Large subunit ribulosebisphosphate carboxylase messenger RNA from Euglena chloroplasts

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.

Maize chloroplast DNA fragment encoding the large subunit of ribulosebisphosphate carboxylase

In vitro linked transcription-translation of chloroplast DNA has been used to show that the large subunit of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39] is encoded by Zea mays chloroplast DNA. A BamHI-generated chloroplast DNA sequence cloned in Escherichia coli is shown to direct the in vitro synthesis of this protein identified as large subunit by its size, serological properties, and limited proteolytic digestion products.

Cloning, expression and purification of cytochrome c(6) from the brown alga Hizikia fusiformis and complete X-ray diffraction analysis of the structure

The primary sequence of cytochrome c(6) from the brown alga Hizikia fusiformis has been determined by cDNA cloning and the crystal structure has been solved at 1.6 A resolution. The crystal belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 84.58, c = 232.91 A and six molecules per asymmetric unit. The genome code, amino-acid sequence and crystal structure of H. fusiformis cytochrome c(6) were most similar to those of red algal cytochrome c(6). These results support the hypothesis that brown algae acquired their chloroplasts via secondary endosymbiosis involving a red algal endosymbiont and a eukaryote host.

Cis-acting elements and trans-acting factors for accurate translation of chloroplast psbA mRNAs: development of an in vitro translation system from tobacco chloroplasts

Translational regulation is an important step of gene expression in chloroplasts. To analyze biochemical mechanisms of translational regulation unique to higher plant chloroplasts, an in vitro translation system has been developed from tobacco chloroplasts. Conditions for chloroplast extraction and the in vitro translation reaction have been optimized with a tobacco psbA-lacZ fusion mRNA. The in vitro system supports accurate translation of a variety of chloroplasts mRNAs. Using a series of mutant psbA mRNAs, we showed that three elements within the 5'-untranslated region of the mRNA are required for translation. Two of them are complementary to the 3'-terminus of chloroplast 16S rRNA (termed RBS1 and RBS2) and the other is an AU-rich sequence (UAAAUAAA) located between RBS1 and RBS2 and is termed the AU box. mRNA competition experiments using the in vitro translation reaction and gel mobility shift assays revealed the existence of a trans-acting factor(s) for translation and its possible interaction with the AU box. We propose a model for the initiation of psbA translation whereby RBS1 and RBS2 bind cooperatively to the 3'-end of 16S rRNA resulting in looping out of the AU box, which facilitates the interaction of a trans-acting factor(s).

Euglena gracilis chloroplast DNA: the untranslated leader of tufA-ORF206 gene contains an intron

Structural features of a dicistronic 1.95 kb mRNA coding for the chloroplast specific elongation factor Tu and ORF206 are described. The unspliced pre-mRNA is composed of 2562 nucleotides and undergoes four splicing events which remove a total of 606 nucleotides. The first intron splits the untranslated leader, two introns dissect the tufA coding region and the forth intron is within ORF206, which codes for a putative protein that is to 34% homologous with the putative protein of chloroplast ORF184 of tobacco. Introns neither belong to group I nor II, and 5' and 3' intron boundaries do not follow consensus sequences. Potential ribosome binding sites are located 58 and 32 positions upstream of the tufA and ORF206 start codon, respectively.

Photo- and Metabolite Regulation of the Synthesis of Ribulose Bisphosphate Carboxylase/Oxygenase and the Phycobiliproteins in the Alga Cyanidium caldarium

In the eukaryotic and unicellular alga Cyanidium caldarium the synthesis of the plastid enzyme ribulose bisphosphate carboxylase/oxygenase (RuBPCase) and the light gathering proteins phycocyanin (PC) and allophycocyanin (APC) is under the control of light and glucose, which is a metabolizable carbon source for this organism. Light promotes the synthesis of these proteins while glucose has a strong inhibitory effect on this process. All subunits of the proteins mentioned above are in vitro translation products of poly (A)(-)-RNA (Steinmüller, Kaling, Zetsche 1983 Planta 159: 308-313). Both factors-light and glucose-exert their effects mainly by modulation of the level of translatable messenger RNA for these proteins. Under autotrophic growth conditions the level of translatable RuBPCase-, PC-, and APC-messenger RNA is high, whereas in the presence of glucose the level of these mRNAs is low or not detectable at all.

