Expression of the Chlamydomonas reinhardtii chloroplast tRNA(Glu) gene in a homologous in vitro transcription system is independent of upstream promoter elements

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Although genomes of mitochondria and plastids are very small compared to those of their bacterial ancestors, the transcription machineries of these organelles are of surprising complexity. With respect to the number of different RNA polymerases per organelle, the extremes are represented on one hand by chloroplasts of eudicots which use one bacterial-type RNA polymerase and two phage-type RNA polymerases to transcribe their genes, and on the other hand by Physcomitrella possessing three mitochondrial RNA polymerases of the phage type. Transcription of genes/operons is often driven by multiple promoters in both organelles. This review describes the principle components of the transcription machineries (RNA polymerases, transcription factors, promoters) and the division of labor between the different RNA polymerases. While regulation of transcription in mitochondria seems to be only of limited importance, the plastid genes of higher plants respond to exogenous and endogenous cues rather individually by altering their transcriptional activities.

The chloroplast trnT-trnF region in the seed plant lineage Gnetales

The trnT-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL intron, a group I intron, and the trnT-trnL and trnL-trnF intergenic spacers. We analyzed the evolution of the region in the three genera of the gymnosperm lineage Gnetales (Gnetum, Welwitschia, and Ephedra), with especially dense sampling in Gnetum for which we sequenced 41 accessions, representing most of the 25-35 species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, while the spacers are so variable in length and composition that homology cannot be found even among the three genera. Palindromic sequences that form hairpin structures were detected in the trnL-trnF spacer, but neither spacer contained promoter elements for the tRNA genes. The absence of promoters, presence of hairpin structures in the trnL-trnF spacer, and high sequence variation in both spacers together suggest that trnT and trnF are independently transcribed. Our model for the expression and processing of the genes tRNA(Thr)(UGU), tRNA(Leu)(UAA), and tRNA(Phe) (GAA) therefore attributes the seemingly neutral evolution of the two spacers to their escape from functional constraints.

Cellular levels of glutamyl-tRNA reductase and glutamate-1-semialdehyde aminotransferase do not control chlorophyll synthesis in Chlamydomonas reinhardtii

5-Aminolevulinic acid (ALA) is the first committed universal precursor in the tetrapyrrole biosynthesis pathway. In plants, algae, and most bacteria, ALA is generated from glutamate. First, glutamyl-tRNA synthetase activates glutamate by ligating it to tRNA(Glu). Activated glutamate is then converted to glutamate 1-semialdehyde (GSA) by glutamyl-tRNA reductase (GTR). Finally, GSA is rearranged to ALA by GSA aminotransferase (GSAT). In the unicellular green alga Chlamydomonas reinhardtii, GTR and GSAT were found in the chloroplasts and were not detected in the mitochondria by immunoblotting. The levels of both proteins (assayed by immunoblotting) and their mRNAs (assayed by RNA blotting) were approximately equally abundant in cells growing in continuous dark or continuous light (fluorescent tubes, 80 micromol photons s(-1) m(-2)), consistent with the ability of the cells to form chlorophyll under both conditions. In cells synchronized to a 12-h-light/12-h-dark cycle, chlorophyll accumulated only during the light phase. However, GTR and GSAT were present at all phases of the cycle. The GTR mRNA level increased in the light and peaked about 2-fold at 2 h into the light phase, and GTR protein levels also increased and peaked 2-fold at 4 to 6 h into the light phase. In contrast, although the GSAT mRNA level increased severalfold at 2 h into the light phase, the level of GSAT protein remained approximately constant in the light and dark phases. Under all growth conditions, the cells contained significantly more GSAT than GTR on a molar basis. Our results indicate that the rate of chlorophyll synthesis in C. reinhardtii is not directly controlled by the expression levels of the mRNAs for GTR or GSAT, or by the cellular abundance of these enzyme proteins.

