Selective in vitro transcription of Euglena chloroplast ribosomal RNA genes by a transcriptionally active chromosome

Multifunctionality of plastid nucleoids as revealed by proteome analyses

Protocols aimed at the isolation of nucleoids and transcriptionally active chromosomes (TACs) from plastids of higher plants have been established already decades ago, but only recent improvements in the mass spectrometry methods enabled detailed proteomic characterization of their components. Here we present a comprehensive analysis of the protein compositions obtained from two proteomic studies of TAC fractions isolated from Arabidopsis/mustard and spinach chloroplasts, respectively, as well as nucleoid fractions from Arabidopsis, maize and pea. Interestingly, different approaches as well as the use of diverse starting materials resulted in the detection of varying protein catalogues with a number of shared proteins. Possible reasons for the discrepancies between the protein repertoires and for missing out some of the nucleoid proteins that have been identified previously by other means than mass spectrometry as well as the repeated identification of "unexpected" proteins indicating potential links between DNA/RNA-associated nucleoid core functions and energy metabolism as well as biosynthetic activities of plastids will be discussed. In accordance with the nucleoid association of proteins involved in key functions of plastids including photosynthesis, the phenotypes of mutants lacking one or the other plastid nucleoid-associated protein (ptNAP) show the importance of nucleoid proteins for overall plant development and growth. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Organelle Nuclei in Higher Plants: Structure, Composition, Function, and Evolution

Plant cells have two distinct types of energy-converting organelles: plastids and mitochondria. These organelles have their own DNAs and are regarded as descendants of endosymbiotic prokaryotes. The organelle DNAs associate with various proteins to form compact DNA-protein complexes, which are referred to as organelle nuclei or nucleoids. Various functions of organelle genomes, such as DNA replication and transcription, are performed within these compact structures. Fluorescence microscopy using the DNA-specific fluorochrome 4',6-diamidino-2-phenylindole has played a pivotal role in establishing the concept of "organelle nuclei." This fluorochrome has also facilitated the isolation of morphologically intact organelle nuclei, which is indispensable for understanding their structure and composition. Moreover, development of an in vitro transcription?DNA synthesis system using isolated organelle nuclei has provided us with a means of measuring and analyzing the function of organelle nuclei. In addition to these morphological and biochemical approaches, genomics has also had a great impact on our ability to investigate the components of organelle nuclei. These analyses have revealed that organelle nuclei are not a vestige of the bacterial counterpart, but rather are a complex system established through extensive interaction between organelle and cell nuclear genomes during evolution. Extensive diversion or exchange during evolution is predicted to have occurred for several important structural proteins, such as major DNA-compacting proteins, and functional proteins, such as RNA and DNA polymerases, resulting in complex mechanisms to control the function of organelle genomes. Thus, organelle nuclei represent the most dynamic front of interaction between the three genomes (cell nuclear, plastid, and mitochondrial) constituting eukaryotic plant cells.

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.

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.

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.

Location, nucleotide sequence and expression of the proton-translocating subunit gene of theE. gracilis chloroplast ATP synthase

A 1700 base pairHindIII restriction fragment from theE. gracilis chloroplast chromosome has been shown to contain the gene for the proton-translocating subunit of the ATP synthase (atpH). The gene was mapped by heterologous hybridization using internal sequences of the gene from wheat and spinach chloroplast DNA. Each chloroplast chromosome contains a single copy of atpH, which is located close to the gene for the alpha subunit of the ATP synthase (atpA). The nucleotide sequence of the gene is uninterrupted by introns. The predicted sequence of 77 amino acids is 70% homologous to that of the wheat and spinach polypeptides. The gene is expressedin vivo as shown by hybridization of atpH probes to cellulose nitrate filter blots of total chloroplast RNA. 5'-proximal to the atpH locus on the clonedHindIII fragment are 38 codons from the carboxy terminus of an open reading frame which may be another ATP synthase subunit. Transcription of the ORF and the atpH gene may be as part of a large polycistronic mRNA.

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.

Biosynthesis of chloroplast transfer RNA in a spinach chloroplast transcription system

We have developed a chloroplast in vitro transcription system capable of transcribing tRNA genes (trn) from the spinach and Euglena gracilis chloroplast genomes. The RNA polymerase contained in the chloroplast extract transcribes the spinach chloroplast trnM2, trnV1, and trnl1 loci and the trnV1-trnN1-trnR1-trnL1 cluster in the EcoG fragment of the Euglena chloroplast genome. Restriction enzyme modified templates were used to demonstrate that the tRNA genes are transcribed in vitro. RNA fingerprint analysis confirmed that tRNAMetm, tRNAlle1 and tRNALeu are correctly processed transcripts from the spinach chloroplast trnM2, trnl1, and Euglena trnL1 loci respectively. CCAOH is added to the mature tRNAs in vitro by a 3' nucleotidyl transferase present in the chloroplast extract. Deletion mutants were constructed from the trnM2 locus to evaluate the role of 5' flanking sequences in transcription initiation and processing. DNA sequences between positions -56 to -85 upstream of the trnM2 locus are required for maximal transcription of tRNAMetm, but are not essential for processing. The RNA polymerase involved in chloroplast trn transcription is distinguishable from the RNA polymerase isolated as a DNA-protein complex from spinach chloroplast that is active in rRNA transcription.

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.

Influence of the ionic environment on the in vitro transcription of the spinach plastid DNA by a selectively bound RNA-polymerase DNA complex

The in vitro transcription of chloroplast DNA (ctDNA) is studied using a DNA-protein complex isolated from spinach plastids. The RNA products are compared to the in vivo synthesized ctRNA by competition for hybridization. At least 80% of the in vitro RNA sequences are present in vivo. Modifications of ionic strength or introduction of heparin in the reaction medium has an important effect on transcriptional activity of the complex. Furthermore, the length of the RNA chains increases ionic strength and amount of heparin. The RNA products are analysed by Southern hybridizations to EcoRI cTDNA fragments. Changes in the ionic strength or in the amount of heparin modify heterogeneously the transcription of the various DNA regions. The quantitative distribution of transcripts among the ctDNA fragments is used as evidence for the selectivity of the transcription. The activity of the DNA-protein complex is much more resistant to high ionic strength than an heterologous transcription system using Escherichia coli RNA polymerase and ctDNA. This latter system transcribes less ctDNA fragments.