Large dataset of octocoral mitochondrial genomes provides new insights into mt-mutS evolution and function

Due to their strict maternal inheritance in most animals and plants, mitochondrial genomes are predicted to accumulate mutations that are beneficial or neutral in females but harmful in males. Although a few male-harming mtDNA mutations have been identified, consistent with this ‘Mother’s Curse’, their effect on females has been largely unexplored. Here, we identify COIIG177S, a mtDNA hypomorph of cytochrome oxidase II, which specifically impairs male fertility due to defects in sperm development and function without impairing other male or female functions. COIIG177S represents one of the clearest examples of a ‘male-harming’ mtDNA mutation in animals and suggest that the hypomorphic mtDNA mutations like COIIG177S might specifically impair male gametogenesis. Intriguingly, some D. melanogaster nuclear genetic backgrounds can fully rescue COIIG177S -associated sterility, consistent with previously proposed models that nuclear genomes can regulate the phenotypic manifestation of mtDNA mutations.

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Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

PeerJ ◽

10.7717/peerj.8356 ◽

2020 ◽

Vol 8 ◽

pp. e8356

Author(s):

Darrin T. Schultz ◽

Jordan M. Eizenga ◽

Russell B. Corbett-Detig ◽

Warren R. Francis ◽

Lynne M. Christianson ◽

...

Keyword(s):

Mitochondrial Genome ◽

Hypothesis Test ◽

Open Reading Frames ◽

Mitochondrial Genomes ◽

Intergenic Sequence ◽

Computational Tools ◽

Protein Coding ◽

Bayesian Hypothesis Test ◽

And Function ◽

Reading Frames

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

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Coding palindromes in mitochondrial genes of Nematomorpha

Nucleic Acids Research ◽

10.1093/nar/gkz517 ◽

2019 ◽

Vol 47 (13) ◽

pp. 6858-6870 ◽

Cited By ~ 1

Author(s):

Kirill V Mikhailov ◽

Boris D Efeykin ◽

Alexander Y Panchin ◽

Dmitry A Knorre ◽

Maria D Logacheva ◽

...

Keyword(s):

Amino Acid ◽

Protein Function ◽

Inverted Repeat ◽

Amino Acid Level ◽

Nucleotide Composition ◽

Mitochondrial Genomes ◽

Inverted Repeats ◽

Protein Coding ◽

Dna Elements ◽

And Function

Abstract Inverted repeats are common DNA elements, but they rarely overlap with protein-coding sequences due to the ensuing conflict with the structure and function of the encoded protein. We discovered numerous perfect inverted repeats of considerable length (up to 284 bp) embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species. Strikingly, both arms of the inverted repeats encode conserved regions of the amino acid sequence. We confirmed enzymatic activity of the respiratory complex I encoded by inverted repeat-containing genes. The nucleotide composition of inverted repeats suggests strong selection at the amino acid level in these regions. We conclude that the inverted repeat-containing genes are transcribed and translated into functional proteins. The survey of available mitochondrial genomes reveals that several other organisms possess similar albeit shorter embedded repeats. Mitochondrial genomes of Nematomorpha demonstrate an extraordinary evolutionary compromise where protein function and stringent secondary structure elements within the coding regions are preserved simultaneously.

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Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense–antisense pairs

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa111 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Jessica M Warren ◽

Daniel B Sloan

Keyword(s):

Molecular Biology ◽

Complete Loss ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Functional Roles ◽