Transcription and processing of the gene for spinach chloroplast threonine tRNA in a homologous in vitro system

An in vitro system was established to study the transcription and processing of threonine tRNA using spinach chloroplast enzyme extract. Experiments using a series of 5' deletion mutants demonstrated that the transcription of trnT gene required no 5' upstream promoter elements. Four plasmid DNA templates containing trnT were constructed for tRNA processing assay. The processing reaction was carried out either with exogenously added precursor-tRNAs made by T7 RNA polymerase or with RNAs synthesized by the transcription activity in the same processing enzyme extract. Both assays demonstrated that the 5' and 3' ends of mature tRNA were processed endonucleolytically and the processing of the 5' end preceded the maturation of the 3' end. The activity of nucleotidyl transferase that adds CCA nucleotides to the 3' end of tRNA was also observed. The use of a coupled transcription and processing system provides us with a better insight to the tRNA processing mechanism of the chloroplast.

The 3' untranslated regions of chloroplast genes in Chlamydomonas reinhardtii do not serve as efficient transcriptional terminators

A general characteristic of the 3' untranslated regions of plastid mRNAs is an inverted repeat sequence that can fold into a stem-loop structure. These stem-loops are superficially similar to structures involved in prokaryotic transcription termination, but were found instead to serve as RNA 3' end processing signals in spinach chloroplasts, and in the atpB mRNA of Chlamydomonas reinhardtii chloroplasts. In order to carry out a broad study of the efficiency of the untranslated sequences at the 3' ends of chloroplast genes in Chlamydomonas to function as transcription terminators, we performed in vivo run-on transcription experiments using Chlamydomonas chloroplast transformants in which different 3' ends were inserted into the chloroplast genome between a petD promoter and a reporter gene. The results showed that none of the 3' ends that were tested, in either sense or antisense orientation, prevented readthrough transcription, and thus were not highly efficient transcription terminators. Therefore, we suggest that most or all of the 3' ends of mature mRNAs in Chlamydomonas chloroplasts are formed by 3' end processing of longer precursors.

The regulation of enzymes involved in chlorophyll biosynthesis

All living organisms contain tetrapyrroles. In plants, chlorophyll (chlorophyll a plus chlorophyll b) is the most abundant and probably most important tetrapyrrole. It is involved in light absorption and energy transduction during photosynthesis. Chlorophyll is synthesized from the intact carbon skeleton of glutamate via the C5 pathway. This pathway takes place in the chloroplast. It is the aim of this review to summarize the current knowledge on the biochemistry and molecular biology of the C5-pathway enzymes, their regulated expression in response to light, and the impact of chlorophyll biosynthesis on chloroplast development. Particular emphasis will be placed on the key regulatory steps of chlorophyll biosynthesis in higher plants, such as 5-aminolevulinic acid formation, the production of Mg(2+)-protoporphyrin IX, and light-dependent protochlorophyllide reduction.

Activity of the Chlamydomonas chloroplast rbcL gene promoter is enhanced by a remote sequence element

The chloroplast gene rbcL encodes the large subunit of ribulose bisphosphate carboxylase. In Chlamydomonas reinhardtii, this gene is transcribed more actively than any other protein-encoding chloroplast gene studied to date. To delineate the rbcL gene promoter, chimeric reporter genes containing fragments of the 5' region of the rbcL gene fused to the coding sequence of the bacterial uidA gene, encoding beta-glucuronidase, were stably introduced into the chloroplast genome of Chlamydomonas by microprojectile bombardment. The relative transcription rates of endogenous and introduced genes were determined in transgenic cell lines in vivo. The basic rbcL promoter is located within the region of the gene extending from positions -18 to +63, taking position +1 as the site of initiation of transcription. A chimeric reporter gene containing only the basic promoter is transcribed only 1-15% as actively as the endogenous rbcL gene, depending on the conditions under which cells are grown and tested. However, a chimeric gene containing rbcL sequences extending to position +170 or beyond is transcribed at about the same rate as the endogenous gene. Deletion of the sequence between positions +170 and +126, well within the protein-encoding region, reduces the rate of transcription to that of reporter genes with the basic promoter alone.

Structure and expression characteristics of the chloroplast DNA region containing the split gene for tRNA(Gly) (UCC) from mustard (Sinapis alba L.)

