Mitochondrial rRNA Research Articles

Origins of Human Malaria: Rare Genomic Changes and Full Mitochondrial Genomes Confirm the Relationship of Plasmodium falciparum to Other Mammalian Parasites but Complicate the Origins of Plasmodium vivax

Despite substantial work, the phylogeny of malaria parasites remains debated. The matter is complicated by concerns about patterns of evolution in potentially strongly selected genes as well as the extreme AT bias of some Plasmodium genomes. Particularly contentious has been the position of the most virulent human parasite Plasmodium falciparum, whether grouped with avian parasites or within a larger clade of mammalian parasites. Here, we study 3 classes of rare genomic changes, as well as the sequences of mitochondrial ribosomal RNA (rRNA) genes. We report 3 lines of support for a clade of mammalian parasites: 1) we find no instances of spliceosomal intron loss in a hypothetical ancestor of P. falciparum and the avian parasite Plasmodium gallinaceum, suggesting against a close relationship between those species; 2) we find 4 genomic mitochondrial indels supporting a mammalian clade, but none grouping P. falciparum with avian parasites; and 3) slowly evolving mitochondrial rRNA sequences support a mammalian parasite clade with 100% posterior probability. We further report a large deletion in the mitochondrial large subunit rRNA gene, which suggests a subclade including both African and Asian parasites within the clade of closely related primate malarias. This contrasts with previous studies that provided strong support for separate Asian and African clades, and reduces certainty about the historical and geographic origins of Plasmodium vivax. Finally, we find a lack of synapomorphic gene losses, suggesting a low rate of ancestral gene loss in Plasmodium.

The occurrence of Pneumocystis jirovecii in people from three different age groups of Warsaw (Poland) community

AbstractThe three age groups of people from Warsaw: children, young adults and elderly people were examined for the prevalence of infection with Pneumocystis jirovecii. Nested PCR was used to amplify fragment of mitochondrial large subunit rRNA of the fungus in samples of oropharyngeal swabs. Nineteen (12.8%) of the 148 examined samples were positive for DNA of P. jirovecii. The samples collected from children were more often positive than the samples from young adults (p = 0.003) or from both groups of adults (p = 0.0029). Moreover, among adults (n = 99) proportion of infected women (n = 6; 12.5%) was significantly higher than men (n = 1; 2%). Results of the research confirm the high prevalence of Pneumocystis infection in children and indirectly point out to children as a possible source of infection for older people.

Phylogeny of the Serrasalmidae (Characiformes) based on mitochondrial DNA sequences

Previous studies based on DNA sequences of mitochondrial (mt) rRNA genes showed three main groups within the subfamily Serrasalminae: (1) a "pacu" clade of herbivores (Colossoma, Mylossoma, Piaractus); (2) the "Myleus" clade (Myleus, Mylesinus, Tometes, Ossubtus); and (3) the "piranha" clade (Serrasalmus, Pygocentrus, Pygopristis, Pristobrycon, Catoprion, Metynnis). The genus Acnodon was placed as the sister taxon of clade (2+3). However, poor resolution within each clade was obtained due to low levels of variation among rRNA gene sequences. Complete sequences of the hypervariable mtDNA control region for a total of 45 taxa, and additional sequences of 12S and 16S rRNA from a total of 74 taxa representing all genera in the family are now presented to address intragroup relationships. Control region sequences of several serrasalmid species exhibit tandem repeats of short motifs (12 to 33 bp) in the 3' end of this region, accounting for substantial length variation. Bayesian inference and maximum parsimony analyses of these sequences identify the same groupings as before and provide further evidence to support the following observations: (a) Serrasalmus gouldingi and species of Pristobrycon (non-striolatus) form a monophyletic group that is the sister group to other species of Serrasalmus and Pygocentrus; (b) Catoprion, Pygopristis, and Pristobrycon striolatus form a well supported clade, sister to the group described above; (c) some taxa assigned to the genus Myloplus (M. asterias, M tiete, M ternetzi, and M rubripinnis) form a well supported group whereas other Myloplus species remain with uncertain affinities (d) Mylesinus, Tometes and Myleus setiger form a monophyletic group.