Base Modification ◽

Trna Structure ◽

Plant Pest ◽

And Function ◽

Common Plant

Abstract Although tRNA structure is one of the most conserved and recognizable shapes in molecular biology, aberrant tRNAs are frequently found in the mitochondrial genomes of metazoans. The extremely degenerate structures of several mitochondrial tRNAs (mt-tRNAs) have led to doubts about their expression and function. Mites from the arachnid superorder Acariformes are predicted to have some of the shortest mt-tRNAs, with a complete loss of cloverleaf-like shape. While performing mitochondrial isolations and recently developed tRNA-seq methods in plant tissue, we inadvertently sequenced the mt-tRNAs from a common plant pest, the acariform mite Tetranychus urticae, to a high enough coverage to detect all previously annotated T. urticae tRNA regions. The results not only confirm expression, CCA-tailing and post-transcriptional base modification of these highly divergent tRNAs, but also revealed paired sense and antisense expression of multiple T. urticae mt-tRNAs. Mirrored expression of mt-tRNA genes has been hypothesized but not previously demonstrated to be common in any system. We discuss the functional roles that these divergent tRNAs could have as both decoding molecules in translation and processing signals in transcript maturation pathways, as well as how sense–antisense pairs add another dimension to the bizarre tRNA biology of mitochondrial genomes.

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Genomic Balance: Two Genomes Establishing Synchrony to Modulate Cellular Fate and Function

Cells ◽

10.3390/cells8111306 ◽

2019 ◽

Vol 8 (11) ◽

pp. 1306 ◽

Cited By ~ 2

Author(s):

St. John

Keyword(s):

Dna Methylation ◽

Mitochondrial Genome ◽

Cell Fate ◽

Nuclear Genome ◽

The Other ◽

Mitochondrial Genomes ◽

Epigenetic Regulators ◽

And Function ◽

Effective Function

It is becoming increasingly apparent that cells require cooperation between the nuclear and mitochondrial genomes to promote effective function. However, it was long thought that the mitochondrial genome was under the strict control of the nuclear genome and the mitochondrial genome had little influence on cell fate unless it was extensively mutated, as in the case of the mitochondrial DNA diseases. However, as our understanding of the roles that epigenetic regulators, including DNA methylation, and metabolism play in cell fate and function, the role of the mitochondrial genome appears to have a greater influence than previously thought. In this review, I draw on examples from tumorigenesis, stem cells, and oocyte pre- and post-fertilisation events to discuss how modulating one genome affects the other and that this results in a compromise to produce functional mature cells. I propose that, during development, both of the genomes interact with each other through intermediaries to establish genomic balance and that establishing genomic balance is a key facet in determining cell fate and viability.

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Hopeful monsters: Unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs

10.1101/2020.09.08.286963 ◽

2020 ◽

Author(s):

Jessica M. Warren ◽

Daniel B. Sloan

Keyword(s):

Mitochondrial Genomes ◽

Trna Genes ◽

Rna Seq ◽

Functional Roles ◽

Base Modification ◽

Plant Pest ◽

And Function ◽

Common Plant ◽

Mitochondrial Trna Genes ◽

Surprising Finding

AbstractAlthough tRNA structure is one of the most conserved and recognizable shapes in molecular biology, aberrant tRNAs are frequently found in the mitochondrial genomes of metazoans. The structure of several mitochondrial tRNAs is so degenerate that doubts have been raised about their expression and function. Mites from the arachnid superorder Acariformes are predicted to have some of the shortest mitochondrial tRNAs, with apparent base mismatches in acceptor stems and a complete loss of cloverleaf-life shape. While performing mitochondrial isolations and recently developed RNA-seq methods to capture mature, CCA-tailed tRNAs in plant tissue, we inadvertently sequenced the mitochondrial tRNAs from a common plant pest, the acariform mite Tetranychus urticae, to a high enough coverage to detect all previously annotated T. urticae tRNA regions. The results not only confirm expression, CCA-tailing and post-transcriptional base modification of these highly divergent tRNAs, but also revealed widespread sense and antisense expression of tRNA genes in the T. urticae mitochondrial genome. Mirrored expression of mitochondrial tRNA genes has been previously hypothesized but not demonstrated to be extensive in any system. We discuss the functional roles that these divergent tRNAs could have as both decoding molecules in translation and processing signals in transcript maturation pathways for other genes, as well as how the surprising finding of sense-antisense tRNA pairs adds another dimension to the bizarre tRNA biology of mitochondrial genomes.

