Mitochondrial oxidative phosphorylation (OXPHOS) fuels cellular ATP demands. OXPHOS defects lead to severe human disorders with unexplained tissue specific pathologies. Mitochondrial gene expression is essential for OXPHOS biogenesis since core subunits of the complexes are mitochondrial-encoded. COX14 is required for translation of COX1, the central mitochondrial-encoded subunit of complex IV. Here we describe a COX14 mutant mouse corresponding to a patient with complex IV deficiency. COX14M19I mice display broad tissue-specific pathologies. A hallmark phenotype is severe liver inflammation linked to release of mitochondrial RNA into the cytosol sensed by RIG-1 pathway. We find that mitochondrial RNA release is triggered by increased reactive oxygen species production in the deficiency of complex IV. Additionally, we describe a COA3Y72C mouse, affected in an assembly factor that cooperates with COX14 in early COX1 biogenesis, which displays a similar yet milder inflammatory phenotype. Our study provides insight into a link between defective mitochondrial gene expression and tissue-specific inflammation.

• MeSH
• Cyclooxygenase 1 * MeSH
• DEAD Box Protein 58 MeSH
• DEAD-box RNA Helicases metabolism   genetics   MeSH
• Liver * metabolism   pathology   MeSH
• Humans MeSH
• Membrane Proteins MeSH
• Mitochondrial Proteins metabolism   genetics   MeSH
• Mitochondria metabolism   MeSH
• Mutation MeSH
• Mice, Inbred C57BL MeSH
• Mice MeSH
• Oxidative Phosphorylation * MeSH
• Protein Biosynthesis MeSH
• Reactive Oxygen Species * metabolism   MeSH
• Electron Transport Complex IV * metabolism   genetics   MeSH
• RNA, Mitochondrial genetics   metabolism   MeSH
• Inflammation * metabolism   genetics   pathology   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Mice MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH

We examined the phylogeography and the variation of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit 1 gene (cox1) of the Chinese liver fluke Clonorchis sinensis (Cobbold, 1875) in two geographic localities in the Russian southern Far East and compared them with those from different geographical regions (China, Korea, Japan and Vietnam). The Russian samples differed from those of the other regions in haplotype frequencies, haplotype and nucleotide diversities, and AT/GC ratios. Only 4 of the 18 haplotypes were common to Russian and Chinese samples, and two haplotypes were common to Russia and other regions. The intraspecific genetic distances ranged from 0 to 1.58% for the entire dataset studied and from 0 to 1.25% among the samples from Russia. Phylogenetic trees revealed no significant genealogical clades of samples corresponding to sampling localities and no strong isolation by distance was estimated with Mantel test. Neutrality test analysis suggested a relatively recent population expansion for C. sinensis, whereas goodness-of-fit tests indicated deviation from the strict model of uniform expansion. Therefore, the sequences of the mtDNA cox1 gene provide useful genetic markers for evaluating intraspecific diversity and generating phylogeographic reconstructions for this fish-borne trematode.

• MeSH
• Clonorchis sinensis classification   genetics   isolation & purification   MeSH
• Phylogeography MeSH
• Genetic Variation * MeSH
• Haplotypes MeSH
• Clonorchiasis parasitology   veterinary   MeSH
• DNA, Mitochondrial chemistry   genetics   MeSH
• Mitochondria genetics   MeSH
• Molecular Sequence Data MeSH
• Fish Diseases parasitology   MeSH
• Electron Transport Complex IV genetics   MeSH
• Fishes MeSH
• Base Sequence MeSH
• Sequence Analysis, DNA veterinary   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Geographicals
• Asia MeSH
• Russia MeSH

The aim of this study is to better understand the cellular gene expression changes upon the RNA interference (RNAi) mediated down-regulation of COX1 resp. COX2 gene expression. The corresponding cell-lines with COX1 resp. COX2 gene expression down regulated will be constructed via RNAi, the synthetic siRNA or plasmid or retrovirus mediated shRNA expression, respectively. The gene expression profile will be determined by DNA microarrays comparing the gene expression with parental cell-line. Based on theresults, experimental, single-purpose DNA microarray containing selected genes will be constructed. Altered physiological function of COX1 resp. COX2 in the absence of one of the isoforms will be discussed.

