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Query: UNIPROT:P06889 (Mol)
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A shortened derivative of the group IIA intron from the mitochondrial cytochrome-c-oxidase subunit I gene (COI I1) of the ascomycete Podospora anserina can undergo self-splicing in vitro. When compared to self-splicing group IIB introns from yeast mitochondria (aI5c, bI1) the autocatalytic reaction shows a lower efficiency and 5' cleavage takes place predominantly by hydrolysis. In order to test the influence on reaction efficiency and mode of 5' cleavage of the long peripheral structure of domain VI (dVI) we generated mutant Podospora introns that have different structural forms of shortened dVI. Our results show that: (1) in general the size and structure of dVI distal from the branch site is essential for 5' transesterification and influences the efficiency of the second splicing step; (2) 5' transesterification as well as the complete self-splicing reaction is more efficient when the structure of dVI is adapted to that of yeast group IIB introns. Moreover, our data indicate that the postulated gamma-gamma' tertiary interaction is also functional for group IIA introns. A weakening or disruption of this interaction in the Podospora intron leads to a greatly reduced cleavage at the 3' splice site and to a selection of cryptic sites downstream in the 3' exon that almost exclusively restore the strong wild-type gamma-gamma' pairing. The so-called "guide" interaction seems to support the selection of 3' cleavage sites but is of secondary importance in relation to the gamma-gamma' interaction.
J Mol Biol 1993 Jun 05
PMID:Self-splicing of a Podospora anserina group IIA intron in vitro. Effects of 3'-terminal intron alterations on cleavage at the 5' and 3' splice site. 851 40

Ten of 12 mitochondrial protein-coding genes and the large (16S) mitochondrial rRNA gene have been identified and mapped within the Romanomermis culicivorax mitochondrial genome. This transcriptional map differs from other nematode mitochondrial DNAs (mtDNAs) with respect to gene order and transcriptional orientation of some genes. Several of these coding regions are components of a 3.0-kilobase mtDNA repeating unit, allowing a direct comparison of nucleotide and amino acid sequence composition for repeated and single copy genes. Analysis of protein-coding regions representing repeated (ND3, ND6) and single copy genes (ATPase 6, cyt.b, COI, COIII, ND1, ND4, ND5), and four repeat-associated open reading frames (ORFs) with unassigned function have revealed striking similarities in nucleotide composition, amino acid frequencies, and codon biases. Although we anticipated that reiterated protein coding regions might be evolving under relaxed selection, our results indicate that both repeated and unique mitochondrial genes appear subject to similar functional constraints.
Mol Biol Evol 1996 Jan
PMID:Similar evolutionary patterning among repeated and single copy nematode mitochondrial genes. 858 95

The complete nucleotide sequence of the mitochondrial DNA of the rainbow trout, Onchorynchus mykiss, has been determined. The total length of the molecule is 16,660 bp. The rainbow trout mitochondrial DNA has the same organization described in eutherian mammals, the clawed frog (Xenopus laevis), and the two fish species, Oriental stream loach (Crossotoma lacustre) and carp (Cyprinus carpio). Alignment and comparison of the deduced amino acid sequences of the 13 proteins encoded by rainbow trout and other vertebrate mitochondrial genomes allowed us to estimate that COI is the most conserved mitochondrial subunit (amino acid identity ranging from 85.6% to 94.8%) whereas ATPase 8 is the most variable one (amino acid identity ranging from 30.8% to 70.4%). Putative secondary structures for the 22 tRNAs found in the molecule are given along with an extensive comparison of tRNA sequences among representative species of each major group of vertebrates. In this sense, an unusual cloverleaf structure for the tRNASer(AGY) is proposed. A stem-loop structure inferred for the origin of the L-strand replication (OL) and the presence of a large polycytidine tract in the OL loop is described. The existence of this stretch instead of the usual T-rich sequence reported so far in mammal mtDNAs is explained in terms of a less-strict template dependence of the RNA primase involved in the initiation of L-strand replication.
J Mol Evol 1995 Dec
PMID:The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. 858 39