Phylogenetic analysis of the order Pleuronectiformes (Teleostei) based on sequences of 12S and 16S mitochondrial genes

The fish order Pleuronectiformes, composed of 14 families, has two suborders: Psettodoidei (with one family) and Pleuronectoidei (with thirteen families). The relationships among families of Pleuronectoidei and among the genera of their families have extensively been debated and a consensus has not yet been reached. In the present study, partial sequences of the 12S and 16S mitochondrial rRNA genes were obtained from 19 species belonging to the families Achiridae, Bothidae, Cynoglossidae, Paralichthyidae, Pleuronectidae, Scophthalmidae, and Soleidae. Additional sequences of 42 pleuronectiform species were obtained from GenBank. Phylogenetic analyses were conducted by the methods of maximum-parsimony, maximum-likelihood and Bayesian inference. Our results corroborate the monophyletic status of all families, excluding Paralichthyidae. In the family Achiridae, the genus Catathyridium (freshwater) was the sister group of Trinectes (saltwater), and Hypoclinemus (freshwater) was the sister group of Achirus (saltwater). Assuming that the putative ancestor of achirids lived in saltwater, it is suggested that the freshwater habitats in South America were colonized independently by different achirid lineages.

Mutacje mitochondrialnego DNA w rozwoju nowotworów głowy i szyi

Data reported until today suggested a pivotal role of nuclear DNA mutations in the process of carcinogenesis. Recently more and more authors claim that disruption of mitochondrial DNA should not be excluded from this analysis. mtDNA have been reported in many cancers of head and neck region. Mitochondrial D-loop has been proven to be mutation hot - spot with majority of mutations in the positions 303 to 315 of poly-C tract. Data show that 37% of patients with premalignant lesions and 62% with carcinoma in situ are positive for mtDNA mutations. Moreover mutations in genes encoding ND2, ND5, COIII, CYTB, and ATP6 were observed in 17% of patients. Mutations in mitochondrial rRNA genes occured in similar number of cases. Neoplastic cells undifferentiation and disease progression is accompanied by multiplication of mtDNA number and increased mtDNA content. mtDNA content corellates with the stage of the disease. mtDNA mutations faciliate cell proliferation and inhibit apoptosis by increasing the production of ractive oxygen species (ROS). Cells harbouring mutated mtDNA have increased proliferation rate, as increased ROS concentration may act as an endogenous growth factor.

Taxonomic Relationships of Ansonia anotis Inger, Tan, and Yambun, 2001 and Pedostibes maculatus (Mocquard, 1890), with a Description of a New Genus (Amphibia, Bufonidae)

Examination of types and recently collected specimens revealed that Ansonia anotis Inger, Tan, and Yambun, 2001 and Pedostibes maculatus (Mocquard, 1890), both described from Kinabalu, Sabah, Malaysia, are hardly differentiated morphologically. Analyses of a total of 2,427 bp of the 12S rRNA, tRNA(val), and 16S mitochondrial rRNA genes revealed that the two species are very close genetically. Thus A. anotis is regarded as conspecific and is synonymized with P. maculatus. Genetically, this species proved to form a lineage distinct from other bufonids from Southeast Asia, including species of Ansonia and Pedostibes. Because the species has also some unique morphological traits different from known bufonid genera, we propose to establish a new genus for Nectophryne maculata Mocquard, 1890.

