RNA polymerases of maize: partial purification and properties of the chloroplast enzyme

Plastid Gene Transcription: An Update on Promoters and RNA Polymerases

Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.

Modeling indicates degradation of mRNA and protein as a potential regulation mechanisms during cold acclimation

Plants are constantly exposed to temperature fluctuations, which have direct effects on all cellular reactions because temperature influences reaction likelihood and speed. Chloroplasts are crucial to temperature acclimation responses of plants, due to their photosynthetic reactions whose products play a central role in plant metabolism. Consequently, chloroplasts serve as sensors of temperature changes and are simultaneously major targets of temperature acclimation. The core subunits of the complexes involved in the light reactions of photosynthesis are encoded in the chloroplast. As a result, it is assumed that temperature acclimation in plants requires regulatory responses in chloroplast gene expression and protein turnover. We conducted western blot experiments to assess changes in the accumulation of two photosynthetic complexes (PSII, and Cytb6f complex) and the ATP synthase in tobacco plants over two days of acclimation to low temperature. Surprisingly, the concentration of proteins within the chloroplast varied negligibly compared to controls. To explain this observation, we used a simplified Ordinary Differential Equation (ODE) model of transcription, translation, mRNA degradation and protein degradation to explain how the protein concentration can be kept constant. This model takes into account temperature effects on these processes. Through simulations of the ODE model, we show that mRNA and protein degradation are possible targets for control during temperature acclimation. Our model provides a basis for future directions in research and the analysis of future results.

Chloroplast RNA polymerases: Role in chloroplast biogenesis

Plastid genes are transcribed by two types of RNA polymerase in angiosperms: the bacterial type plastid-encoded RNA polymerase (PEP) and one (RPOTp in monocots) or two (RPOTp and RPOTmp in dicots) nuclear-encoded RNA polymerase(s) (NEP). PEP is a bacterial-type multisubunit enzyme composed of core subunits (coded for by the plastid rpoA, rpoB, rpoC1 and rpoC2 genes) and additional protein factors (sigma factors and polymerase associated protein, PAPs) encoded in the nuclear genome. Sigma factors are required by PEP for promoter recognition. Six different sigma factors are used by PEP in Arabidopsis plastids. NEP activity is represented by phage-type RNA polymerases. Only one NEP subunit has been identified, which bears the catalytic activity. NEP and PEP use different promoters. Many plastid genes have both PEP and NEP promoters. PEP dominates in the transcription of photosynthesis genes. Intriguingly, rpoB belongs to the few genes transcribed exclusively by NEP. Both NEP and PEP are active in non-green plastids and in chloroplasts at all stages of development. The transcriptional activity of NEP and PEP is affected by endogenous and exogenous factors. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

Plastid gene transcription: promoters and RNA polymerases

Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.

A purification strategy for analysis of the DNA/RNA-associated sub-proteome from chloroplasts of mustard cotyledons

Plant cotyledons are a tissue that is particularly active in plastid gene expression in order to develop functional chloroplasts from pro-plastids, the plastid precursor stage in plant embryos. Cotyledons, therefore, represent a material being ideal for the study of composition, function and regulation of protein complexes involved in plastid gene expression. Here, we present a pilot study that uses heparin-Sepharose and phospho-cellulose chromatography in combination with isoelectric focussing and denaturing SDS gel electrophoresis (two-dimensional gel electrophoresis) for investigating the nucleic acids binding sub-proteome of mustard chloroplasts purified from cotyledons. We describe the technical requirements for a highly resolved biochemical purification of several hundreds of protein spots obtained from such samples. Subsequent mass spectrometry of peptides isolated out of cut spots that had been treated with trypsin identified 58 different proteins within 180 distinct spots. Our analyses indicate a high enrichment of proteins involved in transcription and translation and, in addition, the presence of massive post-translational modification of this plastid protein sub-fraction. The study provides an extended catalog of plastid proteins from mustard being involved in gene expression and its regulation and describes a suitable purification strategy for further analysis of low abundant gene expression related proteins.

Purification and properties of a pea chloroplast DNA polymerase

A DNA polymerase has been purified >3,000-fold from the chloroplasts of pea plants by chromatography on DEAE-cellulose, phosphocellulose, single-stranded DNA-agarose, and sedimentation in a glycerol gradient. Electrophoretic analysis on polyacrylamide gels in the presence of sodium dodecyl sulfate indicates that the final fraction contained a single discernible protein band of 90,000 daltons. Gel filtration on Sephacryl S-200 and glycerol gradient sedimentation under nondenaturing conditions demonstrate that the chloroplast DNA polymerase has a native molecular mass of approximately 87,000 daltons. The purified polymerase lacks any associated nuclease activity. The enzyme activity is inhibited by N-ethylmaleimide (74% at 1.0 mM) and ethidium bromide (90% at 0.23 mM) and is resistant to aphidicolin. The purified enzyme is totally dependent on the presence of added DNA, has an absolute requirement for Mg(2+) (12 mM optimal), is stimulated by K(+) (120 mM optimal), and requires all four deoxynucleoside triphosphates for maximum activity. Native DNA which has been degraded to a limited extent with DNase I is the most efficient template.