The mustard chloroplast gene trnG-UCC is split by a 717-bp group-II intron. Northern hybridization and RNase protection experiments suggest cotranscription with the upstream psbK-psbI operon, but not with the downstream trnR-UCU gene. The ends of most RNase-protected fragments between psbI and trnG correlate with the position of two potential stem-loop structures in this region, which could act as RNA processing elements. However, one RNA 5' end, approximately 75 bp upstream of the trnG 5' exon, does not so correlate and is preceded by prokaryotic-type '-10' and '-35' sequence elements. This suggests the possibility that a fraction of the trnG transcripts is initiated here. All precursor transcripts spanning the trnG region seem to have a common 3' end, which was located 117 bp downstream from the 3' exon, immediately after a stem-loop region. During seedling development, the major 0.8-0.9-kb trnG precursor transcripts show a transient maximum level at around 48 h after sowing, at a time when the mature tRNA begins to accumulate to constant levels. No significant differences in transcript patterns were observed either in the light or in darkness.

Structure and light-regulated expression of the gsa gene encoding the chlorophyll biosynthetic enzyme, glutamate 1-semialdehyde aminotransferase, in Chlamydomonas reinhardtii

The gsa gene, which encodes glutamate 1-semialdehyde (GSA) aminotransferase (GSAT), an enzyme in the chlorophyll and heme biosynthetic pathway, has been cloned from Chlamydomonas reinhardtii by complementation of an Escherichia coli hemL mutant. The deduced C. reinhardtii GSAT amino acid sequence has a high degree of similarity to GSAT sequences from barley, tobacco, soybean and various prokaryotic sources. In vitro enzyme activity assays from E. coli transformed with the C. reinhardtii GSAT cDNA showed that higher levels of GSAT activity are associated with the expression of the cDNA insert. Analysis of changes in mRNA levels in light:dark synchronized C. reinhardtii cultures was done by northern blotting. The level of GSAT mRNA nearly doubled during the first 0.5 h in the light and increased over 26-fold after 2 h in the light. This increase is comparable to previously reported increases in GSAT activity in dark-grown cultures transferred to the light, and is the first report of induction by light of a gene encoding an ALA biosynthetic enzyme in plant or algal cells. The accumulation of GSAT mRNA follows the pattern of chlorophyll accumulation and the pattern of chlorophyll a/b-binding protein (cabII-1) mRNA accumulation in these cells, suggesting that the two genes may be regulated by light through a common mechanism. Additional evidence that the GSAT mRNA may be transcriptionally regulated by light is found in the genomic sequence of the gsa gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Complex formation between glutamyl-tRNA synthetase and glutamyl-tRNA reductase during the tRNA-dependent synthesis of 5-aminolevulinic acid in Chlamydomonas reinhardtii

The formation of a stable complex between glutamyl-tRNA synthetase and the first enzyme of chlorophyll biosynthesis glutamyl-tRNA reductase was investigated in the green alga Chlamydomonas reinhardtii. Apparently homogenous enzymes, purified after previously established purification protocols were incubated in various combinations with ATP, glutamate, tRNA(Glu) and NADPH and formed complexes were isolated via glycerol gradient centrifugation. Stable complexes were detected only after the preincubation of glutamyl-tRNA synthetase, glutamyl-tRNA reductase with either glutamyl-tRNA or free tRNA(Glu), ATP and glutamate, indicating the obligatory requirement of aminoacylated tRNA(Glu) for complex formation. The further addition of NADPH resulting in the reduction of the tRNA-bound glutamate to glutamate 1-semialdehyde led to the dissociation of the complex. Once complexed to the two enzymes tRNA(Glu) was found to be partially protected from ribonuclease digestion. Escherichia coli, Bacillus subtilis and Synechocystis 6803 tRNA(Glu) were efficiently incorporated into the protein-RNA complex. The detected complexes provide the chloroplast with a potential channeling mechanism for Glu-tRNA(Glu) into chlorophyll synthesis in order to compete with the chloroplastic protein synthesis machinery.