Úkolem této studie je porozumění změn v genové expresi na buněčné úrovni v souvislosti se zablokováním exprese COX1 resp. COX2 pomocí RNA interference (RNAi). Pomocí RNAi, syntetických siRNA nebo shRNA exprimujících plasmidů či retrovirů, budou vytvořenybuněčné linie se zablokovanou expresí COX1 resp. COX2. Profil genové exprese bude určen pomocí DNA mikročipů srovnáním s mateřskou linií a ověřením pomocí real-time PCR. Na základě prvních výsledků bude sestaven experimentální jednoúčelový DNA mikročipobsahující vybrané geny. Na základě výsledků bude posouzena fyziologická funkce COX1 a COX2 v souvislosti s absencí jedné z izoforem.

• MeSH
• Cyclooxygenase 1 physiology   MeSH
• Cyclooxygenase 2 physiology   MeSH
• Gene Expression MeSH
• Cyclooxygenase Inhibitors adverse effects   MeSH
• RNA, Small Interfering MeSH
• Microchip Analytical Procedures MeSH
• Polymerase Chain Reaction MeSH
• RNA Interference MeSH
• Inflammation MeSH

• Conspectus
• Biochemie. Molekulární biologie. Biofyzika
• NML Fields
• biologie
• NML Publication type
• závěrečné zprávy o řešení grantu IGA MZ ČR

UNLABELLED: Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts. IMPORTANCE: Uridine insertion/deletion-type RNA editing, which occurs in the mitochondrion of kinetoplastid protists, has been well-studied in the model parasite genera Trypanosoma, Leishmania, and Crithidia. Perkinsela provides a unique opportunity to broaden our knowledge of RNA editing machinery from an evolutionary perspective, as it represents the earliest kinetoplastid branch and is an obligatory endosymbiont with extensive reductive trends. Interestingly, up to 50% of mitochondrial transcripts in Perkinsela contain errors. Our study was complemented by use of newly developed software designed for accurate mapping of extensively edited RNA-seq reads obtained by deep sequencing.

• MeSH
• Amoebozoa parasitology   MeSH
• Gene Deletion * MeSH
• RNA Editing * MeSH
• Kinetoplastida genetics   growth & development   MeSH
• DNA, Mitochondrial chemistry   genetics   MeSH
• Mitochondria genetics   MeSH
• Sequence Analysis, DNA MeSH
• Computational Biology MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

BACKGROUND: Although rapid changes in copy number and gene order are common within plant mitochondrial genomes, associated patterns of gene transcription are underinvestigated. Previous studies have shown that the gynodioecious plant species Silene vulgaris exhibits high mitochondrial diversity and occasional paternal inheritance of mitochondrial markers. Here we address whether variation in DNA molecular markers is correlated with variation in transcription of mitochondrial genes in S. vulgaris collected from natural populations. RESULTS: We analyzed RFLP variation in two mitochondrial genes, cox1 and atp1, in offspring of ten plants from a natural population of S. vulgaris in Central Europe. We also investigated transcription profiles of the atp1 and cox1 genes. Most DNA haplotypes and transcription profiles were maternally inherited; for these, transcription profiles were associated with specific mitochondrial DNA haplotypes. One individual exhibited a pattern consistent with paternal inheritance of mitochondrial DNA; this individual exhibited a transcription profile suggestive of paternal but inconsistent with maternal inheritance. We found no associations between gender and transcript profiles. CONCLUSIONS: Specific transcription profiles of mitochondrial genes were associated with specific mitochondrial DNA haplotypes in a natural population of a gynodioecious species S. vulgaris.Our findings suggest the potential for a causal association between rearrangements in the plant mt genome and transcription product variation.

• MeSH
• DNA, Plant genetics   MeSH
• Haplotypes MeSH
• DNA, Mitochondrial genetics   MeSH
• Genes, Mitochondrial MeSH
• Polymorphism, Restriction Fragment Length MeSH
• Genetics, Population MeSH
• Sequence Analysis, DNA MeSH
• Silene genetics   MeSH
• Gene Expression Profiling MeSH
• Inheritance Patterns MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