Multilocus ribosomal RNA phylogeny of the leaf beetles (Chrysomelidae)

AbstractBasal relationships in the Chrysomelidae (leaf beetles) were investigated using two nuclear (small and partial large subunits) and mitochondrial (partial large subunit) rRNA (≈ 3000 bp total) for 167 taxa covering most major lineages and relevant outgroups. Separate and combined data analyses were performed under parsimony and model‐based tree building algorithms from dynamic (direct optimization) and static (Clustal and BLAST) sequence alignments. The performance of methods differed widely and recovery of well established nodes was erratic, in particular when using single gene partitions, but showed a slight advantage for Bayesian inferences and one of the fast likelihood algorithms (PHYML) over others. Direct optimization greatly gained from simultaneous analysis and provided a valuable hypothesis of chrysomelid relationships. The BLAST‐based alignment, which removes poorly aligned sequence segments, in combination with likelihood and Bayesian analyses, resulted in highly defensible trees obtained in much shorter time than direct optimization, and hence is a viable alternative when data sets grow. The main taxonomic findings include the recognition of three major lineages of Chrysomelidae, including a basal “sagrine” clade (Criocerinae, Donaciinae, Bruchinae), which was sister to the “eumolpine” (Spilopyrinae, Eumolpinae, Cryptocephalinae, Cassidinae) plus “chrysomeline” (Chrysomelinae, Galerucinae) clades. The analyses support a broad definition of subfamilies (i.e., merging previously separated subfamilies) in the case of Cassidinae (cassidines + hispines) and Cryptocephalinae (chlamisines + cryptocephalines + clytrines), whereas two subfamilies, Chrysomelinae and Eumolpinae, were paraphyletic. The surprising separation of monocot feeding Cassidinae (associated with the eumolpine clade) from the other major monocot feeding groups in the sagrine clade was well supported. The study highlights the need for thorough taxon sampling, and reveals that morphological data affected by convergence had a great impact when combined with molecular data in previous phylogenetic analyses of Chrysomelidae.© The Willi Hennig Society 2007.

Deleterious Mutation in the Mitochondrial Arginyl–Transfer RNA Synthetase Gene Is Associated with Pontocerebellar Hypoplasia

Homozygosity mapping was performed in a consanguineous Sephardic Jewish family with three patients who presented with severe infantile encephalopathy associated with pontocerebellar hypoplasia and multiple mitochondrial respiratory-chain defects. This resulted in the identification of an intronic mutation in RARS2, the gene encoding mitochondrial arginine-transfer RNA (tRNA) synthetase. The mutation was associated with the production of an abnormally short RARS2 transcript and a marked reduction of the mitochondrial tRNA(Arg) transcript in the patients' fibroblasts. We speculate that missplicing mutations in mitochondrial aminoacyl-tRNA synthethase genes preferentially affect the brain because of a tissue-specific vulnerability of the splicing machinery.

Pentatricopeptide Repeat Proteins in Trypanosoma brucei Function in Mitochondrial Ribosomes

The pentatricopeptide repeat (PPR), a degenerate 35-amino-acid motif, defines a novel eukaryotic protein family. Plants have 400 to 500 distinct PPR proteins, whereas other eukaryotes generally have fewer than 5. The few PPR proteins that have been studied have roles in organellar gene expression, probably via direct interaction with RNA. Here we show that the parasitic protozoan Trypanosoma brucei encodes 28 distinct PPR proteins, an extraordinarily high number for a nonplant organism. A comparative analysis shows that seven out of eight selected PPR proteins are mitochondrially localized and essential for oxidative phosphorylation. Six of these are required for the stabilization of mitochondrial rRNAs and, like ribosomes, are associated with the mitochondrial membranes. Furthermore, one of the PPR proteins copurifies with the large subunit rRNA. Finally, ablation of all of the PPR proteins that were tested induces degradation of the other PPR proteins, indicating that they function in concert. Our results show that a significant number of trypanosomal PPR proteins are individually essential for the maintenance and/or biogenesis of mitochondrial rRNAs.

