Dataset Information

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

ABSTRACT: 5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator.

SUBMITTER: Valach M

PROVIDER: S-EPMC4267664 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

Valach Matus M Burger Gertraud G Gray Michael W MW Lang B Franz BF

Nucleic acids research 20141127 22

5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 ...[more]

PMID: 25429974

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Project description:BackgroundLow socioeconomic status (SES) residents living in social housing, which is subsidized by government or government-funded agencies, may have higher exposures to pesticides used in indoor residences since pesticides are applied due to structural deficiencies, poor maintenance, etc. OBJECTIVE: To estimate exposure of residents in low-SES social housing built in the 1970s to legacy and current-use pesticides and to investigate factors related to exposures.MethodsTwenty-eight particle-phase pesticides were measured in the indoor air of 46 units in seven low-income social housing, multi-unit residential buildings (MURBs) in Toronto, Canada using portable air cleaners deployed for 1 week in 2017. Pesticides analyzed were legacy and current use in the classes: organochlorines, organophosphates, pyrethroids, and strobilurins.ResultsAt least one pesticide was detected in 89% of the units with detection frequencies (DF) for individual pesticides of up to 50%, including legacy organochlorines and current-use pesticides. Current-use pyrethroids had the highest DF and concentrations, with the highest particle-phase concentration for pyrethrin I at 32,000 pg/m3. Heptachlor, restricted for use in Canada in 1985, had the highest estimated maximum total air (particle plus gas phase) concentration of 443,000 pg/m3. Heptachlor, lindane, endosulfan I, chlorothalonil, allethrin, and permethrin (except in one study) had higher concentrations than those measured in low-income residences reported elsewhere. In addition to the intentional use of pesticides to control pests and their use in building materials and paints, tobacco smoking was significantly correlated with the concentrations of five pesticides used on tobacco crops. The distribution of pesticides with high DF in individual buildings suggested that pest eradication programs by the building management and/or pesticide use by residents were the major sources of measured pesticides.ImpactLow-income social housing fills a much-needed demand, but the residences are prone to pest infestation and hence pesticide use. We found exposure to at least 1 of 28 particle-phase pesticides in 89% of all 46 units tested, with the highest DF and concentrations for current-use pyrethroids and long-banned organochlorines (e.g., DDT, heptachlor) due to very high persistence indoors. Also measured were several pesticides not registered for use indoors, e.g., strobilurins used to treat building materials and pesticides used on tobacco crops. These results, which are the first Canadian data for most pesticides indoors, show widespread exposure to numerous pesticides.

Dataset Information

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

Publications

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

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