scholarly journals Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids

2018 ◽  
Author(s):  
Sarah K. Hewitt ◽  
Kobchai Duangrattanalert ◽  
Tim Burgis ◽  
Leo A.H. Zeef ◽  
Daniela Delneri
Keyword(s):  
Mitochondrial Dna ◽  
Expression Profiles ◽  
Hybrid Cell ◽  
Carbon Sources ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
The Other ◽  
Cellular Functions ◽  
Hybrid Fitness ◽  
Selection Of

AbstractMitochondrial DNA (mtDNA) in budding yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, becoming homoplasmic. Therefore, hybrids between different yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and that the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Here, we crossedSaccharomyces cerevisiaewithS. uvarumunder different environmental conditions and examined the plasticity of the retention of mtDNA in each hybrid. We showed that on fermentable carbon sources at warm temperatures each parental mtDNA was equally likely to be retained, while at colder temperatures, hybrids preferentially retained mtDNA derived fromS. uvarum. On a non-fermentable carbon source, hybrids retainedS. cerevisiaemtDNA, independent of temperature. By acquiring transcriptome data and co-expression profiles for hybrids harbouring different mtDNA in a selection of environments, we found a clear pattern of concerted allelic transcription of one or the other sub-genome for specific biological pathways, supporting the notion that the hybrid cell works preferentially with one set of parental alleles or the other according to specific cellular functions. We argue that the type of mtDNA retained in hybrids affects the expression of the nuclear genome and the organism fitness in different environments, and therefore may have a role in driving the evolution of the hybrid nuclear genome in terms of gene retention and loss.

scholarly journals Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids

2020 ◽  
Vol 8 (4) ◽  
pp. 494 ◽  
Author(s):  
Sarah K. Hewitt ◽  
Kobchai Duangrattanalert ◽  
Tim Burgis ◽  
Leo A.H. Zeef ◽  
Samina Naseeb ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Yeast Species ◽  
Hybrid Cell ◽  
Nuclear Gene ◽  
Cellular Functions ◽  
Hybrid Fitness ◽  
Rich Media ◽  
Hybrid Genome ◽  
Allele Type ◽  
Respiratory Conditions

Mitochondrial DNA (mtDNA) in yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, thus becoming homoplasmic. Therefore, hybrids between the yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Saccharomyces cerevisiae/S. uvarum hybrids preferentially retained S. uvarum mtDNA when formed on rich media at colder temperatures, while S. cerevisiae mtDNA was primarily retained on non-fermentable carbon source, at any temperature. Transcriptome data for hybrids harbouring different mtDNA showed a strong environmentally dependent allele preference, which was more important in respiratory conditions. Co-expression analysis for specific biological functions revealed a clear pattern of concerted allelic transcription within the same allele type, which supports the notion that the hybrid cell works preferentially with one set of parental alleles (or the other) for different cellular functions. Given that the type of mtDNA retained in hybrids affects both nuclear expression and fitness, it might play a role in driving hybrid genome evolution in terms of gene retention and loss.

scholarly journals Mutations in the mitochondrial ATP synthase gamma subunit suppress a slow-growth phenotype of yme1 yeast lacking mitochondrial DNA.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 435-442 ◽  
Author(s):  
E R Weber ◽  
R S Rooks ◽  
K S Shafer ◽  
J W Chase ◽  
P E Thorsness
Keyword(s):  
Mitochondrial Dna ◽  
Atp Synthase ◽  
Slow Growth ◽  
Carbon Sources ◽  
Nuclear Gene ◽  
Genomic Locus ◽  
Gamma Subunit ◽  
Mitochondrial Atp Synthase ◽  
Growth Phenotype ◽  
Slow Growth Phenotype

