stations was investigated by restriction fragment analysis and Southern hybridization. All cms lines showed similar but not identical restriction and hybridization signal patterns, readily distinguishable from those of fertile (N) cytoplasm. Digestion of the mtDNA with BamHI, EcoRI, SalI, and XhoI revealed distinct differences between the sterile lines, and six subtypes of the S cytoplasm could be distinguished. Differences between the sterile lines were confirmed by hybridization with a [Formula: see text] gene probe revealing minor, line-specific hybridization signals. The data presented provide evidence for the existence of considerable variation within the only commercially used source of cms in the sugar beet, the Owen's type of cytoplasm.

Rapid hybridization-based assays for identification by DNA probes of male-sterile and male-fertile cytoplasms of the sugar beet Beta vulgaris L.

Methods are described whereby hybridization of mitochondrial (mt) DNA with different DNA probes can definitely distinguish male-fertile and and male-sterile (cms) cytoplasms of sugar beet Beta vulgaris L. We have developed two types of miniassays. (1) Comparative methods requiring the isolation and restriction of total cellular DNA, hybridization with cloned mtDNA fragments from either fertile or male-sterile cytoplasms, and comparison of the hybridization patterns to the fertile-and sterile-specific patterns of mtDNA of sugar beet for the given mtDNA probe. For these analyses, we routinely used 1 g of plant material to determine the type of cytoplasm. (2) Noncomparative ("plus-minus") methods requiring neither the isolation of pure DNA nor restriction, electrophoresis, or Southern blotting. Instead, alkaline-SDS plant extracts from as little as 50 mg of plant material were dot-blotted and hybridized with fertile-specific (mitochondrial minicircular DNA) and/or cms-specific probes (consisting of a 2.3-kb mtDNA sequence exclusively occurring in the cms cytoplasm). The assays are simple to perform, give definitive results, are nonde-structive to the plants, and may be used in mass screening of sugar beet populations for hybrid production or in in vitro culture processes.

Phosphorylated nonhistone proteins in different fractions of rat liver nuclei obtained by metrizamide gradient centrifugation.

The distribution of nuclear nonhistone proteins (NHPs) labelled in vivo with 32P was investigated in different subnuclear fractions obtained by metrizamide gradient centrifugation of mildly sonicated rat liver nuclei. The bulk chromatin banding at 1.20-1.22 g to cm3 (fraction C) contained only minor amounts both of non-phosphorylated and 32P-labelled NHPs. Nick-translated DNA sequences were found to sediment at a slightly higher density (1.26 g/cm3) in a minor fraction (A). Fraction A also contained a significant portion of the newly synthesized RNA and was enriched additionally with a broad spectrum of NHPs; some of them were highly 32P-labelled. Two hnRNP fractions (R2 and R1) sedimenting at densities greater than 1.28 g/cm3 were analyzed, too. By SDS-PAGE it was shown that the most abundant 32P-NHPs were found in three groups (fraction A, R1, and R2). Two of them, 32-34 KDa, and 37-40 KDa, are components of the major proteins of the hnRNP particles. A group of four moderately labelled 32P-NHPs of approximately 55 K, 64 K, 70 K, and 90 KDa appeared substantially enriched in fraction A. They were found also in RNP fractions R1 and R2, but to a smaller mount. Therefore, we suggest that in fraction A they exist in a complex with hnRNP. Fraction A was also enriched with numerous 32P-NHPs of very high molecular weight found in other types of experiments nearly exclusively in the nuclear residual structures. The 32P-protein pattern of the nucleoli was shown to be different from that of the other subnuclear fractions. Considering our observations on the accumulation of nick-translated DNA sequences, the presence of newly synthesized RNA, the high content of NHPs, and the association of special 32P-NHPs we suggest that fraction A represents transcriptionally active chromatin.

Discrimination of several classes of nonhistone proteins in chromatin fractions from liver and thymus nuclei of rats.

Nonhistone proteins (NHPs) of salt-soluble chromatin (Chromatin S) and of the residual nuclei (Chromatin P) from rat liver and thymus were studied by SDS-polyacrylamide gel electrophoresis. The two chromatin fractions of the liver showed significant differences in their NHP patterns with most of the hnRNP and matrix proteins occurring in Chromatin P. In accordance with the low protein content of thymus nuclei, the corresponding thymus fractions exhibited electrophoretic patterns with a markedly lower amount of NHPs than in liver. Chromatin P from thymus, in contrast to the liver fraction, revealed only a very low content of hnRNP-specific proteins of molecular weight 30,000-40,000 (30 K to 40 K) (informosomal proteins) consistent with the significantly lower RNA content of thymus nuclei. In the region of the matrix proteins (60-75 K) Chromatin P showed only two bands of about 64 K and 73 K in thymus, whereas in liver five strong bands at 64 K, 66 K, 69 K, 73 K, and 75 K were found. RNase digestion was employed to discriminate hnRNP-specific protein from "real" chromosomal NHPs. At least about 65% and 25% of the NHPs from Chromatin P and S of liver, respectively, were found to be RNP-specific. The two chromatin fractions were further fractionated by sucrose gradient centrifugation and isopycnic banding in metrizamide. After centrifugation the main peaks, both of Chromatin S and P, contained only minor amounts of NHPs with a predominating protein of 38 K. By the centrifugation procedures described in this paper, a small subfraction of chromatin could be separated which was enriched in newly synthesized RNA, informosomal proteins, matrix- and other high molecular weight proteins. This subfraction might be related to transcriptionally active chromatin.

Complexes of DNA with arginine-rich and slightly lysine-rich histones. Transcription and electron microscopy.

Calf thymus DNA was reconstituted with arginine-rich histones H3 and H4 and slightly lysine-rich histones H2A and H2B respectively. Complexes containing histones H3 and H4 exhibit nucleosome-like structures when examined in the electron microscope and show a restriction of in vitro transcription similar to that obtained for reconstitutes made up from the four histones H2A, H2B, H3 and H4. One the contrary, complexes of DNA and histones H2A and H2B create different morphological structures of short stretches of bound histones and do not cause a template restriction in vitro.

Effect of RNA synthesis on the binding of 3H-cortisol to nuclear ribonucleoprotein particles from rat liver carrying DNA-like RNA in vivo.

3H-cortisol was found to associate with rat liver nuclear 30S ribonucleoprotein particles carrying D-RNA in vivo. No interaction was detectable when RNA synthesis was inhibited by alpha-amanitine. The association appears to be specifically for RNP carrying RNA synthesized after the administration of cortisol to adrenalectomized rats. The DNA/protein/RNA ratio of rat liver nuclei was not effected by alpha-amanitine under our conditions. However, the drug caused a 5-10 fold decrease in nuclear uptake of cortisol. The results are discussed in relation to a supposed transfer of cortisol-receptor complexes from the chromatin template to the nascent RNA chains.