A New Species of Deiratonotus (Crustacea: Brachyura: Camptandriidae) Found in the Kumanoe River Estuary, Kyushu, Japan

Camptandriid crabs collected in the Kumanoe River Estuary, Kyushu, Japan were studied on the basis of morphological characters and molecular analysis. As a result, a new species, Deiratonotus kaoriae, was recognized. These crabs were found mainly in a creek of the sandy tidal flat within the Kumanoe River Estuary. The new species shares a very diagnostic character, the presence of a transverse ridge on the carapace, with D. cristatus (de Man, 1895) and differs markedly from the other congeners that lack this feature. The new species, however, differs from D. cristatus in the absence of harpoon-shaped setae on the subdistal end of the first gonopod and the presence of an extremely reduced second abdominal segment. According to a molecular analysis based on 12S+16S mitochondrial rRNA gene sequences, with Cleistostoma dilatatum (de Haan, 1833) and Camptandrium sexdentatum Stimpson, 1858 as outgroups, Deiratonotus kaoriae is more closely related to D. cristatus than to D. japonicus (Sakai, 1934).

Phylogenetic analyses of the genera Pipra, Lepidothrix and Dixiphia (Pipridae, Passeriformes) using partial cytochrome b and 16S mtDNA genes

The piprids (manakins) are small‐bodied Neotropical birds characterized by sexual dimorphism of the plumage and elaborate courtship rituals. The phylogenetic relationships of some of piprid genera, in particular Pipra, are not well defined. Recently, Pipra was divided into three distinct groups, and the recognition of two new genera — Lepidothrix and Dixiphia— was suggested, based on the characteristic of the syringial morphology. In the present study, we analyse the phylogenetic relationships among these genera on the basis of data from the mitochondrial genes rRNA 16S and cytochrome b. Bayesian Inference (BI), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods of analyses produced phylogenetic trees with very similar topologies with regard to the groupings formed by the species representing the three genera. These results indicate that the genera Pipra, Lepidothrix and Dixiphia do not constitute a single monophyletic clade, and support the current hypothesis of polyphyletism for the former representatives of the genus Pipra. However, the topologies presented do not coincide exactly with the phylogeny suggested by the morphological data with regard to the relationship between these three groups and the remaining piprid genera analysed here, emphasizing the need for further studies of this group of birds. The agreement between the molecular data presented here and the biogeographical information available for some of the species analysed appears to confirm the potential of using segments of the mitochondrial genome for the study of phylogeographical patterns in this group of organisms.

Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients

Background: Pneumocystis pneumonia (PCP) is conventionally diagnosed by identifying Pneumocystis jirovecii in lower respiratory tract samples using cytochemical stains. Molecular diagnosis of PCP is potentially more sensitive. Methods: A study...

Deletion of the MTO2 gene related to tRNA modification causes a failure in mitochondrial RNA metabolism in the yeast Saccharomyces cerevisiae

We report here the characterization of the yeast mto2 null mutants carrying wild-type mitochondrial DNA or 15S rRNA C1049G allele. The amounts of mitochondrial tRNALys, tRNAGlu, tRNAGln, tRNALeu, tRNAGly and tRNAMet were markedly decreased but those of tRNAArg and tRNAHis were not affected in mto2 strains. The mto2 strains exhibited significant reduction in the aminoacylation of tRNALys, tRNALeu but almost no effect in those of tRNAHis. Interestingly, the strain carrying the C1049G allele exhibited an impairment of aminoacylation of those tRNAs. Furthermore, the steady-state levels of mitochondrial mRNA CYTB, COX1, COX2, COX3, and ATP6 were markedly decreased in mto2 strains. These data strongly indicate that unmodified tRNA caused by the deletion of MTO2 caused the instability of mitochondrial tRNAs and mRNAs and impairment of aminoacylation of tRNAs.

Polymerase chain reaction detection of Pneumocystis jiroveci: evaluation of 9 assays

Various polymerase chain reaction (PCR) amplification strategies have been described for detecting Pneumocystis jiroveci in clinical specimens. Different combinations of primer/target and platforms have been reported to yield varying PCR detection rates. PCR was evaluated on clinical specimens using internal transcribed spacer regions of the rRNA nested, dihydropteroate synthase single and nested, dihydrofolate reductase nested, major surface glycoprotein heminested, mitochondrial large subunit rRNA (mtLSUrRNA) single and nested, 18S rRNA 1-tube nested, and real-time 5S rRNA PCR. The most sensitive PCR was subsequently compared with routine diagnostic immunofluorescence (IF) microscopy. Discrepant PCR and IF results were resolved after review of clinical and histology/cytology records. Major discrepancies were observed among the methods investigated. mtLSUrRNA nested PCR was the most sensitive, produced less false-negative results, and displayed the highest degree of concordance with histology. Direct comparison of mtLSUrRNA nested PCR versus IF yielded low sensitivity and specificity, which were improved for PCR and lowered for IF on review of clinical and laboratory records.