Preferential transcription of cloned maize chloroplast DNA sequences by maize chloroplast RNA polymerase

Zea mays chloroplast DNA-dependent RNA polymerase in vitro preferentially transcribes maize chloroplast DNA sequences incorporated in cloned chimeric bacterial plasmids. Preferential transcription is dependent on the presence of a 27.5-kilodalton polypeptide, the S factor, which has been purified from maize chloroplasts, and also on the template's being in the supercoiled form.

Maize plastid gene expressed during photoregulated development

RNAs larger than about 6 S prepared from etioplasts of dark-grown maize seedlings, and from plastids at later stages of light-induced development, were labeled in vitro and hybridized to separated fragments of maize chloroplast DNA digested with endonucleases. The major nonribosomal RNA present in developing plastids, but virtually undetectable in etioplasts, hybridizes to chloroplast DNA Bam fragment 8 and has been mapped on the maize plastid chromosome. Other aliquots of RNA from plastids were translated in a rabbit reticulocyte-derived system. Developing plastids, and mature chloroplasts, but not etioplasts, contain mRNA for an approximately 34,500 dalton polypeptide. The simultaneous appearance, during light-induced maize plastid development, of RNA which hybridizes to Bam 8 and is translated into a 34,500 dalton protein indicates that photoregulated expression of a single gene is being observed.

The role of phosphorylation in redox regulation of photosynthesis genes psaA and psbA during photosynthetic acclimation of mustard

The long-term response (LTR) to light-quality gradients improves performance and survival of plants in dense stands. It involves redox-controlled transcriptional regulation of the plastome-encoded genes psaAB (encoding the P700 apoproteins of photosystem I) and psbA (encoding the D1 protein of photosystem II) and requires the action of plastid-localized kinases. To study the potential impact of phosphorylation events on plastid gene expression during the LTR, we analyzed mustard seedlings acclimated to light sources favoring either photosystem I or photosystem II. Primer extension analyses of psaA transcripts indicate that the redox regulation occurs at the principal bacterial promoters, suggesting that the plastid encoded RNA polymerase (PEP) is the target for redox signals. Chloroplast protein fractions containing PEP and other DNA-binding proteins were purified from mustard via heparin-Sepharose chromatography. The biochemical properties of these fractions were analyzed with special emphasis on promoter recognition and specificity, phosphorylation state, and kinase activity. The results demonstrate that the LTR involves the action of small DNA-binding proteins; three of them exhibit specific changes in the phosphorylation state. Auto-phosphorylation assays, in addition, exhibit large differences in the activity of endogenous kinase activities. Chloroplast run-on transcription experiments with the kinase inhibitor H7 and the reductant DTT indicate that phosphorylation events are essential for the mediation of redox signals toward psaA and psbA transcription initiation, but require the synergistic action of a thiol redox signal. The data support the idea that redox signals from the thylakoid membrane are linked to gene expression via phosphorylation events; however, this mediation appears to require a complex network of interacting proteins rather than a simple phosphorelay.

A fluorescence-based assay for multisubunit DNA-dependent RNA polymerases

The properties of DNA-dependent RNA polymerases have been studied since the 1960s, but considerable interest in probing RNA polymerase structure/function relationships, the roles of different classes of RNA polymerases in cellular processes, and the feasibility of using RNA polymerases as drug targets still exists. Historically, RNA polymerase activity has been measured by the incorporation into RNA of radioisotopically labeled nucleotides. We report the development of an assay for RNA polymerase activity that uses the dye RiboGreen to detect transcripts by fluorescence and is thus free of the expense, short shelf life, and high handling costs of radioisotopes. The method is relatively quick and can be performed entirely in microplate format, allowing for the processing of dozens to hundreds of samples in parallel. It should thus be well-suited to use in drug screening and analysis of chromatographic fractions. As RiboGreen fluorescence is enhanced by binding to either RNA or DNA, template DNA must be removed by DNase digestion and ultrafiltration between the transcription and the detection phases of the assay procedure. Although RiboGreen fluorescence is sensitive to changes in solvent environment, solvent exchange in the ultrafiltration step allows comparison of transcription levels even under extremes of salt, pH, etc.

Viroids with hammerhead ribozymes: some unique structural and functional aspects with respect to other members of the group

Viroids, subviral pathogens of plants, are composed of a single-stranded circular RNA of 246-399 nucleotides. Within the 27 viroids sequenced, avocado sunblotch, peach latent mosaic and chrysanthemum chlorotic mottle viroids (ASBVd, PLMVd and CChMVd, respectively) can form hammerhead structures in both of their polarity strands. These ribozymes mediate self-cleavage of the oligomeric RNAs generated in the replication through a rolling circle mechanism, whose two other steps are catalyzed by an RNA polymerase and an RNA ligase. ASBVd, and presumably PLMVd and CChMVd, replicate and accumulate in the chloroplast, whereas typical viroids replicate and accumulate in the nucleus. PLMVd and CChMVd do not adopt a rod-like or quasi rod-like secondary structure as typical viroids do but have a highly branched conformation. A pathogenicity determinant has been mapped in a defined region of the CChMVd molecule.