Abstract In Saccharomyces cerevisiae, inactivation of the nuclear gene YME1 causes several phenotypes associated with impairment of mitochondrial function. In addition to deficiencies in mitochondrial compartment integrity and respiratory growth, yme1 mutants grow extremely slowly in the absence of mitochondrial DNA. We have identified two genetic loci that, when mutated, act as dominant suppressors of the slow-growth phenotype of yme1 strains lacking mitochondrial DNA. These mutations only suppressed the slow-growth phenotype of yme1 strains lacking mitochondrial DNA and had no effect on other phenotypes associated with yme1 mutations. One allele of one linkage group had a collateral respiratory deficient phenotype that allowed the isolation of the wild-type gene. This suppressing mutation was in ATP3, a gene that encodes the gamma subunit of the mitochondrial ATP synthase. Recovery of two of the suppressing ATP3 alleles and subsequent sequence analysis placed the suppressing mutations at strictly conserved residues near the C terminus of Atp3p. Deletion of the ATP3 genomic locus resulted in an inability to utilize nonfermentable carbon sources. atp3 deletion strains lacking mitochondrial DNA grew slowly on glucose media but were not as compromised for growth as yme1 yeast lacking mitochondrial DNA.

scholarly journals Extensive Variation in Nuclear Mitochondrial DNA Content Between the Genomes of Phytophthora sojae and Phytophthora ramorum

2006 ◽  
Vol 19 (12) ◽  
pp. 1329-1336 ◽  
Author(s):  
Konstantinos Krampis ◽  
Brett M. Tyler ◽  
Jeffrey L. Boore
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Genome ◽  
Sequence Divergence ◽  
Nuclear Gene ◽  
Phytophthora Sojae ◽  
Phytophthora Ramorum ◽  
Mtdna Sequences ◽  
Sequence Comparisons ◽  
Mitochondrial Dna Content ◽  
Mitochondrial Dnas

Fragments of mitochondrial DNA (mtDNA) transferred to the nuclear genome are called nuclear mitochondrial DNAs (NUMTs). We report here a comparison of NUMT content between genomes from two species of the same genus. Analysis of the genomes of Phytophthora sojae and P. ramorum revealed large differences in the NUMT content of the two genomes: 16.27 × 10−3 and 2.28 × 10−3% of each genome, respectively. Substantial differences also exist between the two species in the sizes of the NUMTs found in each genome, with ranges of 20 to 405 bp for P. sojae and 19 to 137 bp for P. ramorum. Furthermore, in P. sojae, fragments from the mitochondrial genes rns, rnl, cox1, and nad (various subunits) are found most frequently, whereas P. ramorum NUMTs most often originate from the cox3, rps14, nad4, and nad5 genes. The large differences in the presumptive mtDNA insertions suggest that the insertions occurred subsequent to the divergence of the two species, and this is supported by sequence comparisons among the NUMTs and the mtDNA sequences of the two species. P. sojae mtDNA sequences inserted in the nuclear genome appear to have been altered as a result of insertions, deletions, inversions, and translocations and provide insights into active mechanisms of sequence divergence in this plant pathogen. No clear examples were found of NUMTs forming functional nuclear genes or of NUMTs inserted into exons or introns of any nuclear gene.

Progress in mitochondrial epigenetics

2013 ◽  
Vol 4 (4) ◽  
pp. 381-389 ◽  
Author(s):  
Hari Manev ◽  
Svetlana Dzitoyeva
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Expression Patterns ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Methylation Pattern ◽  
Mitochondrial Activity ◽  
Epigenetic Mechanisms ◽  
Molecular Events ◽  
Recent Developments

AbstractMitochondria, intracellular organelles with their own genome, have been shown capable of interacting with epigenetic mechanisms in at least four different ways. First, epigenetic mechanisms that regulate the expression of nuclear genome influence mitochondria by modulating the expression of nuclear-encoded mitochondrial genes. Second, a cell-specific mitochondrial DNA content (copy number) and mitochondrial activity determine the methylation pattern of nuclear genes. Third, mitochondrial DNA variants influence the nuclear gene expression patterns and the nuclear DNA (ncDNA) methylation levels. Fourth and most recent line of evidence indicates that mitochondrial DNA similar to ncDNA also is subject to epigenetic modifications, particularly by the 5-methylcytosine and 5-hydroxymethylcytosine marks. The latter interaction of mitochondria with epigenetics has been termed ‘mitochondrial epigenetics’. Here we summarize recent developments in this particular area of epigenetic research. Furthermore, we propose the term ‘mitoepigenetics’ to include all four above-noted types of interactions between mitochondria and epigenetics, and we suggest a more restricted usage of the term ‘mitochondrial epigenetics’ for molecular events dealing solely with the intra-mitochondrial epigenetics and the modifications of mitochondrial genome.

scholarly journals Quasi-Mendelian Paternal Inheritance of mitochondrial DNA: A notorious artifact, or anticipated mtDNA behavior?