Mitochondrial genes reveal cryptic diversity in plant-breeding frogs from Madagascar (Anura, Mantellidae, Guibemantis)

One group of mantellid frogs from Madagascar (subgenus Pandanusicola of Guibemantis) includes species that complete larval development in the water-filled leaf axils of rainforest plants. This group consists of six described species: G. albolineatus, G. bicalcaratus, G. flavobrunneus, G. liber, G. pulcher, and G. punctatus. We sequenced the 12S and 16S mitochondrial rRNA genes (∼1.8 kb) from multiple specimens (35 total) of all six species to assess phylogenetic relationships within this group. All reconstructions strongly supported G. liber as part of the Pandanusicola clade, even though this species does not breed in plant leaf axils. This result confirms a striking reversal of reproductive specialization. However, all analyses also indicated that specimens assigned to G. liber include genetically distinct allopatric forms that do not form a monophyletic group. Most other taxa that were adequately sampled ( G. bicalcaratus, G. flavobrunneus, and G. pulcher) likewise consist of several genetically distinct lineages that do not form monophyletic groups. These results suggest that many of the recognized species in this group are complexes of cryptic species.

Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer ofZygozymaspecies toLipomycesandBabjevia anomalatoDipodascopsis

Phylogenetic relationships among species assigned to genera of the family Lipomycetaceae were determined from analysis of the nearly entire large, subunit rRNA gene, the small subunit rRNA gene, mitochondrial small subunit rRNA gene and the translation elongation factor-1alpha gene. Monophyly of the Lipomycetaceae was strongly supported, and currently described species appear genetically unique. The multigene analysis provided no support for maintaining the genera Kawasakia, Smithiozyma, Waltomyces or Zygozyma, and it is proposed that species in these genera be assigned to the genus Lipomyces. The monotypic genus Babjevia is a member of the Dipodascopsis clade and it is proposed to reassign Babjevia anomala to Dipodascopsis. The proposed changes will result in the Lipomycetaceae having two ascosporic genera, Lipomyces and Dipodascopsis, and the anamorphic genus Myxozyma.

Complete sequence of the mitochondrial genome of Taenia saginata: Comparison with T. solium and T. asiatica

The complete sequence of the Taenia saginata mitochondrial genome was determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The mitochondrial genome was 13,670 bp long, contained 12 protein-coding genes, two ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). It did not encode the atp8 gene. Overlapping regions were found between nad4L and nad4, nad1 and trnN, and cox1 and trnT. The ATG initiation codon was used for 10 protein-coding genes, and the GTG initiation codon was used for the remaining 2 genes ( nad4 and atp6). The size of the protein-coding genes of the three human Taenia tapeworms did not vary, except for Taenia solium nad1 (891 aa) and nad4 (1212 aa) and Taenia asiatica cox2 (576 aa). The tRNA genes were 57–75 bp long, and the predicted secondary structures of 18 of these genes had typical clover-leaf shapes with paired dihydrouridine (DHU) arms. The genes in all human Taenia tapeworms for the two mitochondrial rRNA subunits rrnL and rrnS are separated by trnC. The putative T. saginata rrnL and rrnS are 972 and 732 bp long, respectively. The non-coding regions of the mt genome of T. saginata consisted of 2 regions: a short non-coding region (SNR, 66 nucleotides) and a long non-coding region (LNR, 159 nucleotides). The overall sequence difference in the full mitochondrial genome between T. saginata and T. asiatica was 4.6%, while T. solium differed by 11%. In conclusion, the complete sequence of the T. saginata mitochondrial genome will serve as a resource for comparative mitochondrial genomics and systematic studies of the parasitic cestodes.