Organellar RNA polymerases of higher plants

The nuclear genome of the model plant Arabidopsis thaliana contains a small gene family consisting of three genes encoding RNA polymerases of the single-subunit bacteriophage type. There is evidence that similar gene families also exist in other plants. Two of these RNA polymerases are putative mitochondrial enzymes, whereas the third one may represent the nuclear-encoded RNA polymerase (NEP) active in plastids. In addition, plastid genes are transcribed from another, entirely different multisubunit eubacterial-type RNA polymerase, the core subunits of which are encoded by plastid genes [plastid-encoded RNA polymerase (PEP)]. This core enzyme is complemented by one of several nuclear-encoded sigma-like factors. The development of photosynthetically active chloroplasts requires both PEP and NEP. Most NEP promoters show certain similarities to mitochondrial promoters in that they include the sequence motif 5'-YRTA-3' near the transcription initiation site. PEP promoters are similar to bacterial promoters of the -10/-35 sigma 70 type.

Detection of avocado sunblotch viroid in chloroplasts of avocado leaves by in situ hybridization

In situ hybridization experiments were carried out to detect avocado sunblotch viroid (ASBVd) in foliar tissue of avocado, using a digoxigenin-labelled RNA probe complementary to the ASBVd-RNA in sections of aldehyde-fixed, LRGold-embedded leaf samples. Detection of the probe was made through anti-digoxigenin antibody and protein-A colloidal gold (20 nm). Seventy to 80% of the signals came from chloroplast while the cytoplasm and vacuole were labelled with ca. 10% of the gold particles. This is in contrast with the subcellular localization of potato spindle tuber viroid and some other related viroids, which are mainly found in the nucleus.

Separation of two classes of plastid DNA-dependent RNA polymerases that are differentially expressed in mustard (Sinapis alba L.) seedlings

Chloroplast and etioplast in vitro transcription systems from mustard have different functional properties, which is reflected in differences in phosphorylation status. Here we report another transcription control mechanism, which involves two plastid DNA-dependent RNA polymerases designated as peak A and peak B enzymes. Both are large multi-subunit complexes, but differ in their native molecular mass (> 700 kDa for peak A and ca. 420 kDa for peak B) and in their polypeptide composition. The A enzyme is composed of at least 13 polypeptides, while the B enzyme contains only four putative subunits. Peak B activity is inhibited by rifampicin, whereas that of peak A is resistant. RNA polymerase activity was compared for plastids from cotyledons of 4-day-old seedlings that were grown either under continuous light (chloroplasts) or in darkness (etioplasts), or were first dark-grown and then transferred to light for 16 h ('intermediate-type' plastids). While the total activity was approximately the same in all three cases, enzyme B was the predominant activity obtained from etioplasts and enzyme A that obtained from chloroplasts. Both had equal activity in preparations from the 'intermediate-type' plastid form. Both activation/inactivation and differential gene expression seem to play a role in the regulation of the plastid transcription machinery.

Evidence that sigma factors are components of chloroplast RNA polymerase

Plastid genes are transcribed by DNA-dependent RNA polymerase(s), which have been incompletely characterized and have been examined in a limited number of species. Plastid genomes contain rpoA, rpoB, rpoC1, and rpoC2 coding for alpha, beta, beta', and beta" RNA polymerase subunits that are homologous to the alpha, beta, and beta' subunits that constitute the core moiety of RNA polymerase in bacteria. However, genes with homology to sigma subunits in bacteria have not been found in plastid genomes. An antibody directed against the principal sigma subunit of RNA polymerase from the cyanobacterium Anabaena sp. PCC 7120 was used to probe western blots of purified chloroplast RNA polymerase from maize, rice, Chlamydomonas reinhardtii, and Cyanidium caldarium. Chloroplast RNA polymerase from maize and rice contained an immunoreactive 64-kD protein. Chloroplast RNA polymerase from C. reinhardtii contained immunoreactive 100- and 82-kD proteins, and chloroplast RNA polymerase from C. caldarium contained an immunoreactive 32-kD protein. The elution profile of enzyme activity of both algal chloroplast RNA polymerases coeluted from DEAE with the respective immunoreactive proteins, indicating that they are components of the enzyme. These results provide immunological evidence for sigma-like factors in chloroplast RNA polymerase in higher plants and algae.

Nascent transcript-binding protein of the pea chloroplast transcriptionally active chromosome

This study describes the nascent RNA-binding protein of the pea chloroplast transcriptional complex. The protein has been identified by photoaffinity labelling of the transcriptionally active chromosome (TAC) which utilizes the endogenous plastid DNA as template. UV irradiation of lysed chloroplast or the isolated TAC under conditions optimized for transcription photocross-links nascent radiolabelled transcripts (up to 250 nucleotides in length) to a 48 kDa protein. The photoaffinity labelling of the transcript-binding protein is dependent on UV irradiation, is maximal after about 30 min of irradiation, and is completely dependent on transcriptional activity; no cross-linkage has been observed with pre-synthesized RNA. Cross-linkage is influenced by salts and inhibitors in accordance with their effects on transcription. The photoconjugate is composed of protein and RNA moieties, and can be hydrolysed by several proteases. However, the cross-linked transcript is protected from nucleases until the protein is removed. Manganese enhances photoaffinity labelling of the transcript-binding protein, and this is paralleled by an increase in total transcriptional activity of TAC. This protein was isolated by 2-dimensional polyacrylamide gel electrophoresis and the sequence of 15 amino acid residues at the amino terminus was determined. The nascent transcript-binding protein appears to be involved in the transcription of all three classes of chloroplast genes. We also found a polypeptide of identical molecular weight to get cross-linked to nascent transcripts in chloroplasts isolated from other legumes such as Cicer arietenum, Vigna radiata and Phaseolus vulgaris, and monocots like Zea mays, Oryza sativa and Pennisetum americanum.