The loss of Surf1 protein leads to a severe COX deficiency manifested as a fatal neurodegenerative disorder, the Leigh syndrome (LS(COX)). Surf1 appears to be involved in the early step of COX assembly but its function remains unknown. The aim of the study was to find out how SURF1 gene mutations influence expression of OXPHOS and other pro-mitochondrial genes and to further characterize the altered COX assembly. Analysis of fibroblast cell lines from 9 patients with SURF1 mutations revealed a 70% decrease of the COX complex content to be associated with 32-54% upregulation of respiratory chain complexes I, III and V and accumulation of Cox5a subunit. Whole genome expression profiling showed a general decrease of transcriptional activity in LS(COX) cells and indicated that the adaptive changes in OXPHOS complexes are due to a posttranscriptional compensatory mechanism. Electrophoretic and WB analysis showed that in mitochondria of LS(COX) cells compared to controls, the assembled COX is present entirely in a supercomplex form, as I-III₂-IV supercomplex but not as larger supercomplexes. The lack of COX also caused an accumulation of I-III₂ supercomplex. The accumulated Cox5a was mainly present as a free subunit. We have found out that the major COX assembly subcomplexes accumulated due to SURF1 mutations range in size between approximately 85-140kDa. In addition to the originally proposed S2 intermediate they might also represent Cox1-containing complexes lacking other COX subunits. Unlike the assembled COX, subcomplexes are unable to associate with complexes I and III.

• MeSH
• Cell Extracts MeSH
• Cell Line MeSH
• Cyclooxygenase 1 genetics   metabolism   MeSH
• Cyclooxygenase 2 genetics   metabolism   MeSH
• Cytochrome-c Oxidase Deficiency genetics   metabolism   MeSH
• Fibroblasts cytology   metabolism   MeSH
• Leigh Disease genetics   metabolism   MeSH
• Humans MeSH
• Membrane Proteins genetics   metabolism   MeSH
• Mitochondrial Proteins genetics   metabolism   MeSH
• Mitochondria genetics   metabolism   MeSH
• Mutation genetics   MeSH
• Oxidative Phosphorylation MeSH
• Protein Subunits genetics   metabolism   MeSH
• Electron Transport Complex I genetics   metabolism   MeSH
• Electron Transport Complex III genetics   metabolism   MeSH
• Electron Transport Complex IV genetics   metabolism   MeSH
• Electron Transport physiology   MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced. The genome comprises 729,765 bp, encoding 80 identified genes of which 36 are protein-coding, 40 tRNA, four rRNA genes, and three pseudogenes. An intronic region from the cox1 gene was identified that encodes an endonuclease enzyme that is present in the other sequenced species of Lentibulariaceae. Chloroplast genes (pseudogene and complete) inserted in the MT genome were identified, showing possible horizontal transfer between organelles. In addition, 50 pairs of long repeats from 94 to 274 bp are present, possibly playing an important role in the maintenance of the MT genome. Phylogenetic analysis carried out with 34 coding mitochondrial genes corroborated the positioning of the species listed here within the family. The molecular dynamism in the mitogenome (e.g. the loss or pseudogenization of genes, insertion of foreign genes, the long repeats as well as accumulated mutations) may be reflections of the carnivorous lifestyle where a significant part of cellular energy was shifted for the adaptation of leaves into traps molding the mitochondrial DNA. The sequence and annotation of G. tuberosa's MT will be useful for further studies and serve as a model for evolutionary and taxonomic clarifications of the group as well as improving our comprehension of MT evolution.

• MeSH
• Phylogeny MeSH
• Genome, Mitochondrial * genetics   MeSH
• Lamiales * genetics   MeSH
• DNA, Mitochondrial MeSH
• Genes, Mitochondrial MeSH
• RNA, Transfer genetics   MeSH
• Publication type
• Journal Article MeSH

Arguably, the most bizarre mitochondrial DNA (mtDNA) is that of the euglenozoan eukaryote Diplonema papillatum. The genome consists of numerous small circular chromosomes none of which appears to encode a complete gene. For instance, the cox1 coding sequence is spread out over nine different chromosomes in non-overlapping pieces (modules), which are transcribed separately and joined to a contiguous mRNA by trans-splicing. Here, we examine how many genes are encoded by Diplonema mtDNA and whether all are fragmented and their transcripts trans-spliced. Module identification is challenging due to the sequence divergence of Diplonema mitochondrial genes. By employing most sensitive protein profile search algorithms and comparing genomic with cDNA sequence, we recognize a total of 11 typical mitochondrial genes. The 10 protein-coding genes are systematically chopped up into three to 12 modules of 60-350 bp length. The corresponding mRNAs are all trans-spliced. Identification of ribosomal RNAs is most difficult. So far, we only detect the 3'-module of the large subunit ribosomal RNA (rRNA); it does not trans-splice with other pieces. The small subunit rRNA gene remains elusive. Our results open new intriguing questions about the biochemistry and evolution of mitochondrial trans-splicing in Diplonema.