2019 ◽  
Author(s):  
Sofia Annis ◽  
Zoe Fleischmann ◽  
Mark Khrapko ◽  
Melissa Franco ◽  
Kevin Wasko ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Selective Advantage ◽  
Somatic Tissue ◽  
Biparental Inheritance ◽  
Mtdna Copy Number ◽  
Mendelian Segregation ◽  
Paternal Haplotype ◽  
Mtdna Haplotype

AbstractA recent report by Luo et al (2018) in PNAS (DOI:10.1073/pnas.1810946115) presented evidence of biparental inheritance of mitochondrial DNA. The pattern of inheritance, however, resembled that of a nuclear gene. The authors explained this peculiarity with Mendelian segregation of a faulty gatekeeper gene that permits survival of paternal mtDNA in the oocyte. Three other groups (Vissing, 2019; Lutz-Bonengel and Parson, 2019; Salas et al, 2019), however, posited the observation was an artifact of inheritance of mtDNA nuclear pseudogenes (NUMTs), present in the father’s nuclear genome. We present justification that both interpretations are incorrect, but that the original authors did, in fact, observe biparental inheritance of mtDNA. Our alternative model assumes that because of initially low paternal mtDNA copy number these copies are randomly partitioned into nascent cell lineages. The paternal mtDNA haplotype must have a selective advantage, so ‘seeded’ cells will tend to proceed to fixation of the paternal haplotype in the course of development. We use modeling to emulate the dynamics of paternal genomes and predict their mode of inheritance and distribution in somatic tissue. The resulting offspring is a mosaic of cells that are purely maternal or purely paternal – including in the germline. This mosaicism explains the quasi-Mendelian segregation of the paternal mDNA. Our model is based on known aspects of mtDNA biology and explains all of the experimental observations outlined in Luo et. al., including maternal inheritance of the grand-paternal mtDNA.

scholarly journals A battle for transmission: the cooperative and selfish animal mitochondrial genomes

Open Biology ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 180267 ◽  
Author(s):  
Anna Klucnika ◽  
Hansong Ma
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Energy Production ◽  
Nuclear Genome ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Cellular Processes ◽  
Mitochondrial Replacement Therapy ◽  
Mtdna Evolution ◽  
Organismal Fitness

The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.

Note on Selection of Coordinate Systems for Geodynamics

1975 ◽  
Vol 26 ◽  
pp. 395-407
Author(s):  
S. Henriksen
Keyword(s):  
Sea Level ◽  
The Other ◽  
Coordinate Systems ◽  
Mean Sea Level ◽  
The Earth ◽  
The One ◽  
Static Systems ◽  
Selection Of

The first question to be answered, in seeking coordinate systems for geodynamics, is: what is geodynamics? The answer is, of course, that geodynamics is that part of geophysics which is concerned with movements of the Earth, as opposed to geostatics which is the physics of the stationary Earth. But as far as we know, there is no stationary Earth – epur sic monere. So geodynamics is actually coextensive with geophysics, and coordinate systems suitable for the one should be suitable for the other. At the present time, there are not many coordinate systems, if any, that can be identified with a static Earth. Certainly the only coordinate of aeronomic (atmospheric) interest is the height, and this is usually either as geodynamic height or as pressure. In oceanology, the most important coordinate is depth, and this, like heights in the atmosphere, is expressed as metric depth from mean sea level, as geodynamic depth, or as pressure. Only for the earth do we find “static” systems in use, ana even here there is real question as to whether the systems are dynamic or static. So it would seem that our answer to the question, of what kind, of coordinate systems are we seeking, must be that we are looking for the same systems as are used in geophysics, and these systems are dynamic in nature already – that is, their definition involvestime.

