Nucleotide sequence of a 1.1 kb fragment of the pea chloroplast genome containing three tRNA genes, one of which is located within an open reading frame of 91 codons.

The nucleotide sequence of a 1082 bp fragment from the pea (Pisum sativum) chloroplast genome is presented. This fragment contains genes for tRNAGlu, tRNATyr and tRNAAsp as well as an open reading frame (ORF) of 91 codons on one strand and two ORFs of 52 and 59 codons on the complementary strand. The tRNAAsp gene is located entirely within the ORF of 91 codons. The first 366 bp of the fragment correspond to 376 bp at one end of a recently published (1) sequence from the broad bean (Vicia faba) chloroplast genome. These regions contain the tRNAGlu and tRNATyr genes, which are identical and separated by 60 bp in both species. These two genes are probably cotranscribed. The intergenic regions in the corresponding segments from the two species are, except for a 10 bp deletion in the pea sequence, 94% homologous.     

Three mitochondrial tRNA genes from Arabidopsis thaliana: evidence for the conversion of a tRNAPhe gene into a tRNATyr gene.

Three tRNA genes have been isolated from a genomic library of Arabidopsis thaliana: a tRNASer (GCU), a tRNATyr (GUA) and a tRNAGlu (UUC) genes. These genes are located closely on the same DNA fragment. The tRNASer and the tRNAGlu genes have both 99% sequence similarity with their mitochondrial counterparts from higher plants indicating that these three tRNA genes are mitochondrial. The tRNATyr gene shows a particular high sequence similarity with the mitochondrial tRNAPhe pseudogene from maize, and both genes are flanked by a tRNASer gene in the upstream region. Extensive sequence comparisons of the Arabidopsis thaliana mitochondrial sequence containing the three tRNA genes and the corresponding region from maize and soybean mitochondria have shown evidence that the tRNA Tyr gene has been generated from a mitochondrial tRNAPhe gene. The conversion was accomplished by three genetic events: a 4 base-pair deletion, a mutation and a recombination, which led to the transformation of the acceptor stem and the anticodon.     

太湖新银鱼m tDNA COII和Cytb基因的克隆与序列分析

设计了5对特异性引物,扩增、拼接并测定出太湖新银鱼线粒体tRNAAsp-COII-tRNALys和tRNAGlu-Cytb-tRNAThr两段基因序列片段。基因定位和序列分析发现,太湖新银鱼线粒体COII基因全序列长度为691 bp,序列AT含量为52.80%,编码230个氨基酸;线粒体Cytb基因序列全长为1141 bp,AT含量为48.90%,它编码380个氨基酸。分别位于线粒体COII和Cytb基因两翼的4个tRNA基因(tRNAAsp、tRNALys、tRNAGlu和tRNAThr)同时被测定出来。将太湖新银鱼与有明银鱼、小齿日本银鱼的同源序列进行比对分析,并基于线粒体COII Cytb基因合并数据的核苷酸和氨基酸两种序列形式,以黑斑蛙为外群,对10种鱼类进行分子系统树的构建,结果一致表明:小齿日本银鱼与有明银鱼的亲缘关系近于太湖新银鱼;鲱科与鲑科的亲缘关系近于银鱼科鱼类;此外在本研究硬骨鱼类的4个科中,白鲟科作为原始而古老的类群,是在系统进化的过程中首先分化出来的一支。     

Nucleotide sequence and evolution of the rat mitochondrial cytochrome b gene containing the ochre termination codon

The nucleotide sequences of the genes for cytochrome b and three potential transfer RNAs (tRNAPro, tRNAThr and tRNAGlu) in cloned rat mitochondrial DNA were determined. The derived amino acid sequence of the cytochrome b protein from the light strand indicated that the C-terminal amino acid is asparagine and the ochre termination codon is encoded in the DNA, in contrast to the the lack of termination codon in the reading frame of human [Anderson et al., Nature 290 (1981) 457] or mouse [Bibb et al., Cell 26 (1981) 167] mitochondrial DNA. The first ATG codon of the cytochrome b gene was spaced five nucleotides from the 5'-end of the tRNAGlu gene on the heavy strand. There was a single nucleotide spacing between the termination codon of the cytochrome b gene and the 5' end of the tRNAThr gene in the light strand. There was also a single nucleotide spacing between the 3'-end of the tRNAThr gene and the 3'-end of the tRNAPro gene on the heavy strand. The amino acid and nucleotide sequences of the cytochrome b genes of mammals and yeast [Nobrega and Tzagoloff, J. Biol. Chem. 255 (1980) 9828] were compared to reveal structural differences in two very different species. At the same time, amino acid substitutions in particular regions of the mammalian gene corresponding to the exon-intron boundaries in the yeast gene were noted. These genetic features are discussed in relation to the extreme compression of genetic information in the mammalian mitochondrial genome as related to the evolution of the gene organization and its sequence.     

