Euglena gracilis chloroplast transfer RNA transcription units. Nucleotide sequence analysis of a tRNAThr-tRNAGly-tRNAMet-tRNASer-tRNAGln gene cluster

The genes aroA and trnQ are located upstream of psbO in the chromosome of Synechocystis 6803

We have identified the existence of two genes, trnQ and aroA, located upstream of the psbO gene in Synechocystis sp. PCC 6803. The trnQ gene encodes a glutamine-specific transfer RNA (tRNA(Gln)) and the sequence given is the first reported for any cyanobacterium. The gene seems to exist as a single copy since its deletion results in non-viable mutation. The aroA gene encodes for 5-enolpyruvylshikimate 3-phosphate synthase and its discovery in the genome of Synechocystis 6803 is the first genetic evidence for the existence of the shikimate biosynthetic pathway in cyanobacteria. Interestingly, the partial sequence shares close homologies with the sequences of aroA from Gram-positive bacteria.

Genes for the plastid elongation factor Tu and ribosomal protein S7 and six tRNA genes on the 73 kb DNA from Astasia longa that resembles the chloroplast DNA of Euglena

The nucleotide sequence of a 6156 bp segment of the circular 73 kb DNA from Astasia longa resembling the chloroplast DNA of Euglena was determined. The genes for the plastid elongation factor Tu (tufA) and the ribosomal protein S7 (rps7), six tRNA genes (trnQ, trnS, trnG, trnM, trnT, trnR), and three open reading frames were identified. These genes show a high degree of sequence similarity (73%-99%) to the corresponding genes on the Euglena chloroplast genome. The tufA gene contains two small AT-rich introns within its coding region. Northern analysis revealed the in vivo transcription of the tufA gene and of a reading frame of 456 codons into monocistronic mRNAs of 1.3 and 1.4 kb, respectively. The arrangement and organization of the genes on the 73 kb DNA of the colourless heterotrophic flagellate Astasia and the chloroplast DNA of autotrophic Euglena are compared.

Characterization of the TrnD, TrnK, PsaA locus of Euglena gracilis chloroplast DNA

The EcoRI fragment Eco J' of Euglena gracilis chloroplast DNA has previously been identified as a tRNA coding locus. The nucleotide sequence of a 2.3-kb region of the Eco J' fragment known to contain the tRNA genes has been determined. This locus was found to contain two tRNA genes, trnD-GTC and trnK-TTT. Separated from the trnK locus by a 43-bp spacer is an open reading frame of 398 codons. The open reading frame is 73-75% homologous to the amino-terminal coding regions of the spinach and maize genes for the P700 chlorophyll a apoprotein of photosystem I. It has been identified as exon I of an intron-containing psaA gene. The exon is followed by an intron of at least 214 bp that has features characteristic of other Euglena chloroplast introns. Major chloroplast RNA transcripts of sizes 5.5, 4.7, and 2.3 kb hybridize to a psaA-specific probe. The gene for a second photosystem I P700 apoprotein, psaB, has been located on an adjacent EcoRI fragment, Eco C.

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.

Characterization of the spinach chloroplast genes for the S4 ribosomal protein, tRNA(Thr) (UGU) and tRNA (Ser) (GGA)

The map location and nucleotide sequence of the genes for the S4 ribosomal protein (rps4) and for tRNA(Thr) (UGU) (trnT) and tRNA(Ser) (GGA) (trnS) on spinach chloroplast DNA have been determined. rps4 lies approximately 5 kb 3' to atpBE in the large single copy region and is transcribed in the same direction as atpBE. It has a 178 bp leader sequence, a 603 bp coding region and 620 bp 3' tail. The sequence of the coding region is 83% homologous with that of maize rps4 (29) and the deduced amino acid sequences from the two species are 7% homologous. The spinach and Escherichia coli S4 proteins are only 36% homologous. As in the case of maize, trnT lies upstream from and on the same strand as rps4 whereas trnS lies downstream and on the opposite strand. Transcription of rps4 apparently proceeds past trnS.

Localization and nucleotide sequences of the tRNA GCC (Gly) , tRNA GUC (Asp) and tRNA GCA (Cys) genes from wheat chloroplast

The location on the wheat chloroplast DNA map and the nucleotide sequences of the genes coding for tRNA GCC (Gly) (trnG-GCC), tRNA GUC (Asp) (trnD-GUC) and tRNA GCA (Cys) (trnC-GCA) have been determined. These three genes are located in the large single copy region of the chloroplast genome, about half-way between one of the inverted repeats and the gene for the α subunit of ATP synthase. They are located on two Bam H1 fragments, called B6 and B18 by Bowmanet al. (1), which are separated by about 450 bp and which were cloned in our laboratory to allow sequencing. ThetrnD-GUC andtrnC-GCA sequences show 98.6 and 89% homology, respectively, with the corresponding spinach chloroplast tRNA genes sequences (2), which are the only other higher plant chloroplasttrnD-GUC andtrnC-GCA sequenced so far, while no othertrnG-GCC sequence has been published. ThetrnG-GCC sequence shows only 58% homology with the corresponding gene sequence inEuglena chloroplasts (3).

