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81 results for “Organelle”
Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP
<p>We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. <em>Barthelona </em>spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one <em>Barthelona </em>strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substratelevel phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.</p>
Data from: Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes
Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed. Here, we present a large-scale comparative transcriptomic study of MROs across a major eukaryotic group, Metamonada, examining lineage-specific gain and loss of metabolic functions in the MROs of Trichomonas, Giardia, Spironucleus and their free-living relatives. Our analyses uncover a complex history of ATP production machinery in diplomonads such as Giardia, and their closest relative, Dysnectes; and a correlation between the glycine cleavage machinery and lifestyles. Our data further suggest the existence of a previously undescribed biochemical class of MRO that generates hydrogen but is incapable of ATP synthesis.
Data from: A liquid-like organelle at the root of motile ciliopathy
Motile ciliopathies are characterized by specific defects in cilia beating that result in chronic airway disease, subfertility, ectopic pregnancy, and hydrocephalus. While many patients harbor mutations in the dynein motors that drive cilia beating, the disease also results from mutations in so-called Dynein Axonemal Assembly Factors (DNAAFs) that act in the cytoplasm. The mechanisms of DNAAF action remain poorly defined. Here, we show that DNAAFs concentrate together with axonemal dyneins and chaperones into organelles that form specifically in multiciliated cells, which we term DynAPs, for Dynein Axonemal Particles. These organelles display hallmarks of biomolecular condensates, and remarkably, DynAPs are enriched for the stress granule protein G3bp1, but not for other stress granule proteins or P-body proteins. Finally, we show that both the formation and the liquid-like behaviors of DynAPs are disrupted in a model of motile ciliopathy. These findings provide a unifying cell biological framework for a poorly understood class of human disease genes and add motile ciliopathy to the growing roster of human diseases associated with disrupted biological phase separation.
Supplementary files for manuscript: Acacia organelle genome assembly
<p>Supplementary files to accompany manuscript regarding genome assembly of organelles from <em>Acacia pycnantha. </em></p> <p>This manuscript assembles a mitochondrial genome (the mitome) and a chloroplast genome (the plastome). Results are referred to in the manuscript, and included here. </p> <p>For each organelle genome, there are 14 assemblies in fasta format, and associated GFA format file if available (not all stages produce this file), as well as the Spades GFA from Unicycler. For each Unicycler assembly there is a set of annotation files that include GenBank and GFF3 formats, and outputs from HMMER, ARAGORN, and tRNAscan-SE. There is also a bam file of reads mapped to alternate assembly paths for the mitome to explore the 90 Kbp contig of interest. A copy of the assembly script (assembler.sh) is included and is also available at this repository - https://github.com/AnnaSyme/organelle-assembly - with instructions on how to run the script and the required inputs and tools.</p> <p>(This Zenodo version is an update, with some duplicated files removed from the annotation folders, and information about the files now included.) </p>
Data from: Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes
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Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP
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Data from: A liquid-like organelle at the root of motile ciliopathy
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Stage-specific changes in the water, Na+, Cl- and K+ contents of organelles during apoptosis, demonstrated by a targeted cryo correlative analytical approach
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Ciliopathy patient variants reveal organelle-specific functions for TUBB4B in axonemal microtubules
GEO Series GSE246488. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response
GEO Series GSE26801. Saccharomyces cerevisiae. 14 samples. Type: Expression profiling by array.
Organelle dysfunction upon asrij depletion causes aging-like changes in mouse hematopoietic stem cells
GEO Series GSE192948. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide rearrangement of protein translation levels for cell and organelle proliferation in a simple unicellular alga
GEO Series GSE273424. Cyanidioschyzon merolae. 4 samples. Type: Other.
Dyw2-DYW2_OTP100: Identification of the transcriptome defects (nuclear and organelles) of the T-DNA KO mutants of DYW2 and OTP100
GEO Series GSE100298. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Physiologic media renders human iPSC-derived macrophages permissive for M. tuberculosis by rewiring organelle function and metabolism
GEO Series GSE255475. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Peroxisome function relies on organelle-associated mRNA translation
GEO Series GSE113567. Saccharomyces cerevisiae. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
Impact of Drp1 Loss on Organelle Interaction, Metabolism, and Inflammation in Mouse Liver
GEO Series GSE296127. Mus musculus. 4 samples. Type: Expression profiling by array.
ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
GEO Series GSE102004. Homo sapiens. 52 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Impact of oxygen availability on the organelle-specific redox potentials and stress in recombinant protein producing Komagataella phaffii
GEO Series GSE277464. Komagataella phaffii CBS 7435. 16 samples. Type: Expression profiling by high throughput sequencing.
Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system
GEO Series GSE34132. Saccharomyces cerevisiae. 3 samples. Type: Other.
A cooperative organelle biogenesis program in mammalian cells
GEO Series GSE201573. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
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