Identification of the template binding polypeptide in the pea chloroplast transcriptional complex

We have identified the template-binding polypeptide in the pea chloroplast transcriptional complex by photoaffinity labelling. This polypeptide has an apparent molecular weight of about 150 kDa and binds to both, chloroplast ribosomal (16S rRNA) and messenger (psbA) promoters. The 16S rRNA and psbA promoters were amplified from chloroplast DNA by the polymerase chain reaction and labelled with a photoactive analogue of TTP, 5-bromodeoxy UTP, as well as with alpha-32P-dCTP. Using the filter-binding assay, the conditions for binding of the RNA polymerase complex to chloroplast promoters were optimized. The polypeptide directly interacting with the template was photo-crosslinked to it and resolved by denaturing gel electrophoresis. The photoaffinity labelling of the 150 kDa polypeptide was dependent on photoactivation by UV irradiation, and the presence of chloroplast promoters. Competition experiments showed that the protein formed a strong interaction with the plastid promoters which could not be displaced by lambda-phage DNA or synthetic polynucleotides. The photo-crosslinked and nuclease-treated promoter-polypeptide complex was resistant to further digestion with DNase and RNase, but could be hydrolyzed by Proteinase K. Binding of the promoters by the 150 kDa polypeptide could not be surpressed by transcription inhibitors like rifampicin and alpha-amanitin. However, heparin (0.001%) inhibited the formation of the enzyme-promoter complex, and interfered with the photoaffinity labelling of the 150 kDa polypeptide. The extent of photoaffinity labelling of 150 kDa polypeptide exhibits some degree of correlation to total transcriptional activity under various salt concentrations. The results demonstrate that the 150 kDa polypeptide is a functional template binding polypeptide of the pea chloroplast transcription complex.

The chloroplast transcription apparatus from mustard (Sinapis alba L.). Evidence for three different transcription factors which resemble bacterial sigma factors

A chloroplast protein fraction with sigma-like activity [Bülow, S. & Link, G. (1988) Plant Mol. Biol. 10, 349-357], was further purified and characterized. Chromatography on heparin-Sepharose, DEAE-Sepharose and Sephacryl S-300 led to the separation of three sigma-like factors (SLF) polypeptides with Mr 67,000 (SLF67), 52,000 (SLF52) and 29,000 (SLF29). None of these polypeptides bind to DNA itself, but each one confers enhanced binding and transcriptional activity when added to Escherichia coli RNA-polymerase core enzyme and DNA fragments carrying a chloroplast promoter. SLF67, SLF52, and SLF29 differ in their ionic-strength requirements for activity. They each mediate the binding to promoters of the chloroplast genes psbA, trnQ, and rps16, with different efficiencies. It is suggested that chloroplast transcription in vivo might be controlled at least in part by these functionally distinct factors.

Highly purified pea chloroplast RNA polymerase transcribes both rRNA and mRNA genes

Pea chloroplast RNA polymerase has been obtained with about 2000-fold purification using DEAE-cellulose and phosphocellulose chromatography. The purified enzyme contained ten prominent polypeptides of 150, 130, 115, 110, 95, 85, 75, 48, 44 and 39 kDa and four other minor polypeptides of 90, 34, 32 and 27 kDa. Purification of this enzyme using chloroplast 16S rDNA promoter affinity column chromatography also yielded an enzyme with similar polypeptides. Purified polyclonal antibodies against the purified chloroplast RNA polymerase were found to recognize most of the polypeptides of the enzyme in Western blot experiments. Primary mobility shift of the 16S rRNA gene and ribulose-1,5-bisphosphate carboxylase large subunit (rbc-L) gene promoters observed with the chloroplast RNA polymerase was abolished by these antibodies. The specific in vitro transcription of these rRNA and mRNA genes was also inhibited by these antibodies. The transcription of the rRNA and mRNA genes was also abolished by tagetitoxin, a specific inhibitor of chloroplast RNA polymerase. The chloroplast RNA polymerase was found to bind specifically to the chloroplast 16S rRNA gene promoter region as visualized in electron microscopy. The presence of the polypeptides of 130, 110, 75-95 and 48 kDa in the DNA-enzyme complex was confirmed by a novel approach using immunogold labeling with the respective antibodies. The polypeptides of this purified RNA polymerase were found to be localized in chloroplasts by an indirect immunofluorescence.