• MeSH
• Chromosomes chemistry   MeSH
• Euglenozoa genetics   MeSH
• Transcription, Genetic MeSH
• Genome, Mitochondrial MeSH
• DNA, Mitochondrial chemistry   MeSH
• Genes, Mitochondrial MeSH
• Mitochondrial Proteins genetics   metabolism   MeSH
• Mitochondria genetics   metabolism   MeSH
• Molecular Sequence Data MeSH
• Sequence Analysis, DNA MeSH
• Trans-Splicing MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

The biogenesis of eukaryotic COX (cytochrome c oxidase) requires several accessory proteins in addition to structural subunits and prosthetic groups. We have analysed the assembly state of COX and SCO2 protein levels in various tissues of six patients with mutations in SCO2 and SURF1. SCO2 is a copper-binding protein presumably involved in formation of the Cu(A) centre of the COX2 subunit. The function of SURF1 is unknown. Immunoblot analysis of native gels demonstrated that COX holoenzyme is reduced to 10-20% in skeletal muscle and brain of SCO2 and SURF1 patients and to 10-30% in heart of SCO2 patients, whereas liver of SCO2 patients' contained normal holoenzyme levels. The steady-state levels of mutant SCO2 protein ranged from 0 to 20% in different SCO2 patient tissues. In addition, eight distinct COX subcomplexes and unassembled subunits were found, some of them identical with known assembly intermediates of the human enzyme. Heart, brain and skeletal muscle of SCO2 patients contained accumulated levels of the COX1.COX4.COX5A subcomplex, three COX1-containing subcomplexes, a COX4.COX5A subcomplex and two subcomplexes composed of only COX4 or COX5A. The accumulation of COX1.COX4.COX5A subcomplex, along with the virtual absence of free COX2, suggests that the lack of the Cu(A) centre may result in decreased stability of COX2. The appearance of COX4.COX5A subcomplex indicates that association of these nucleus-encoded subunits probably precedes their addition to COX1 during the assembly process. Finally, the consequences of SCO2 and SURF1 mutations suggest the existence of tissue-specific functional differences of these proteins that may serve different tissue-specific requirements for the regulation of COX biogenesis.

• MeSH
• Fibroblasts enzymology   MeSH
• Financing, Organized MeSH
• Liver enzymology   MeSH
• Infant MeSH
• Muscle, Skeletal enzymology   MeSH
• Humans MeSH
• Membrane Proteins MeSH
• Mitochondrial Proteins MeSH
• Brain enzymology   MeSH
• Mutation genetics   MeSH
• Myocardium enzymology   MeSH
• Organ Specificity MeSH
• Protein Subunits chemistry   metabolism   MeSH
• Child, Preschool MeSH
• Proteins genetics   metabolism   MeSH
• Gene Expression Regulation, Enzymologic MeSH
• Electron Transport Complex IV biosynthesis   chemistry   metabolism   MeSH
• Carrier Proteins MeSH
• Check Tag
• Infant MeSH
• Humans MeSH
• Child, Preschool MeSH

The genus Brachylecithum was for the first time subject to molecular taxonomic phylogenetic analysis in order to ascertain relationships among its component taxa. We used two markers-the nuclear ribosomal 28S ribosomal DNA (rDNA) gene and the mitochondrial cox1 gene, for six species of the genus; 11 sequences of partial 28S rDNA and partial cox1 were obtained from adult B. capilliformis, B. glareoli, B. kakea, B. laniicola, B. lobatum, and B. strigis, and from larval stages obtained from snails of the genus Cepaea. We propose to synonymize B. strigis with B. lobatum, while the genetic differences in the 28S rDNA gene and mitochondrial cox1 gene confirm the species status of B. capilliformis and indicate a distinct group within Brachylecithum, including B. kakea and B. laniicola. Cercarial and metacercarial isolates from the snails showed 100 % similarity to B. lobatum; thus, it is the first record of Cepaea snails as intermediate hosts of this species and the first report on life cycle abbreviation within the Dicrocoeliidae.

• MeSH
• Cercaria MeSH
• Dicrocoeliidae genetics   physiology   MeSH
• Phylogeny MeSH
• Snails parasitology   MeSH
• Host Specificity MeSH
• Host-Parasite Interactions MeSH
• Genes, Mitochondrial MeSH
• DNA, Ribosomal genetics   MeSH
• Life Cycle Stages MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH