DNA sequences for the Zea mays tRNA genes tV-UAC and tS-UGA: tV-UAC contains a large intron

Comparative and functional anatomy of group II catalytic introns--a review

The 70 published sequences of group II introns from fungal and plant mitochondria and plant chloroplasts are analyzed for conservation of primary sequence, secondary structure and three-dimensional base pairings. Emphasis is put on structural elements with known or suspected functional significance with respect to self-splicing: the exon-binding and intron-binding sites, the bulging A residue involved in lariat formation, structural domain V and two isolated base pairs, one of them involving the last intron nucleotide and the other one, the first nt of the 3' exon. Separate sections are devoted to the 29 group II-like introns from Euglena chloroplasts and to the possible relationship of catalytic group II introns to nuclear premessenger introns. Alignments of all available sequences of group II introns are provided in the APPENDIX.

Structure and organization of Marchantia polymorpha chloroplast genome. II. Gene organization of the large single copy region from rps'12 to atpB

The nucleotide sequence (56,410 base-pairs) of the large single-copy region of chloroplast DNA from the liverwort Marchantia polymorpha has been determined. The sequence starts from one end (JLA) of the large single-copy region and encompasses genes for 21 tRNAs, six ATPase subunits (atpA, atpB, atpE, atpF, atpH and atpI), two photosystem I polypeptides (psaA and psaB), four photosystem II polypeptides (psbA, psbC, psbD and psbG), five ribosomal proteins (rps2, rps4, rps7, rps'12 and rps14), and three RNA polymerase subunits (rpoB, rpoC1 and rpoC2). In addition, we detected 18 open reading frames ranging from 29 to 2136 amino acid residues long, four of which share significant amino acid sequence homology to those of an Escherichia coli malK protein (designated mbpX), human mitochondrial ND2 (ndh2) and ND3 (ndh3) of a respiratory chain NADH dehydrogenase, or a bacterial antenna protein of a light-harvesting complex (lhcA). Sequence analysis suggests that four tRNA genes and six protein genes might be split by introns; they are trnG(UCC), trnK(UUU), trnL(UAA), trnV(UAC), atpF, ndh2, rpoC1, rps'12, ORF135 and ORF167. In the large single-copy region described here, the gene organization deduced is highly conserved with respect to that of higher plants, but an inversion of some 30,000 base-pairs flanked by trnL(CAA) and trnD(GUC) was seen between the liverwort and tobacco chloroplast genomes.

Pea chloroplast tRNA(Lys) (UUU) gene: transcription and analysis of an intron-containing gene

The pea chloroplast trnK gene which encodes tRNA(Lys) (UUU) was sequenced. TrnK is located 210 bp upstream from the promoter of psbA and immediately downstream from the 3'-end of rbcL. The gene is transcribed from the same DNA strand as psbA and rbcL. A 2447 bp intron with class II features is located in the trnK anticodon loop. The intron contains a 506 amino acid open reading frame which could encode an RNA maturase. The primary transcript of trnK is 2.9 kb long; its 5'-end was identified as a site of transcription initiation by in vitro transcription experiments. The 5'-terminus is adjacent to DNA sequences previously identified as transcription promoter elements. The most abundant trnK transcript is 2.5 kb long with termini corresponding to the 5' and 3' ends of the trnK exons. Intron specific RNAs were not detected. This suggests that RNA processing which produces tRNA(Lys) leads to rapid degradation of intron sequences.

Insertion/deletion mutations in the Zea chloroplast genome

The chloroplast (cp) genomes of Zea species are distinguished by at least four restriction fragment length (insertion/deletion) mutations. All four mutations occur in the large unique sequence region of the genome. Restriction fragments containing three of these mutations were cloned. The large and small forms of two of the mutated fragments were sequenced. This revealed 80 and 83 bp insertion/deletions. The inserted/deleted segments are not parts of tandem repeats nor were they flanked by direct repeats. Two other insertion/deletion mutations were not sequenced, but their sizes were estimated to be 150 and 250 bp by size fractionation on agarose gels. Use of Tripsacum pilosum and Sorghum bicolor as outgroups suggests that three of the fragment length mutations arose via deletions. The fourth could not be polarized. The three species of section Luxuriantes of Zea were identical to one another for each of the four length mutations, and they were consistently distinguished from the taxa of section Zea by these mutations. These data support the division of Zea into the above named sections.

Structures of tobacco chloroplast genes for tRNA(Ile) (CAU), tRNA (Leu) (CAA), tRNA (Cys) (GCA), tRNA (Ser) (UGA) and tRNA (Thr) (GGU): a compilation of tRNA genes from tobacco chloroplasts

The location and nucleotide sequences of tobacco chloroplast genes for tRNA(Ile) (CAU), tRNA(Leu) (CAA), tRNA(Cys) (GCA), tRNA(Ser) (UGA) and tRNA(Thr) (GGU) (trnI-CAU, trnL-CAA, trnC-GCA, trnS-UGA and trnT-GGU, respectively) have been determined. The trnI and trnL are located in the inverted repeat region. The trnC, trnS and trnT are present in the large single copy region. These five tRNA genes together with the 25 different tRNA genes previously published have been compiled and compared. These 30 tRNA genes corresponding to 20 amino acids are most likely to be all of the tRNA genes encoded in tobacco chloroplast genome.

Nucleotide sequence of the split tRNAleu(UAA) gene from Sorghum bicolor chloroplasts

The nucleotide (nt) sequence of the split tRNAleu(UAA) gene and 328 nt of its flanking regions from sorghum chloroplasts (cp) has been determined. This gene is located in the BamHI-6 fragment in a map position very similar to that of maize. The exon of sorghum tRNAleu gene has an identical nt sequence to its counterpart in maize. Although the 450 nt of intron in sorghum is 8 nt shorter than that of maize, the nt sequence between them shows 97% homology. Like maize and broad bean, the intron from sorghum cp tRNAleu gene could be folded into a secondary structure which is similar to the postulated structure of the intron from the auto-spliceable rRNA precursor of Tetrahymena. Both introns from sorghum and maize contain open reading frames (ORFs) which are conserved at the N terminus. The putative AUG initiation codon for both ORFs is located in the stem region of a 12-bp secondary structure of highly A + T-rich sequences.

Nucleotide sequences of transfer RNA genes in the Pisum sativum chloroplast DNA

Eight transfer RNA (tRNA) genes which were previously mapped to five regions of the Pisum sativum (pea) chloroplast DNA (ctDNA) have been sequenced. They have been identified as tRNA(Val)(GAC), tRNA(Asn)(GUU), tRNA(Arg)(ACG), tRNA(Leu)(CAA), tRNA(Tyr)(GUA), tRNA(Glu)(UUC), tRNA(His)(GUG), and tRNA(Arg)(UCU) by their anticodons and by their similarity to other previously identified tRNA genes from the chloroplast DNAs of higher plants or from E. gracilis. In addition,two other tRNA genes, tRNA(Gly) (UCC) and tRNA(Ile)(GAU), have been partially sequenced. The tRNA genes are compared to other known chloroplast tRNA genes from higher plants and are found to be 90-100% homologous. In addition there are similarities in the overall arrangement of the individual genes between different plants. The 5' flanking regions and the internal sequences of tRNA genes have been studied for conserved regions and consensus sequences. Two unusual features have been found: there is an apparent intron in the D-loop of the tRNA(Gly)(UCC), and the tRNA(Glu)(UUC) contains GATTC in its T-loop.

Organization and sequence of five tRNA genes and of an unidentified reading frame in the wheat chloroplast genome: evidence for gene rearrangements during the evolution of chloroplast genomes

The genes for the initiator tRNA(Met)CAU, tRNA(Gly)UCC, tRNA(Thr)GGU, tRNA(Glu)UUC and tRNA(Tyr)GUA and an open reading frame of 62 codons have been identified by sequencing a 2,358 bp BamHI and a 1,378 bp BamHI-Sst2 DNA fragments from wheat chloroplasts. A comparison of the organization of these five tRNA genes and of the open reading frame on the wheat, tobacco and spinach chloroplast genomes suggests that at least three genomic inversions must have occurred during the evolution of the wheat chloroplast genome from a spinach-like ancestor genome. Furthermore, it seems that in wheat the 91 bp intergenic region between the genes for the initiator tRNA(Met) and the gene for tRNA(Gly)UCC is one end-point of the 20 kbp genomic inversion proposed by Palmer and Thompson in the case of maize (Palmer and Thompson 1982). A 119 bp duplication is located at this junction: the first copy comprises the 91 bp of the intergenic region and the first 28 bp of the tRNA(Met) gene, the second copy is found downstream of the tRNA(Met) gene.

Location and nucleotide sequence of the genes for tobacco chloroplast tRNAArg (ACG) and tRNALeu(UAG)

The location and nucleotide sequence of the genes and flanking regions for tRNAArg(ACG) and tRNALeu(UAG) on tobacco chloroplast DNA have been determined. The gene arrangement is 5S rRNA-260 bp-tRNAArg-581 bp-tRNAAsn-5.2 kbp-tRNALeu. The tRNAArg and tRNALeu genes are expressed in the chloroplasts. The opposite strand of the tRNAArg gene contains a tRNAArg-like sequence. The tRNAArg, tRNAAsn and tRNALeu coding regions are contained in open reading frames.