Recalibrated tree of leaf beetles (Chrysomelidae) indicates independent diversification of angiosperms and their insect herbivores.

BackgroundThe great diversity of the “Phytophaga” (weevils, longhorn beetles and leaf beetles) has been attributed to their co-radiation with the angiosperms based on matching age estimates for both groups, but phylogenetic information and molecular clock calibrations remain insufficient for this conclusion.MethodologyA phylogenetic analysis of the leaf beetles (Chrysomelidae) was conducted based on three partial ribosomal gene markers (mitochondrial rrnL, nuclear small and large subunit rRNA) including over 3000 bp for 167 taxa representing most major chrysomelid lineages and outgroups. Molecular clock calibrations and confidence intervals were based on paleontological data from the oldest (K-T boundary) leaf beetle fossil, ancient feeding traces ascribed to hispoid Cassidinae, and the vicariant split of Nearctic and Palearctic members of the Timarchini.Principal FindingsThe origin of the Chrysomelidae was dated to 73–79 Mya (confidence interval 63–86 Mya), and most subfamilies were post-Cretaceous, consistent with the ages of all confirmed body fossils. Two major monocot feeding chrysomelid lineages formed widely separated clades, demonstrating independent colonization of this ancient (early Cretaceous) angiosperm lineage.ConclusionsPrevious calibrations proposing a much older origin of Chrysomelidae were not supported. Therefore, chrysomelid beetles likely radiated long after the origin of their host lineages and their diversification was driven by repeated radiaton on a pre-existing diverse resource, rather than ancient host associations.

Climate and genotypes of Pneumocystis jirovecii

This study explored whether seasonal and/or climatic factors influenced detection of specific genotypes of Pneumocystis jirovecii. Between 1989 and 2001, 155 isolates of P. jirovecii were obtained from patients undergoing bronchoscopic alveolar lavage. For each isolate, the month and climatic conditions were noted. Genotypes of P. jirovecii were distinguished by polymorphisms in the mitochondrial large-subunit rRNA gene. There were monthly and seasonal variations in the frequency of detection of mixed genotypes (p 0.018 and p 0.031, respectively) and genotype 2 (p 0.029 and p 0.086, respectively). There was no association between month/season and genotypes 1, 3 and 4, or between monthly temperature or rainfall and any genotype.

A Comparative Genomics Analysis of Codon Reassignments Reveals a Link with Mitochondrial Proteome Size and a Mechanism of Genetic Code Change Via Suppressor tRNAs

Using a comparative genomics approach we demonstrate a negative correlation between the number of codon reassignments undergone by 222 mitochondrial genomes and the mitochondrial genome size, the number of mitochondrial ORFs, and the sizes of the large and small subunit mitochondrial rRNAs. In addition, we show that the TGA-to-tryptophan codon reassignment, which has occurred 11 times in mitochondrial genomes, is found in mitochondrial genomes smaller than those which have not undergone the reassignment. We therefore propose that mitochondrial codon reassignments occur in a wide range of phyla, particularly in Metazoa, due to a reduced "proteomic constraint" on the mitochondrial genetic code, compared to the nuclear genetic code. The reduced proteomic constraint reflects the small size of the mitochondrial-encoded proteome and allows codon reassignments to occur with less likelihood of lethality. In addition, we demonstrate a striking link between nonsense codon reassignments and the decoding properties of naturally occurring nonsense suppressor tRNAs. This suggests that natural preexisting nonsense suppression facilitated nonsense codon reassignments and constitutes a novel mechanism of genetic code change. These findings explain for the first time the identity of the stop codons and amino acids reassigned in mitochondrial and nuclear genomes. Nonsense suppressor tRNAs provided the raw material for nonsense codon reassignments, implying that the properties of the tRNA anticodon have dictated the identity of nonsense codon reassignments.