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Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

International Journal of Molecular Sciences ◽

10.3390/ijms22041811 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1811

Author(s):

Liina Kinkar ◽

Robin Gasser ◽

Bonnie Webster ◽

David Rollinson ◽

D. Littlewood ◽

...

Keyword(s):

Structural Variation ◽

Mitochondrial Genomes ◽

Nanopore Sequencing ◽

Coding Region ◽

High Coverage ◽

Protein Coding ◽

Oxford Nanopore ◽

Long Read ◽

Genomic Dnas ◽

And Function

Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.

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Conformation of Ribosomes from Escherichia Coli

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051062 ◽

1974 ◽

Vol 32 ◽

pp. 210-211

Author(s):

M. Boublik ◽

W. Hellmann ◽

F. Jenkins

Keyword(s):

Binding Sites ◽

Ribosomal Proteins ◽

Fluorescent Dyes ◽

Protein Biosynthesis ◽

Three Dimensional ◽

Spatial Arrangement ◽

Dimensional Structure ◽

Complete Understanding ◽

And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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The Effect of Oxidized Cholesterol on the Aorta of Rabbits- Scanning Electron Microscopic Observations

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100054327 ◽

1982 ◽

Vol 40 ◽

pp. 340-341

Author(s):

S. K. Pena ◽

C. B. Taylor ◽

J. Hill ◽

J. Safarik

Keyword(s):

Cholesterol Biosynthesis ◽

Cholesterol Content ◽

Arterial Injury ◽

Electron Microscopic ◽

Aortic Smooth Muscle ◽

Oxidized Cholesterol ◽

Initial Event ◽

Membrane Structure And Function ◽

Scanning Electron Microscopic ◽

And Function

Introduction: Oxidized cholesterol derivatives have been demonstrated in various cell cultures to be very potent inhibitors of 3-hvdroxy-3- methylglutaryl Coenzyme A reductase which is a principle regulator of cholesterol biosynthesis in the cell. The cholesterol content in the cells exposed to oxidized cholesterol was found to be markedly decreased. In aortic smooth muscle cells, the potency of this effect was closely related to the cytotoxicity of each derivative. Furthermore, due to the similarity of their molecular structure to that of cholesterol, these oxidized cholesterol derivatives might insert themselves into the cell membrane, alter membrane structure and function and eventually cause cell death. Arterial injury has been shown to be the initial event of atherosclerosis.

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Ultrastructure of developing visual cortical synapses in the cat superior colliculus

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100085083 ◽

1991 ◽

Vol 49 ◽

pp. 156-157

Author(s):

Caroline A. Miller ◽

Laura L. Bruce

Keyword(s):

Superior Colliculus ◽

Phosphate Buffer ◽

Receptive Fields ◽

Visual Cortical Area ◽

Cortical Synapses ◽

Visual Cortical ◽

And Function ◽

Phosphate Buffered Saline ◽

The Brain ◽

Cat Superior Colliculus

The first visual cortical axons arrive in the cat superior colliculus by the time of birth. Adultlike receptive fields develop slowly over several weeks following birth. The developing cortical axons go through a sequence of changes before acquiring their adultlike morphology and function. To determine how these axons interact with neurons in the colliculus, cortico-collicular axons were labeled with biocytin (an anterograde neuronal tracer) and studied with electron microscopy.Deeply anesthetized animals received 200-500 nl injections of biocytin (Sigma; 5% in phosphate buffer) in the lateral suprasylvian visual cortical area. After a 24 hr survival time, the animals were deeply anesthetized and perfused with 0.9% phosphate buffered saline followed by fixation with a solution of 1.25% glutaraldehyde and 1.0% paraformaldehyde in 0.1M phosphate buffer. The brain was sectioned transversely on a vibratome at 50 μm. The tissue was processed immediately to visualize the biocytin.

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