Maize chloroplast RNA polymerase: the 180-, 120-, and 38-kilodalton polypeptides are encoded in chloroplast genes

Prominent polypeptides with apparent molecular masses of 180, 120, 85, and 38 kDa are found in an extensively purified preparation of maize chloroplast DNA-dependent RNA polymerase that retains the capacity to initiate transcription of the cloned chloroplast gene rbcL correctly and the requirement for a supercoiled DNA template for specific and active transcription. Amino-terminal amino acid sequences of the 180-, 120-, and 38-kDa polypeptides have been determined and found to correspond precisely to the sequences deduced from the 5' ends of the maize chloroplast rpoC2, rpoB, and rpoA genes, respectively. These experiments show that these chloroplast rpo genes encode the prominent polypeptides in the highly enriched maize chloroplast RNA polymerase preparation and support the conclusion that these polypeptides are functional components of the enzyme. The rpoB, rpoC1, and rpoC2 genes have been mapped on the maize chloroplast chromosome.

Interaction of a 3' RNA region of the mustard trnK gene with chloroplast proteins

The 3' flanking region of the chloroplast trnK gene for tRNALys of mustard contains a palindromic sequence previously implicated with transcription termination and/or processing of the precursor RNA. Here we have investigated whether RNA sequences from the trnK 3' region are capable of interacting with chloroplast proteins in vitro. We find specific binding to an RNA region which is located further downstream from the palindromic sequence. The approximate length and position of this 3' binding region is reflected by a 41 nt spanning RNA segment which is protected against RNase T1 digestion by chloroplast protein(s). Competition experiments and sequence analyses suggest that U residues play an essential role in the RNA-protein interaction. Only a small number of proteins, possibly one single species, is in contact with the trnK 3' RNA.

Binding and transcription of relaxed DNA templates by fractions of maize chloroplast extracts

Preparations of partially purified chloroplast DNA-dependent RNA polymerase from maize and some other plants transcribe cloned chloroplast genes preferentially and much more actively from appropriately negatively supercoiled templates than from relaxed templates. We have found that the polymerase in such fractions does not bind to promoter regions of the maize chloroplast genes psbA and rbcL on small linear DNA fragments but that some protein(s) in unfractionated chloroplast extracts does bind. DEAE chromatography of the extracts has permitted the separation of a DNA-binding fraction from the bulk of the RNA polymerase activity. The binding fraction contains plastid RNA polymerase activity that is relatively independent of template topology.

In organello transcription in maize mitochondria and its sensitivity to inhibitors of RNA synthesis

Purified mitochondrial preparations from etiolated maize shoots support the incorporation of radioactivity from labeled UTP into RNA. The incorporation is linear with time for up to 2 hours, shows Michaelis-Menton kinetics with respect to the concentration of the labeled substrate, UTP, and has salt and pH optima which are different than those previously reported for RNA synthesis by isolated chloroplasts. When a crude mitochondrial preparation is subjected to isopycnic sucrose gradient centrifugation, the bulk of the RNA synthetic activity co-sediments with mitochondrial marker enzymes and with the mitochondrial 26S and 18S rRNAs. Maize mitochondrial RNA synthesis is prevented by actinomycin D and ethidium bromide but unaffected by alpha-amanitin. It is strongly inhibited by rifampicin at concentrations which have no effect on nuclear and chloroplast RNA synthesis, but only moderately inhibited by rifampicin at concentrations which completely inhibit bacterial RNA synthesis. The optimization, cell fractionation, and inhibitor data all suggest that contaminating organelles and bacteria do not contribute appreciably to the RNA synthesis in purified mitochondrial preparations.

Transcript levels of two adjacent chloroplast genes during mustard (Sinapis alba L.) seedling development are under differential temporal and light control

Transcript levels of two plastid genes were investigated during early seedling development of mustard (Sinapis alba L.) until 96 h after sowing. The two genes, which are closely linked and have the same polarity, are the psbA gene encoding the Mr 32-35000 herbicide-binding QB-protein of photosystem II and the trnK gene encoding plastid tRNA(Lys) (UUU) and potentially an intron-derived maturase-related protein. By using Northern and dot blot hybridization techniques with sensitive RNA probes, the 1.2 kb psbA transcript was found to be present in low amounts during the initial phase of seed germination. Thereafter, it increases in concentration both in light- and dark-grown seedlings until approximately 48 h after sowing. A further increase in psbA transcript concentration during the subsequent phase until 96 h was observed in light-grown, but not in dark-grown seedlings. The 2.8 kb trnK transcript is one to two orders of magnitude less abundant than the psbA transcript throughout the time period investigated. The concentration of this transcript is light-independent and shows a transient peak level at around 48 h, i.e. at the onset of light-enhanced accumulation of the psbA transcript.

Abortive and productive elongation catalysed by purified spinach chloroplast RNA polymerase

Experimental conditions are reported under which purified spinach chloroplast RNA polymerase catalyses the abortive elongation reaction on a synthetic poly[d(A-T)] template. The reaction only occurs under very stringent conditions and absolutely requires Mn2+ as the metal activator. No reaction can be detected in the presence of Mg2+. Furthermore, the rate of abortive elongation with the chloroplast enzyme is extremely sensitive to the presence of added salts, such as KCl or (NH4)2SO4, in the reaction assays. In the combined presence of Mn2+ and Mg2+, a marked inhibition of abortive elongation is associated with an activation of productive elongation and an increased length of RNA chains. Thus, whereas Mn2+ is more active than Mg2+ for phosphodiester bond formation, it appears that Mg2+ favors the stabilization of the ternary transcription complexes. These results are compared with those obtained under similar conditions for wheat germ RNA polymerase II and Escherichia coli RNA polymerase.