The genes for the ribosomal proteins S12 and S7 are clustered with the gene for the EF-Tu protein on the chloroplast genome of Euglena gracilis

We characterize a DNA segment of the Euglena gracilis chloroplast DNA fragment Eco . N by nucleotide sequencing and S1 nuclease analysis. We show that this region, which is upstream of the previously sequenced tuf A gene, contains the genes for the ribosomal proteins S12 and S7. The gene arrangement is 5'-rps 12-80 bp spacer-rps 7-174 bp spacer-tuf A, somewhat similar to the str operon of E. coli. The chloroplast S12 and S7 proteins contain 124 and 155 aminoacids, respectively, and are to 68% and 38% homologous with the corresponding E. coli proteins. The region is transcribed into a distronic mRNA of about 1.1 to 1.2 kb. The rps 12 and rps 7 genes, contrary to the tuf A gene, are not split.

Nucleotide sequence of a Euglena gracilis chloroplast genome region coding for the elongation factor Tu; evidence for a spliced mRNA

We characterize a 1.95 kb transcription product of the Euglena gracilis chloroplast DNA fragment Eco-N + Q by S1 nuclease analysis and DNA sequencing and show that it is the product of three splicing events. Exon 1 (0.45 kb), exon 2 (0.74 kb) and 175 nucleotides of exon 3 (0.53 kb) code for the chloroplast elongation factor protein (EF-Tu). The remaining part of exon 3 and exon 4 (0.23 kb) have unidentified open reading frames. The chloroplast EF-Tu protein has 408 aminoacids and is to 70% homologous with the E. coli EF-Tu protein. The active site for aminoacyl-tRNA binding is highly conserved, while the active site for GTP/GDP binding lacks the cysteine present in the E. coli EF-Tu protein. The two introns separating exons 1, 2 and 3 are, respectively, 103 and 110 nucleotides long. The size of the third intron is not yet determined. The splicing rules for eukaryote mRNA are not followed.

Photocontrol of the polypeptide composition ofEuglena : Analysis by two-dimensional gel electrophoresis

Two-dimensional gel electrophoresis resolved total cellular protein fromEuglena gracilis Klebs var.bacillaris Cori into 650 polypeptides detectable by silver staining. Exposure of dark-grown restingEuglena to light for 72 h increased the relative amounts of 79 polypeptides and decreased the relative amounts of 72 polypeptides. Four polypeptides whose level increased upon light exposure were undetectable in the bleached mutant W3BUL. Since W3BUL has lost most if not all of its chloroplast genome, these polypeptides may be coded by the chloroplast genome. Although the majority of the polypeptides studied appear to be coded by the nuclear or mitochondrial genomes, seven polypeptides which were present in W3BUL were not detectable in another chloroplast-DNA-deficient, bleached mutant, W10BSmL. It appears that a number of nonchloroplast genes are no longer expressed in this mutant. Exposure of dark-grown resting cells of the bleached mutant, W3BUL, to light increased the relative amounts of 12 polypeptides and decreased the relative amounts of 14 polypeptides. Since W3BUL lacks detectable protochlorophyll(ide), the chloroplast photoreceptor, the levels of these polypeptides are regulated by light acting through a nonchloroplast photoreceptor. Exposure of cells to light had no detectable effect on the relative amounts of those polypeptides which were present in W10BSmL, even though W10BSmL has a nonchloroplast photoreceptor. EitherEuglena contains multiple nonchloroplast photoreceptors, some of which are absent from W10BSmL, or the nonchloroplast photoreceptor present in W10BSmL is uncoupled from some of the events normally controlled by that photoreceptor.

