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

Identification of essential subunits in the plastid-encoded RNA polymerase complex reveals building blocks for proper plastid development

The major RNA polymerase activity in mature chloroplasts is a multisubunit, Escherichia coli-like protein complex called PEP (for plastid-encoded RNA polymerase). Its subunit structure has been extensively investigated by biochemical means. Beside the "prokaryotic" subunits encoded by the plastome-located RNA polymerase genes, a number of additional nucleus-encoded subunits of eukaryotic origin have been identified in the PEP complex. These subunits appear to provide additional functions and regulation modes necessary to adapt transcription to the varying functional situations in chloroplasts. However, despite the enormous progress in genomic data and mass spectrometry techniques, it is still under debate which of these subunits belong to the core complex of PEP and which ones represent rather transient or peripheral components. Here, we present a catalog of true PEP subunits that is based on comparative analyses from biochemical purifications, protein mass spectrometry, and phenotypic analyses. We regard reproducibly identified protein subunits of the basic PEP complex as essential when the corresponding knockout mutants reveal an albino or pale-green phenotype. Our study provides a clearly defined subunit catalog of the basic PEP complex, generating the basis for a better understanding of chloroplast transcription regulation. In addition, the data support a model that links PEP complex assembly and chloroplast buildup during early seedling development in vascular plants.

The atpB and rbcL promoters in plastid DNAs of a wide dicot range

The plastid atpB-rbcL intergene has been analyzed within a wide range of plants covering the major dicot lineages. New sequences from 13 plant species were determined and aligned with three already-known sequences. The promoters of the rbcL and the atpB genes were localized and analyzed according to published observations in spinach and tobacco. The evolutionary conservation of two atpB promoters, separated by 113-262 nucleotides, is strong support that both are functionally active, and it also allows a discrimination between the previously reported atpB transcripts. Moreover, the radically distinct sequences of the two atpB promoters suggest that they interact with two distinct initiation complexes. The alignment also confirms the much higher conservation of the leader sequence in the rbcL mRNA than in the atpB mRNA among dicots, presuming a function at the posttranscriptional level.

In Vitro Analysis of Light-Induced Transcription in the Wheat psbD/C Gene Cluster Using Plastid Extracts from Dark-Grown and Short-Term-Illuminated Seedlings

We describe a plastid in vitro transcription system that reflects characteristic features of the light-regulated transcription observed in vivo. Multiple transcripts of the wheat (Triticum aestivum) psbD/C gene cluster comprise six distinct 5[prime] ends including four transcription initiation sites designated as D/C-1 through D/C-4. Transcripts from one particular site, D/C-3, were found to be conspicuously enhanced in abundance after 4 h of illumination in vivo. The plastid extract prepared from 5-d-old dark-grown wheat seedlings was capable of transcribing from the D/C-2 and D/C-4 sites in vitro but had almost no transcription activity from the light-responsive D/C-3 site (the D/C-1 site was not examined). The plastid extract from 4-h-illuminated seedlings initiated transcription from the light-responsive site (D/C-3). Transcription from the D/C-2 and D/C-4 sites was not enhanced by using the extract from 4-h-illuminated seedlings, indicative of specific activation of the light-responsive promoter on the D/C-3 site by the extract from 4-h-illuminated seedlings. The plastid extract from 4-h-illuminated seedlings was divided into two fractions on a heparin-Sepharose column, into which the light-induced component(s) responsible for activation of the D/C-3 promoter and RNA polymerase were separated. The fraction containing the component(s) activating the D/C-3 promoter induced the transcription activity from the D/C-3 site in the plastid extract from dark-grown seedlings. It is concluded that the plastid extract from 4-h-illuminated seedlings contains some light-regulatory component(s) that activate specifically the light-responsive promoter.

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.

The 110-kDa polypeptide of spinach plastid DNA-dependent RNA polymerase: single-subunit enzyme or catalytic core of multimeric enzyme complexes?

Highly purified RNA polymerase preparations from spinach chloroplasts contain seven major polypeptides of 150, 145, 110, 102, 80, 75, and 38 kDa. I find that RNA polymerase activity can be separated under defined conditions into three different fractions by heparin-Sepharose chromatography. Immunological analysis has shown that the first fraction contains RNA polymerase activity associated with all seven major polypeptides, and other studies have shown that some of these polypeptides (150, 145, 80, and 38 kDa) are associated with an RNA polymerase similar to the Escherichia coli enzyme. However, similar analyses of the remaining fractions show activity associated only with the 110-kDa polypeptide, suggesting the existence of a second kind of chloroplast RNA polymerase. Samples of this 110-kDa polypeptide purified by SDS/PAGE actively synthesize RNA in a reaction dependent on a supercoiled DNA template and the four ribonucleoside triphosphates. Hence, this polypeptide has all of the properties expected of a single-subunit RNA polymerase of the T7 bacteriophage type.

Two distinct transcriptional activities of pea (Pisum sativum) chloroplasts share immunochemically related functional polypeptides

An RNA polymerase activity has been purified from pea (Pisum sativum) chloroplast extracts with a distinct transcriptional specificity for a chloroplast messenger gene. This activity (ms-RNA pol) differs from the pea RNA polymerase preparation reported by Sun, Shapiro, Wu & Tewari [(1986) Plant Mol. Biol. 6, 429-439], which specifically transcribes only the rRNA gene (rb-RNA pol). The specificity of transcription has been assessed by the synthesis in vitro of discrete transcripts of predicted sizes using cloned promoter regions of the chloroplast psbA and 16 S rRNA genes. The ms-RNA pol preparation, with polypeptides ranging in apparent molecular mass from 22 to 180 kDa, correctly initiates transcription from recombinant plasmids containing the psbA promoter and does not support 16 S rRNA promoter-directed transcription. The two activities differ also in their response to Mn2+ ions. To investigate whether the two transcriptional activities share common functional polypeptides, monoclonal antibodies were developed against the rb-RNA pol preparation. Three clones were selected on the basis of their ability to inhibit transcription in vitro of the 16 S rRNA gene by rb-RNA pol. The antibodies from these clones independently recognized three polypeptides with molecular masses of 27, 90 and 95 kDa on immunoblots. Antibodies cross-reacting with the 90 kDa polypeptide completely eliminated the specific retardation of an end-labelled 16 S rRNA promoter fragment in a mobility-shift assay, whereas the antibodies against the 95 kDa polypeptide resulted in the formation of a ternary complex (enzyme-DNA-antibody). The antibodies cross-reacting with the 27 kDa polypeptide, however, did not alter the mobility of the retarded DNA-enzyme complex on the gel. These antibodies also inhibited transcription in vitro of the psbA gene by ms-RNA pol and recognized polypeptides of identical molecular masses in the ms-RNA pol. These results show that the three polypeptides are functional components of the chloroplast transcriptional complex and appear to be involved in the transcription of both rRNA and mRNA genes. Transcriptional specificity is probably conferred by ancillary transcription factor(s) which remain to be identified.