Organization and nucleotide sequence of the genes for spinach chloroplast tRNA(Glu) and tRNA (Tyr.)

The map location and nucleotide sequence of the genes and flanking regions for tRNAUUC (Glu) (trnE) and tRNAGUA (Tyr) (trnY) from spinach (Spinacia oleracea) chloroplast DNA have been determined. The genes lie approximately midway between the genes for tRNAGGU (Thr) (trnT) and tRNAGUC (Asp) (trnD) on BamH1 fragment 8b, the arrangement being trnT, 458 bp, trnE, 64 bp, trnY, 409 bp, trnD. trnE and trnY are encoded by the same DNA strand as trnD and the direction of their transcription is divergent with respect to the transcription of trnT. trnE and trnY are 89% and 74% homologous, respectively, with the corresponding Euglena gracilis chloroplast genes. The corresponding homologies between the spinach chloroplast and E. coli genes are 72% and 61%. trnE is unusual in that it has the sequence 5'ATTCNA rather than 5'GTTCNA in the TΨ arm. Northern hybridizations to chloroplast RNA with restriction fragments carrying trnE and trnY sequences indicated that both genes are transcribed in vivo.

The nucleotide sequence of bacteriophage T5 glutamine transfer RNA

Uniformly 32P-labeled phage-specific tRNAGln has been isolated from bacteriophage T5-infected Escherichia coli cells and its nucleotide sequence has been determined using thin-layer chromatography on cellulose to fractionate the oligonucleotides. The sequence is: pUGGGGAUUAGCUUAGCUUGGCCUAAAGCUUCGGCCUUUGAAG psi CGAGAUCAUUGGT psi CAAAUCCAAUAUCCCCUGCCAOH. The main feature of this tRNA is the absence of Watson-Crick pairing between the 5'-terminal base and the fifth base from its 3'-end. The structure of tRNA was confirmed by DNA sequencing of its gene.

Transfer RNA genes of Euglena gracilis chloroplast DNA : A review

Transfer RNA genes have been mapped to at least nine different loci on the physical map of the Euglena gracilis chloroplast genome. One of these loci in the ribosomal RNA operons is present three times per genome. The DNA sequences of six of the nine different loci, containing 21 different tRNA genes, have been determined. Genes corresponding to the amino acids Ala, Arg, Asn, Cys, Gln, Gly (2), Glu, His, Ile, Leu (2), Met (2), Phe, Ser, Thr, Trp, Tyr, Val, and one unassigned species have been identified. All genes except one are found in clusters of 2-6 genes. None of the known genes contains introns, nor codes for the 3'-CCA terminus. In addition to these genes, two pseudo tRNA genes are present in the rDNA leader region.

Intervening sequences in chloroplast genomes

Chloroplast DNAs from the green algae Euglena gracilis and from broad beans (Vicia faba) were hybridized with homologous chloroplast RNA. The hybrids were analyzed by electron microscopy. Almost all transcribed regions of the Euglena genome, except for the rRNA genes, contain intervening sequences. A minimum of 50 introns was observed amounting to about 32 kb of the 145 kb genome. Only four spliced transcripts with a total number of six introns (about 0.8 kb each) were detected in the bean chloroplast RNA. A complete transcription map of the Euglena chloroplast genome was established. Transcribed regions occur on the strand that codes for the rRNAs (plus strand) as well as on the complementary strand (minus strand). The polarity of transcription reverses at least six times.

Accurate processing and pseudouridylation of chloroplast transfer RNA in a chloroplast transcription system

The trancription of a cloned trnV1-trnN1-trnR1 cluster from Euglena gracilis chloroplast (ct) DNA and the processing of a tRNA(Val)-tRNA(Asn)-tRNA(Arg) polycistronic precursor were studied in a spinach ct transcription extract. A soluble ct RNA polymerase selectively transcribes the trnV1-trnN1-trnR1-trnL1 locus in the EcoG fragment from the Euglena ct genome. Restriction enzyme modified templates and RNA fingerprint analysis were used to confirm that the tRNA genes were correctly transcribed. The tRNA(Val)-tRNA(Asn)-tRNA(Arg) polycistronic precursor transcribed by RNA polymerase III in a HeLa cell extract was used as a substrate to demonstrate that a ct tRNA precursor molecule is correctly processed by the ct tRNA processing enzymes. The oligonucleotide pattern of tRNAs processed in vitro from the tRNA(Val)-tRNA(Asn)-RNA(Arg) polycistronic precursor is indistinguishable from tRNA(Val), tRNA(Asn) and tRNA(Arg) transcribed by the ct RNA polymerase and processed in the ct transcription extract. The 3'-CCAOH is added to the tRNAs by a 3' nucleotidyltransferase after correct processing of the 3' terminus. Correct pseudouridylation was demonstrated for uridine residues in a tRNA(Met) m molecule transcribed from a spinach ct trnM1 locus. Thus, the enzymatic activities involved in tRNA biosynthesis in vitro include DNA-dependent (tDNA) RNA polymerase, a 5'-processing activity (RNase P-like), a 3'-exonuclease, an endoribonuclease involved in 3'-tRNA maturation, a tRNA nucleotidyltransferase, and pseudouridylate synthetase.