The nucleotide sequence of the mitochondrial ND2, COI, COII, ATPase8, srRNA and nine tRNA genes have been sequenced from two individual of the meadow grasshopper Chorthippus parallelus. Comparisons are made to other insects for which the same regions are completely sequenced. Percentage A + T is found to be relatively low in C. parallelus though consistent with that of the other Orthopteran, Locusta migratoria. The relative number of substitutions observed in the different protein-coding genes was analysed between pairs of insect species sharing different levels of relatedness. A clear change in this rate was observed between the within-genus and between-genera comparisons. This change is interpreted in terms of the functional constraints acting on these four different genes. The patterns seem to result from an early saturation of COI and COII genes with synonymous substitutions, and a tolerance of ND2 and ATPase8 function to high levels of amino acid replacements. This analysis highlights a need for further sequence studies and comparisons between taxa of different levels of divergence in order to understand the patterns of mtDNA evolution on which many evolutionary investigations are based.
Insect Mol Biol 1996 May
PMID:The sequence and structure of the meadow grasshopper (Chorthippus parallelus) mitochondrial srRNA, ND2, COI, COII ATPase8 and 9 tRNA genes. 867 63

The complete mitochondrial DNA (mtDNA) molecule of the gorilla was sequenced. The entire sequence, 16,412 nucleotides, was determined by analysis of natural (not polymerase chain reaction) restriction fragments covering the whole molecule. The sequence was established from one individual and thus nonchimeric. After comparison with the COII gene of gorilla specimens with known geographical origin, the sequence was identified as characteristic of the Western lowland gorilla, Gorilla gorilla gorilla. With the exception of the NADH2 gene, all genes have a methionine start codon. The inferred start codon of NADH2 is ATT (isoleucine). The COIII, NASDH4, and cytochrome b genes are not terminated by a stop codon triplet, and the COI gene is probably terminated by an AAA triplet rather than by a regular stop codon. The great majority of genic sequences (rRNAs, peptide-coding genes, tRNAs) of the complete mtDNAs of Gorilla, Pan, and Homo show a greater similarity between Pan and Homo than between either of these genera to Gorilla. The analysis of the peptide-coding genes suggest that relative to comparison between Homo and Pan a certain degree of transition saturation has taken place in codon position 3 in comparisons between Gorilla to either Homo or Pan.
Mol Biol Evol 1996 May
PMID:A complete sequence of the mitochondrial genome of the western lowland gorilla. 867 44

Polymerase chain reaction (PCR) products corresponding to 803 bp of the cytochrome oxidase subunits I and II region of mitochondrial DNA (mtDNA COI-II) were deduced to consist of multiple haplotypes in three Sitobion species. We investigated the molecular basis of these observations. PCR products were cloned, and six clones from one individual per species were sequenced. In each individual, one sequence was found commonly, but also two or three divergent sequences were seen. The divergent sequences were shown to be nonmitochondrial by sequencing from purified mtDNA and Southern blotting experiments. All seven nonmitochondrial clones sequenced to completion were unique. Nonmitochondrial sequences have a high proportion of unique sites, and very few characters are shared between nonmitochondrial clones to the exclusion of mtDNA. From these data, we infer that fragments of mtDNA have been transposed separately (probably into aphid chromosomes), at a frequency only known to be equalled in humans. The transposition phenomenon appears to occur infrequently or not at all in closely related genera and other aphids investigated. Patterns of nucleotide substitution in mtDNA inferred over a parsimony tree are very different from those in transposed sequences. Compared with mtDNA, nonmitochondrial sequences have less codon position bias, more even exchanges between A, G, C and T, and a higher proportion of nonsynonymous replacements. Although these data are consistent with the transposed sequences being under less constraint than mtDNA, changes in the nonmitochondrial sequences are not random: there remains significant position bias, and probable excesses of synonymous replacements and of conservative inferred amino acid replacements. We conclude that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition. We believe that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes. However, our data highlight the need to establish the true evolutionary relationships between sequences in comparative investigations.
Mol Biol Evol 1996 Mar
PMID:Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). 874 40