Structure and evolution of a mouse tRNA gene cluster encoding tRNAAsp, tRNAGly and tRNAGlu and an unlinked, solitary gene encoding tRNAAsp

We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al., 1981, Nucleic Acids Res. 9, 2239-2250). The mouse and rat tRNAAsp and tRNAGly coding regions are identical. The tRNAGlu coding regions differ at two positions. The flanking sequences contain 3 non-homologous areas: a c. 100 bp insertion in the first mouse spacer, short tandemly repeated sequences in the second spacers and unrelated sequences at the 3' ends of the clusters. In contrast, most of the flanking regions are homologous, consisting of strings of consecutive, identical residues (5-17 bp) separated by single base differences and short insertions/deletions. The latter are often associated with short repeats. The homology of the flanking regions is c. 75%, similar to other murine genes. The second lambda clone contains a solitary mouse tRNAAsp gene. The coding region is identical to that of the clustered tRNAAsp gene. The 5' flanking regions of the two genes contain homologous areas (10-25 bp) separated by unrelated sequences. Overall, the flanking regions of the two mouse tRNAAsp genes are less homologous than those of the mouse and rat clusters.     

Nucleotide sequences of genes for ribosomal protein L41 and tRNAThr(AGU) from Coprinus cinereus.

The nucleotide sequences of genes for the homolog in Coprinus cinereus of the eukaryotic ribosomal protein L41 and for tRNAThr(AGU) are reported. The gene for tRNAThr(AGU) was located upstream of the gene for the L41 ribosomal protein, and these genes were adjacent to each other but in opposite orientations. The deduced amino acid sequence of ribosomal protein L41 exhibited strong homology to those of L41 proteins of several yeasts. The 56th amino acid of the deduced protein was proline, as it is in the L41 protein of a cycloheximide-sensitive strain of yeast. The putative secondary structure of the tRNA gene resembled the characteristic cloverleaf structure of tRNAs. Elements resembling an A-box and a B-box were found in the gene for tRNAThr(AGU). These boxes are known as internal promoter elements in genes for eukaryotic tRNAs.     

麦穗鱼线粒体基因组序列测定及分析

利用麦穗鱼Pseudorasbora parva和相关鱼类的部分线粒体基因序列,设计出2对长批引物和30对短批引物,采用基于长PCR的2次PCR扩增法测定并注释麦穗鱼线粒体基因组全序列。结果表明,麦穗鱼线粒体基因组长16600bp,A+T含量为58.9%,37个基因位置及组成与其它硬骨鱼一致,均由13个蛋白编码基因、22个tRNA、2个rRNA基因和1个控制区(D-loop)组成。其中L链仅含8个tRNA(Pro、T yr、Ser、Ala、Asn、Cys、Glu、Gln)及ND6基因,其余基因皆由H链编码。基因排列紧密,间隔序列共计13处64bp,长度从1～32bp不等;基因重叠区7处23bp,重叠碱基数在1～7bp之间。13个蛋白编码基因中,除COI起始密码子为GTG外,其余均以ATG为起始密码子;有8个基因(ND1、ND2、COI、ATP6、ATP8、ND4L、ND5、ND6)3’端有完全的TAA或TAG终止密码子,其它5个基因终止密码子为不完整的TA(ND3和ND4)或T(COⅡ,COⅢ,Cyt b)。除tRNASer(AGY)外,其余21个tRNA基因的二级结构均为典型的三叶草结构。预测的lrRNA二级结构共有6个结构域,53个茎环结构,srRNA二级结构包含43个茎环结构。控制区(D-loop)存在3个结构区:终止序列区(TAS)、中央保守区(CSB-F、CSB-D)和保守序列区(CSB-1、CSB-2、CSB-3),其中TAS与DNA复制终止相关,出现茎环结构。     

Complete mitochondrial genome of Chinese big-headed turtle, Platysternon megacephalum, with a novel gene organization in vertebrate mtDNA