The gene for the large subunit of ribulose-1,5-bisphosphate carboxylase in Euglena gracilis chloroplast DNA: location, polarity, cloning, and evidence for an intervening sequence

The gene for the large subunit (LS) of ribulose-1,5,-bisphosphate carboxylase of Euglena gracilis Z chloroplast DNA has been mapped by heterologous hybridization with DNA restriction fragments containing internal sequences from the Zea mays and Chlamydomonas reinhardii LS genes. The Euglena LS gene which has the same polarity as the Euglena rRNA genes has been located with respect to Pst I, Pvu I, and HindIII sites within the Eco RI fragment Eco A. The region of Euglena chloroplast DNA complementary to an 887 bp internal fragment from the Chlamydomonas chloroplast LS gene is interrupted by a 0.5-1.1 kbp non-complementary sequence. This is the first chloroplast protein gene located on the Euglena genome, and the first evidence for an intervening sequence within any chloroplast protein gene.

Euglena gracilis Chloroplast DNA Codes for Polyadenylated RNA

Polyadenylated RNA, isolated from total cellular RNA of photoautotrophically grown Euglena gracilis, comprised 2.1% of the total cellular RNA and contained 6.2% polyadenylic acid. Polyadenylated RNA, labeled in vitro with (125)I, hybridized at saturating levels to an average 7.7% of the chloroplast DNA. In the presence of excess chloroplast rRNA, hybridization of polyadenylated RNA was reduced, but was still observed at a level corresponding to 2.8% of the chloroplast DNA. Polyadenylic acid was not detected in mRNA prepared from chloroplast polyribosomes, indicating a level of less than 0.1% polyadenylic acid in mature chloroplast mRNA. Of the total RNA isolated from cytoplasmic polyribosomes, 2.0% contained polyadenylic acid. This latter polyadenylated RNA did not hybridize to chloroplast DNA.

The synthesis of chloroplast high-molecular-weight ribosomal ribonucleic acid in spinach

Illuminated suspensions of chloroplasts isolated from young spinach leaves show incorporation of [3H]uridine into several species of RNA. One such RNA species of Mr 2.7 x 10(6) shows sequence homology with both the chloroplast 23-S rRNA (Mr = 1.05 x 10(6)) and 16-S rRNA (Mr = 0.56 x 10(6)), as judged by DNA/RNA competition hybridization. Leaves labelled in vivo with [32P]orthophosphate in the presence of chloramphenicol accumulate labelled RNAs of Mr 1.28 x 10(6), 0.71/0.75 x 10(6) and 0.47 x 10(6). The 1.28 x 10(6)-Mr RNA shows 80.5% sequence homology with the 1.05 x 10(6)-Mr rRNA and the 0.71/0.75 x 10(6)-Mr RNA mixture shows 76% sequence homology with the 0.56 x 10(6)-Mr rRNA. We conclude that the pathway of rRNA maturation in spinach chloroplasts is similar to that of Escherichia coli.

Messenger RNA of the large subunit of ribulose-1,5-bisphosphate carboxylase from Chlamydomonas reinhardi. Isolation and properties

Polysomes specifically synthesizing the large subunit of ribulose-1,5-bisphosphate carboxylase were isolated from Chlamydomonas reinhardi cells by the indirect immunoprecipitation method. Electrophoretic analysis showed that the immunoprecipitated polysomes were of chloroplast origin. The mRNA coding for the large subunit which was purified from immunoprecipitated polysomes migrated at the 19-S position on sucrose density gradients, and its molecular weight was estimated to be 7.3 x 10(5) by acid-urea/agarose gel electrophoresis. The mRNA was translated in vivo with a cell-free protein-synthesizing system derived from Escherichia coli to give full-length large-subunit polypeptides.

Cell suspensions for kinetic studies of inhibitor action : The rapid initial action of dikegulac on membrane properties in situ

Because of uniformity and small distances for transport, cell suspensions offer a system for rapid measurements of initial reactions of phytotoxic compounds. We had previously shown that a growth regulator, dikegulac (2,3:4,6 di-o-isopropylidine-2-keto-L-gulonate) inhibits amino acid incorporation into proteins. Using Solanum nigrum suspension cultures, it was found that dikegulac rapidly inhibits amino acid uptake into cells, before inhibiting incorporation, with time points starting at a few minutes, and kinetics that can be extrapolated back to time zero. With more rapid kinetics this compound induces leakage of a preloaded dye. The rate of leakage was less with stationary cells in suspension, reiterating that they are more resistant to the effects of this compound. It was thus concluded that at the concentrations used, the first effect of dikegulac (or one very close to the first effect) is on the cell membrane.