Transcription analysis of the maize chloroplast gene for the ribosomal protein S4

Maize seedlings contain several RNA species complementary to the rpS4 coding strand of the maize chloroplast ribosomal protein gene rpS4. All of these have the same 5' end about 182 bp upstream of the translation start codon for the protein S4. Northern and S1 nuclease analyses of RNA isolated from seedlings at different stages of greening show that the size of the pool of rpS4 transcripts does not change significantly upon illumination of dark-grown seedlings. The rpS4 gene has also been analyzed by in vitro transcription using maize chloroplast RNA polymerase preparations. The site of initiation in vitro has been mapped by S1 nuclease analysis to the same location as the 5' terminus of in vivo transcripts. A sequence resembling other plastid promoters occurs just upstream of this initiation site. The sensitivity of in vitro transcription to DNA template superhelicity has been assessed for the rpS4 gene promoter; its negative superhelicity-transcription rate profile resembles that of rbcL.

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.

Accurate transcription and processing of 19 Euglena chloroplast tRNAs in a Euglena soluble extract

The transcription and accurate processing of 19 different Euglena gracilis chloroplast tRNAs in a homologous chloroplast soluble extract is described. The chloroplast DNA dependent-RNA polymerase present in the extract selectively transcribes the tRNA genes (Greenberg et al., 1984, J. Biol. Chem., 259: 14880-14887). Two dimensional polyacrylamide gel electrophoresis and RNA fingerprint analysis were used to show that the tRNAs are correctly processed at the 5'- and 3'-ends. The Euglena chloroplast soluble extract contains a 5'-processing or 'RNase P-like' activity and RNases responsible for processing tRNA termini. However, it was not determined if the 3'-CCA was added. Therefore, the soluble extract contains activities that are quite similar to an extract of spinach chloroplasts (Greenberg et al. (1984), Plant Mol. Biol., 3: 97-109). After transcription of total chloroplast DNA in the Euglena soluble extract, thirty-three tRNA sized products were resolved by two dimensional polyacrylamide gel electrophoresis. Nineteen tRNAs could be identified in this mixture.

Identification and mutational analysis of the promoter for a spinach chloroplast transfer RNA gene

A transcription extract from purified spinach chloroplast was used to test chloroplast DNA sequences for their function as promoter elements. Chloroplast tRNA genes are correctly transcribed in the extract by a soluble RNA polymerase, and precursor molecules are processed into mature tRNAs. Transcription of the spinach chloroplast tRNA2Met gene (trnM2) in vitro requires 5' upstream DNA sequences. Deletion of 5' DNA sequences with exonuclease Bal31 was used to establish the 5' boundary of the promoter region. This boundary is part of a DNA sequence with partial homology to the prokaryotic -35 region. Seventeen base pairs downstream from this sequence a DNA sequence occurs which is homologous to the prokaryotic -10 region. We used synthetic oligonucleotides fused to trnM2 5' deletion mutants to create insertions, deletions and base substitutions in these regions. Internal deletion mutants demonstrated that the -10 promoter element is also required for transcription in vitro. The arrangement of DNA sequences recognised by the chloroplast RNA polymerase resembles the prokaryotic promoter organization.

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.

An in vitro system for accurate transcription initiation of chloroplast protein genes

We have developed an homologous in vitro system from spinach chloroplasts that correctly initiates transcription of the plastid genes for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) and the beta subunit of the plastid ATPase (atpB). The transcriptionally active extracts from spinach chloroplasts require circular DNA templates for specific initiation. The RNA polymerase activity is insensitive to rifampicin. The extent of transcription in vitro is a function of the extract:template ratio. The efficiency of the rbcL transcription in vitro is more than one transcript per one hundred templates per hour.

Hybridization study of developmental plastid gene expression in mustard (Sinapsis alba L.) with cloned probes for most plastid DNA regions

An approach to assess the extent of developmental gene expression of various regions of plastid (pt)DNA in mustard (Sinapis alba L.) is described. It involves cloning of most ptDNA regions. The cloned regions then serve as hybridization probes to detect and assess the abundance of complementary RNA sequences represented in total plastid RNA. By comparison of the hybridization pattern observed with plastid RNA from either dark-grown or light-grown plants it was found that many ptDNA regions are constitutively expressed, while several 'inducible' regions account for much higher transcript levels in the chloroplast than in the etioplast stage. The reverse situation, i.e. 'repressed' regions which would account for higher transcript levels in the etioplast, was not observed. The hybridization results obtained with RNA from 'intermediatetype' plastids suggest that transient gene expression is a common feature during light-induced chloroplast development. The time-course of gene expression differs for various ptDNA regions.