A large number of studies in evolutionary biology utilize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among distantly related lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitochondrial genes might potentially produce misleading evolutionary inferences and hence might not constitute an adequate representation neither of the entire mitochondrial genome nor of the evolutionary history of the organisms from which they are derived. We investigated the performance of all mitochondrial protein-coding genes to recover two expected phylogenies of tetrapods and mammals. According to these tests, mitochondrial protein-coding genes can be roughly classified into three groups of good (ND4, ND5, ND2, cytb, and COI), medium (COII, COIII, ND1, and ND6), and poor (ATPase 6, ND3, ATPase 8, and ND4L) phylogenetic performers in recovering these expected trees among phylogenetically distant relatives. How general our findings are is unclear. Simple length differences and rate differences between these genes cannot account for their different phylogenetic performance. The phylogenetic performance of these mitochondrial genes might depend on various factors that play a role in determining the probability of discovering the correct phylogeny such as the density of lineage creation events in time, the phylogenetic "depth" of the question, lineage-specific rate heterogeneity, and the completeness of taxa representation.
Mol Biol Evol 1996 Sep
PMID:Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. 875 2

The mRNAs of the nuclear encoded genes, ornithine decarboxylase (ODCase) and poly(ADP)ribose polymerase (PADPRP), and the mitochondrial encoded genes, cytochrome oxidase I and II (COI and COII) and ATPase 6, are differentially expressed during spermatogenesis (Alcivar et al., 1989: Biol Reprod 41:1133; 1989: Dev Biol 135:263; 1991: Biol Reprod 46:201). In this study, we use Northern blotting to examine the steady state levels of ODCase, PADPRP, COI, COII, and ATPase 6 mRNAs in testes of hypophysectomized male rats following testosterone administration. Four weeks after hypophysectomy, rats received 24 cm subcutaneous implants of testosterone-filled polydimethylsiloxane (PDS) and were killed at 3, 7, 14, 28, and 56 days thereafter. After hypophysectomy, the steady state levels for the PADPRP, COI, COII, and ATPase 6 mRNAs were not significantly different from controls, although hypophysectomy caused a 44% loss of preleptotene spermatocytes and an 88% loss of pachytene spermatocytes, the testicular cell types expressing the highest levels of these mRNAs. In contrast, the levels of the two ODCase mRNAs were greatly decreased after hypophysectomy and mirrored the number of germinal cells present in the testis. After testosterone treatment, ODCase mRNA levels remained low 3 days after treatment and gradually increased at days 14, 28, and 56. No major hybridization signal changes in PADPRP, COI, COII, and ATPase mRNA were observed after testosterone treatment. We conclude that the steady state mRNA levels for the housekeeping ODCase gene respond differently after hypophysectomy and testosterone treatment of male rats than the PADPRP and mitochondrial DNA transcripts.
Mol Reprod Dev 1996 Mar
PMID:Differential expression of ornithine decarboxylase, poly(ADP)ribose polymerase, and mitochondrial mRNAs following testosterone administration to hypophysectomized rats. 886 40

A cDNA encoding mitochondrial cytochrome c oxidase subunit I (mt COI) from Manduca sexta (Lepidoptera: Sphingidae) was cloned and sequenced. AT (adenine-thymine) content is high and codon usage is biased and likely reflects the role of mt COI in electron transport. The encoded protein is 514 amino acids long, contains seven invariant His residues observed in COIs in all organisms and would be predicted to be composed of 12 transmembrane regions.
Comp Biochem Physiol B Biochem Mol Biol 1996 Apr
PMID:Mitochondrial cytochrome C oxidase subunit I of Manduca sexta and a comparison with other invertebrate genes. 892 45

Marine invertebrate collections have historically been maintained in ethanol following fixation in formalin. These collections may represent rare or extinct species or populations, provide detailed time-series samples, or come from presently inaccessible or difficult-to-sample localities. We tested the viability of obtaining DNA sequence data from formalin-fixed, ethanol-preserved (FFEP) deep-sea crustaceans, and found that nucleotide sequences for mitochondrial 16S rRNA and COI genes can be recovered from FFEP collections of varying age, and that these sequences are unmodified compared with those derived from frozen specimens. These results were repeatable among multiple specimens and collections for several species. Our results indicate that in the absence of fresh or frozen tissues, archived FFEP specimens may prove a useful source of material for analysis of gene sequence data by polymerase chain reaction (PCR) and direct sequencing.
Mol Mar Biol Biotechnol 1996 Dec
PMID:DNA sequencing of formalin-fixed crustaceans from archival research collections. 898 99


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