INTERFERENSI GRAMATIKAL DALAM KUMPULAN CERPEN BIARKAN AKU MEMULAI KARYA NURUL F. HUDA

2019 ◽  
Vol 1 (01) ◽  
pp. 16-23
Author(s):  
Zimmatul Liviana
Keyword(s):  
Short Stories ◽  
Data Collection ◽  
Qualitative Method ◽  
Language Variation ◽  
The Other ◽  
Qualitative Descriptive ◽  
Ofthe Object ◽  
Selection Of ◽  
Descriptive Qualitative

The research grammatical interference in a collection ofshort stories Biarkan Aku Memula iwork Nurul F. Hudaisa collection ofshort storiesset in the back that Is start work Let Nurul F. Huda contains many grammatical interference.The problem of this   study were(1)how   the various morphologi calinterference containedin   a   collection of short stories Biarkan Aku Memulai work Nurul F. Huda. (2)how the various syntactic interference contained in a collection of short stories Biarkan Aku Memulai work Nurul F. Huda. The purposeof this studyis to describe the morphological and         Syntactic interference contained in a collection of short stories Biarkan Aku Memulai work Nurul F. Huda. Sociolinguistics is the study of language variation and use in society. Interference is the event of the use of language elements of one into the other language elements that occur in the speakers themselves. This research uses descriptive qualitative method because to describe the actual realityin order to obtainan accurateand objective. Qualitative descriptive methods were used to analyzethe elements ofa word orphrase that incorporated elements of other languages with the analysis and description of the formulation of the problem is the answer. Data collection techniques using observation techniques, the determination ofthe object of research, the selection of short stories.Based on the analysis of the data in this study can be found that there are six forms of interference morphology, namely (1) the prefix nasal N-sound, (2) the addition of the suffix, (3) the exchange prefix, (4) exchange suffixes, (5) exchange konfiks, (6) removal affixes. While the syntactic interference only on the words and phrases in a sentence. The results of the study it can be concluded that the interference morphology more common than syntactic interference.

The Propaganda Feedback Loop

2018 ◽  
Author(s):  
Yochai Benkler ◽  
Robert Faris ◽  
Hal Roberts
Keyword(s):  
Case Studies ◽  
Feedback Loop ◽  
The Other ◽  
Hillary Clinton ◽  
Donald Trump ◽  
The Public ◽  
False Reporting ◽  
Media Ecosystem ◽  
Crowd Out ◽  
Selection Of

This chapter presents a model of the interaction of media outlets, politicians, and the public with an emphasis on the tension between truth-seeking and narratives that confirm partisan identities. This model is used to describe the emergence and mechanics of an insular media ecosystem and how two fundamentally different media ecosystems can coexist. In one, false narratives that reinforce partisan identity not only flourish, but crowd-out true narratives even when these are presented by leading insiders. In the other, false narratives are tested, confronted, and contained by diverse outlets and actors operating in a truth-oriented norms dynamic. Two case studies are analyzed: the first focuses on false reporting on a selection of television networks; the second looks at parallel but politically divergent false rumors—an allegation that Donald Trump raped a 13-yearold and allegations tying Hillary Clinton to pedophilia—and tracks the amplification and resistance these stories faced.

Development of a mito-CRISPR system for generating mitochondrial DNA-deleted strain in Saccharomyces cerevisiae

2020 ◽  
Vol 85 (4) ◽  
pp. 895-901
Author(s):  
Takamitsu Amai ◽  
Tomoka Tsuji ◽  
Mitsuyoshi Ueda ◽  
Kouichi Kuroda
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitochondrial Dna ◽  
Ethidium Bromide ◽  
Nuclear Genome ◽  
Target Sequence ◽  
Guide Rna ◽  
Crispr System ◽  
Mitochondrial Target ◽  
Gene Treatment ◽  
Mtdna Deletion

ABSTRACT Mitochondrial dysfunction can occur in a variety of ways, most often due to the deletion or mutation of mitochondrial DNA (mtDNA). The easy generation of yeasts with mtDNA deletion is attractive for analyzing the functions of the mtDNA gene. Treatment of yeasts with ethidium bromide is a well-known method for generating ρ° cells with complete deletion of mtDNA from Saccharomyces cerevisiae. However, the mutagenic effects of ethidium bromide on the nuclear genome cannot be excluded. In this study, we developed a “mito-CRISPR system” that specifically generates ρ° cells of yeasts. This system enabled the specific cleavage of mtDNA by introducing Cas9 fused with the mitochondrial target sequence at the N-terminus and guide RNA into mitochondria, resulting in the specific generation of ρ° cells in yeasts. The mito-CRISPR system provides a concise technology for deleting mtDNA in yeasts.

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