Synthesis of the large subunit of ribulose-1,5-bisphosphate carboxylase in anin vitro partially definedE. coli system

Thein vitro DNA- or RNA-directed synthesis of the large subunit (LS) of spinach chloroplast ribulose-1,5-biphosphate carboxylase (RuP2C) has been examined in a highly definedE. coli transcription-translation system. Spinach chloroplast DNA, RNA and recombinant plasmids containing the spinach chloroplast LS gene (rbcL) have been used as templates in thein vitro system and a quantitative assay has been developed to measure LS formation. Thein vitro formed product contains formylmethionine at the N-terminal position and sediments primarily as a monomer. There is no detectable enzymatic activity associated with thein vitro product. To determine where theE. coli RNA polymerase used in these systems initiates, we have examined the transcripts produced by this enzymein vitro. Measurements of run-off transcripts indicate thatE. coli RNA polymerase initiates at the same position on the gene as is seenin vivo. In addition, the complete nucleotide sequence of therbcL gene including previously unsequenced 3' and 5' flanking regions has been determined. The sequence agrees, except at two nucleotide positions, with previously published sequencing data for this gene (Zurawski, G, Perrot, B, Bottomley, W, Whitfeld, PR, 1981. Nucleic Acids Res. 9:3251-3270).

Chloroplast RNA polymerase from spinach: purification and DNA-binding proteins

Spinach DNA dependent RNA polymerase was purified from isolated chloroplasts by two different procedures. Analysis of the protein composition of the two preparations by SDS-polyacrylamide gel electrophoresis always shows six abundant polypeptides with Mr of 150, 110, 102, 80, 75 and 38 Kd and one less abundant polypeptide of 25 Kd. Some other proteins ranging from 40-70 Kd in Mr are also detected but in a minor and variable amount. The two preparations have an optimum of enzyme activity at 30°C and at 15 mM (NH4)2SO4 when tested with denatured calf thymus DNA.Binding experiments with two different nick translated fragments of spinach chloroplast DNA show that the 80 and 75 Kd polypeptides possess a strong DNA binding capacity.

Selective in vitro transcription of chloroplast genes

Transcription of Euglena gracilis chloroplast genes has been investigated by using in vitro transcription systems. A DNA-dependent RNA polymerase responsible for the transcription of rRNA genes has been isolated as a nucleoprotein complex (transcriptionally active chromosome). The RNA polymerase remains tightly bound to the chloroplast DNA template and does not initiate transcription with cloned chloroplast genes. A transcriptionally active extract has been prepared from intact Euglena chloroplasts. The soluble RNA polymerase in this extract recognizes cloned chloroplast tRNA genes and tRNA-sized products have been detected after transcription. The tRNA-sized molecules specifically hybridize to the tRNA genes in the plasmid DNA. At least five tRNA-sized products have been identified from transcription of a trnY1trnH1-trnM1-trnE1-trnW1-trnG1 cluster. Evidence is also presented that processing enzymes in the chloroplast-extract can recognize a polycistronic tRNAVal-tRNAAsn-tRNAArg precursor and process it into tRNA-sized molecules. Truncated templates have been used to demonstrate that the chloroplast tRNA genes are actively transcribed. From a comparison of 5' flanking sequences in chloroplast tRNA genes, a consensus sequence which might function as a promoter, has been identified. The properties of the RNA polymerase involved in the transcription of chloroplast rRNA genes and tRNA genes have been investigated and compared.

Properties and characterization of a spinach chloroplast RNA polymerase isolated from a tanscriptionally active DNA-protein complex

A chloroplast RNA polymerase has been isolated from a transcriptionally active spinach plastid DNA-protein complex. The properties of the complex and of the reconstituted system have been compared. The crude enzyme is at least sevenfold less active when compared with the complex. RNA synthesis by the reconstituted system is sensitive to high ionic strength and heparin, contrarily to RNA synthesis by the chloroplast DNA-protein complex. On the other hand, rifampicin has no inhibitory effect whatever on the transcriptional system used. The RNA polymerase isolated is more efficient with denatured DNA than with double-stranded DNA and the best template is chloroplast DNA. The crude RNA polymerase isolated migrates in a peak of 11 S in glycerol gradient centrifugation and is located in a single band in non-denaturing polyacrylamide gel electrophoresis. About 30 polypeptides (Mr 15 000--180 000) are part of the complex and only eight of them are found in the RNA polymerase preparation. Only five polypeptides are always present with the same yield. They are probably the subunits of the RNA polymerase. The molecular weight of these subunits ranged from 15 000--69 000, even if the isolation of the enzyme was performed in the presence of protease inhibitors.

Capacity for RNA synthesis in 70S ribosome-deficient plastids of heat-bleached rye leaves

In the leaves of rye seedlings (Secale cereale L.) grown at an elevated temperature of 32°C the formation of plastidic 70S ribosomes is specifically prevented. The resulting plastid ribosome-deficient leaves, which are chlorotic in light, represent a system for the identification of translation products of the 80S ribosomes among the chloroplastic proteins. Searching for the primary heat-sensitive event causing the 70S ribosome-deficiency, the thermostability of the chloroplastic capacity for RNA synthesis was investigated. The RNA polymerase activity of isolated normal chloroplasts from 22°-grown rye leaves was not inactivated in vitro at temperatures between 30° and 40°C. The ribosome-deficient plastids purified from bleached 32°-grown leaf parts contained significant RNA polymerase activity which was, however, lower than in functional chloroplasts. After application of [(3)H]uridine to intact leaf tissues [(3)H]uridine incorporation was found in ribosome-deficient plastids of 32°C-grown leaves. The amount of incorporation was similar to that in the control chloroplasts from 22°C-grown leaves. According to these results, it is unlikely that the non-permissive temperature (32°C) causes a general inactivation of the chloroplastic RNA synthesis in rye leaves.