Use of aurintricarboxylic acid as an inhibitor of nucleases during nucleic acid isolation

Aurintricarboxylic acid (ATA) is a general inhibitor of nucleases. ATA has been shown to inhibit the following enzymes in vitro: DNAse I, RNAse A, S1 nuclease, exonuclease III, and restriction endonucleases Sal I, Bam HI, Pst I and Sma I. The observed inhibition is consistent with the proposal by Blumenthal and Landers (BBRC 55, 680, 1973) that most nucleic acid binding proteins will be sensitive to ATA. The action of ATA as a nuclease inhibitor can be used to advantage in the isolation of cellular nucleic acids.

Identification and Properties of the Messenger RNA Activity in Chlamydomonas reinhardi Coding for the Large Subunit of d-ribulose-1,5-bisphosphate Carboxylase

Properties of the mRNA coding for the large subunit of ribulose-1,5-bisphosphate carboxylase from Chlamydomonas reinhardi were determined. Large subunit synthesis, directed by RNA from partially purified whole cell extracts, was detected by specific immunoprecipitation of polypeptide products synthesized in a heterologous translation system derived from Escherichia coli. Large subunit synthesis showed sharp RNA concentration dependence in an E. coli translation system, and at optimal RNA concentrations, immunoprecipitable large subunit synthesis accounted for 2% of the total incorporation. Large subunit messenger activity sedimented at 12 to 14S on nondenaturing sucrose gradients and did not bind to oligo(dT)-cellulose suggesting the mRNA is not polyadenylated. The immunoprecipitable products translated in vitro are not complete polypeptide chains, but are smaller peptides identifiable as large subunit fragments by tryptic fingerprint analysis. No immunoprecipitable product was obtained when similar RNA fractions were tested in a wheat germ translation system.

Poly(A)-associated RNA from the mitochondrial fraction of the fungus Trichoderma

Total RNA was extracted from purified mitochondrial and cytoplasmic fractions of germinating conidia of Trichoderma viride and bound to oligo(dT)-cellulose at 22 and 4 degrees C. Under chromatographic conditions which retained very short poly(A) segments (i.e., 4 degrees C), up to 10% of short-term 32PO4-lebeled RNA from the mitochondrial fraction were selectively bound. The poly(A)-associated RNAs from the mitochondrial and cytoplasmic fractions showed the following characteristics. (a) On polyacrylamide gels mitochondrial fraction RNA had a distinctive pattern with a major peak at about 22 S and a smaller one at about 29 S; in contrast, cytoplasmic fraction RNA was heterogenously distributed along the gel. (b) The poly(A) segment released by RNAase digestion of mitochondrial fraction poly(A)-associated RNA migrated on polyacrylamide gels as molecules 20-25-nucleotides long, while that of the cytoplasmic fraction showed an apparent size of 50-60 nucleotides. (c) Mitochondrial fraction RNA bound to oligo(dT)-cellulose in the cold had a guanine + cytosine content of 21% versus 34% for bulk mitochondrial RNA and 48% for cytoplasmic poly(A)-associated RNA; the oligo(dT)-bound RNAs were further identified by their high percentages of adenine residues (46% for the mitochondria and 30% for the cytoplasm). (d) The poly(A)-associated RNA fraction was translated, in vitro, in a cell-free protein-synthesizing system from wheat germ. The products induced by cytoplasmic RNA showed a complex pattern on polyacrylamide gels of many polypeptides ranging in molecular weights from 10000 to 40000. The pattern induced by mitochondrial fraction RNA however, was much simpler, revealing two discrete, main products: a major one at Mr approximately 13000 and a minor one at Mr approximately 20000.