The mitochondrial genome of the Chinese big-headed turtle, Platysternon megacephalum, was obtained using polymerase chain reaction (PCR). The entire mtDNA sequence, the longest mitochondrial genome in turtles reported so far, is 19161 bp. This mitochondrial genome exhibits a novel gene order, which greatly differs from that of any other vertebrates. It is characterized by four distinctive features: 1) the translocation of a gene cluster including three tRNA genes (tRNAHis, tRNASer, tRNALeu(CUN)) and ND5 gene, 2) two tRNAThr pseudogenes, 3) a duplication of pseudo tRNAThr/tRNAPro/D-loop region and 4) 3 non-coding spacers. These unique identities represent a new mitogenomic gene order in vertebrates. The TDRL model was proposed to account for the generation of the gene order in P. megacephalum.     

Wheat germ splicing endonuclease is highly specific for plant pre-tRNAs.

Intron-containing pre-tRNAs from organisms as different as yeast, Nicotiana, Xenopus and man are efficiently spliced and processed in a HeLa cell extract. They are also correctly processed in a wheat germ extract; however, the intron is removed only from the tobacco pre-tRNA. To determine whether plant pre-tRNA introns have any specific structural and/or sequence feature we have cloned two intron-containing tRNATyr genes from the plant Arabidopsis. Comparison of these genes, of the Nicotiana tRNATyr gene and of a Glycine max tRNAMet gene reveals that plant introns from three different species have no sequence homology and are only 11 to 13 nucleotides long. Thus, short length may be one important feature of plant introns. Furthermore, the 5' and 3' splice sites are separated by 4 bp in the extended anticodon stems of these pre-tRNA structures. In contrast, yeast and vertebrate introns are rather variable in length and the splice sites are separated by 5 or 6 bp. These differences in distance and relative helical orientation of the splice sites in plant pre-tRNAs versus pre-tRNAs from other organisms are obviously tolerated by the vertebrate splicing endonuclease, but not at all by the plant enzyme.     

Expression of a X. laevis tRNATyr gene in mammalian cells.

Expression of a X. laevis tRNATyr gene has been studied in mammalian cells. This tRNATyr gene has a 13 base intervening sequence adjacent to its anticodon. A fragment containing the tRNATyr gene was cloned into the late region of SV40. Cells infected with a recombinant virus stock vastly overproduce a tRNATyr that is properly spliced, processed and modified. It was also found that the X. laevis tRNATyr is identical or nearly identical to an endogenous tRNATyr of monkey kidney cells. The possibility of using the X. laevis tRNATyr gene to create an amber suppressor for mammalian cells is discussed.     

Characterization of a rat tRNA gene cluster: comparison of nucleotide sequences of the gene for tRNALeu newly found in repeating units

In the rat, DNA carrying a cluster of the genes for tRNAAsp, tRNAGly, and tRNAGlu, aligned in that order, is repeated about 10 times. Seven DNA clones corresponding to the independent repeating units were isolated from a rat gene library. Nucleotide sequence analysis of these clones revealed the presence of a fourth tRNA gene, the gene for tRNALeu, in the cluster. The tRNALeu gene is located about 600 base pairs (bp) upstream from the tRNAAsp gene and its polarity differs from those of the other three tRNA genes. Among the repeating units, the nucleotide sequence of tRNALeu is conserved to a relatively high degree.     

Organization of tRNA and rRNA genes in N. crassa mitochondria: intervening sequence in the large rRNA gene and strand distribution of the RNA genes.

Through analysis of cloned fragments of N. crassa mitochondrial DNA, we have derived a physical map for the region of the mitochondrial genome which encodes the ribosomal RNAs and most of the tRNAs. We have located RNA genes on this map by hybridization of purified 32P end-labeled RNA probes, and our findings are as follows. First, the gene for the large ribosomal RNA contains an intervening sequence of approximately 2000 bp. Second, the genes for the small and large ribosomal RNAs are not adjacent, as previously reported, and the region between them contains a number of tRNA genes, including that for the mitochondrial tRNATyr, which is located close to the small rRNA gene on the same strand of the mitochondrial DNA. Third, there is a second cluster of tRNA genes on the mitochondrial DNA following the large ribosomal RNA gene, but there is no evidence for the presence of tRNA genes in the intervening sequence of the large ribosomal RNA. Fourth, hybridization of labeled ribosomal and transfer RNAs to the separated strands of a cloned 16 kbp DNA fragment covering this region indicates that the two ribosomal RNAs and most, if not all, of the mitochondrial tRNAs are encoded on one strand of the mitochondrial DNA.