Peptide maps comparing subunits of maize chloroplast and type II nuclear DNA-dependent RNA polymerases

Both one- and two-dimensional peptide mapping techniques have been used to compare the 180-kilodalton subunits from maize chloroplast and type II nuclear DNA-dependent RNA polymerases (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). Despite their similar molecular mass, these 180-kilodalton subunits are not the same. Also, two-dimensional tryptic maps of the 160-, 43-, and 28-kilodalton polypeptides from maize type II nuclear RNA polymerase and of the 140-, 42-, and 27-kilodalton polypeptides from maize chloroplast RNA polymerase show that each of these six polypeptides is unique.

Transcription activity of a DNA-protein complex isolated from spinach plastids

A DNA . protein complex of about 150 S is isolated from purified spinach chloroplasts by Sepharose 4B gel filtration. A DNA-dependent RNA polymerase activity is found associated with the complex. This DNA protein complex is able to initiate RNA chains in vitro. The RNA synthesis is more dependent on CTP than other nucleoside triphosphates. 50% of the activity is still present with 0.6 M KCl. The temperature optimum occurs between 30 degrees C and 35 degrees C. Rifampicin and rifamycin SV have no inhibitory effect. TNA products have been characterized by gel filtration and by hybridization with chloroplast DNA (ctDNA). At the beginning of transcription DNA products are linked to the transcription complex and are later detached. The molecular weight of the product ranges between 0.07 X 10(6) and 2 X 10(6). A part of the product (3--4%) has a molecular weight higher than 2 X 10(6). No endogenous RNase activity was present during the molecular weight determinations experiments. Hybridization experiments show that at least 75% of the RNA products are hybridizable with ctDNA and that 40% of these products are composed of chloroplast ribosomal RNA, showing that rDNA is preferentially transcribed.

Synthesis of chloroplast ribonucleic acid in Chlamydomonas reinhardtii toluene-treated cells

Chlamydomonas reinhardtii cells treated with toluene at 0 degrees C and 25 degrees C incorporate ribonucleoside triphosphates (NTPs) into chloroplast RNA at 25 degrees C and also at 35 degrees C. The incorporation requires all four NTPs and Mg2+, and is completely inhibited by DNase, RNase, actinomycin D (40 microgram/ml) and rifampicin (350 microgram/ml). However, the incorporation is almost totally insensitive to both alpha-amanitin and streptolydigin at 200 microgram/ml.

Comparison of the Molecular Weights of Proteins Synthesized by Isolated Chloroplasts with Those Which Appear during Greening in Zea mays

The proteins of prolamellar bodies of etioplasts and of thylakoid membranes of greening and mature chloroplasts from Zea mays were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Three classes of proteins were distinguished: those present in etioplasts and disappearing during greening, those absent in etioplasts and appearing during greening, and those present in both etioplasts and chloroplasts. The largest number of proteins belonged to this last class.The molecular weights of chloroplast thylakoid proteins were compared to the molecular weights of the membrane-associated proteins synthesized by isolated, mature chloroplasts. Thirteen of the 15 to 20 membrane-bound proteins made by isolated chloroplasts corresponded in size to proteins present in chloroplasts. Most of the 13 are present in both etioplasts and chloroplasts although a few were the same size as proteins which increase during greening. Production of most of the membrane proteins made in the plastids is not stringently regulated by light in vivo. The polypeptide subunits of the light-harvesting pigment-protein complex, the most abundant proteins of the chloroplast thylakoids, were absent from etioplasts. They were not synthesized by isolated chloroplasts.

Amatoxins, phallotoxins, phallolysin, and antamanide: the biologically active components of poisonous Amanita mushrooms

This review gives a comprehensive account of the molecular toxicology of the bicyclic peptides obtained from the poisonous mushrooms of the genus Amanita. The discussion of the biochemical events will be preceded by a consideration of the chemistry of the toxic peptides. The structural features essential for biological activities of both the amatoxins and the phallotoxins will be discussed, also including the most important analytical data. Similar consideration will be given to antamanide, a cyclic peptide, which counteracts phalloidin. In addition, the phallolysins, three cytolytic proteins from Amanita phalloides will be discussed. The report on the biological activity of the amatoxins will deal with the sensitivity of the different RNA-polymerases towards the toxins and with their action on various cell types. Consideration will also be given to systems in which alpha-amanitin was used and can be used as a molecular tool; in the past, many investigators used the inhibitor in molecular biology, genetics, and even in physiological research. As for the phallotoxins, discussion of the affinity of these toxins for actin is provied. Further discussion attempts to understand the course of intoxication by filling in the gap between the first molecular event, formation of microfilaments, and the various lesions in hepatocytes during the intoxication.