scholarly journals Mitochondrial genomes are retained by selective constraints on protein targeting

2015 ◽  
Vol 112 (33) ◽  
pp. 10154-10161 ◽  
Author(s):  
Patrik Björkholm ◽  
Ajith Harish ◽  
Erik Hagström ◽  
Andreas M. Ernst ◽  
Siv G. E. Andersson
Keyword(s):  
Endoplasmic Reticulum ◽  
Membrane Proteins ◽  
Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Nuclear Genome ◽  
Protein Domains ◽  
Eukaryotic Cell ◽  
Mitochondrial Genomes ◽  
Hydrophobic Membrane ◽  
Selective Constraints

Mitochondria are energy-producing organelles in eukaryotic cells considered to be of bacterial origin. The mitochondrial genome has evolved under selection for minimization of gene content, yet it is not known why not all mitochondrial genes have been transferred to the nuclear genome. Here, we predict that hydrophobic membrane proteins encoded by the mitochondrial genomes would be recognized by the signal recognition particle and targeted to the endoplasmic reticulum if they were nuclear-encoded and translated in the cytoplasm. Expression of the mitochondrially encoded proteins Cytochrome oxidase subunit 1, Apocytochrome b, and ATP synthase subunit 6 in the cytoplasm of HeLa cells confirms export to the endoplasmic reticulum. To examine the extent to which the mitochondrial proteome is driven by selective constraints within the eukaryotic cell, we investigated the occurrence of mitochondrial protein domains in bacteria and eukaryotes. The accessory protein domains of the oxidative phosphorylation system are unique to mitochondria, indicating the evolution of new protein folds. Most of the identified domains in the accessory proteins of the ribosome are also found in eukaryotic proteins of other functions and locations. Overall, one-third of the protein domains identified in mitochondrial proteins are only rarely found in bacteria. We conclude that the mitochondrial genome has been maintained to ensure the correct localization of highly hydrophobic membrane proteins. Taken together, the results suggest that selective constraints on the eukaryotic cell have played a major role in modulating the evolution of the mitochondrial genome and proteome.

scholarly journals From simple to supercomplex: mitochondrial genomes of euglenozoan protists

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 392 ◽  
Author(s):  
Drahomíra Faktorová ◽  
Eva Dobáková ◽  
Priscila Peña-Diaz ◽  
Julius Lukeš
Keyword(s):  
Gene Expression ◽  
Mitochondrial Genome ◽  
World Ocean ◽  
Eukaryotic Cell ◽  
Mitochondrial Genomes ◽  
Gradual Reduction ◽  
Rna Molecules ◽  
The World ◽  
Complex Protein ◽  
Endosymbiotic Origin

Mitochondria are double membrane organelles of endosymbiotic origin, best known for constituting the centre of energetics of a eukaryotic cell. They contain their own mitochondrial genome, which as a consequence of gradual reduction during evolution typically contains less than two dozens of genes. In this review, we highlight the extremely diverse architecture of mitochondrial genomes and mechanisms of gene expression between the three sister groups constituting the phylum Euglenozoa - Euglenida, Diplonemea and Kinetoplastea. The earliest diverging euglenids possess a simplified mitochondrial genome and a conventional gene expression, whereas both are highly complex in the two other groups. The expression of their mitochondrial-encoded proteins requires extensive post-transcriptional modifications guided by complex protein machineries and multiple small RNA molecules. Moreover, the least studied diplonemids, which have been recently discovered as a highly abundant component of the world ocean plankton, possess one of the most complicated mitochondrial genome organisations known to date.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp., and Dicyema japonicum

2018 ◽  
Author(s):  
Helen. E. Robertson ◽  
Philipp. H. Schiffer ◽  
Maximilian. J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Small Subunit ◽  
Mitochondrial Genomes ◽  
List Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cell Layers

AbstractThe Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a divergent gene order compared to other metazoans. The data we present from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical across the Metazoa. The cox1 gene from dicyemid species has a series of conserved in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.Key FindingsWe report the first almost-complete mitochondrial genome from an orthonectid parasite, Intoshia linei, including 12 protein-coding genes; 20 tRNAs and putative sequences for large and small subunit rRNAs. We find that the I. linei mitochondrial genome is exceptionally AT-rich and has a novel gene order compared to other published metazoan mitochondrial genomes. These findings are indicative of the rapid rate of evolution that has occurred in the I. linei mitochondrial genome.We also report nine and eight protein-coding genes, respectively, from the dicyemid species Dicyema sp. and Dicyema japonicum, and use the cox1 genes from both species for phylogenetic inference of the internal phylogeny of the dicyemids.We find that the cox1 gene from dicyemids has a series of four conserved in-frame deletions which appear to be unique to this group.

scholarly journals Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

2020 ◽  
Vol 21 (2) ◽  
pp. 483
Author(s):  
Wei Liu ◽  
Yingli Cai ◽  
Qianqian Zhang ◽  
Fang Shu ◽  
Lianfu Chen ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Mycorrhizal Fungi ◽  
Plant Cell Wall ◽  
Physical Map ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Nuclear Genome ◽  
Cell Wall Degrading Enzymes ◽  
Total Length ◽  
Morchella Crassipes

Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

2018 ◽  
Vol 4 ◽  
Author(s):  
Helen E. Robertson ◽  
Philipp H. Schiffer ◽  
Maximilian J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Limited Support ◽  
Cell Layers

Abstract The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14 247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.

scholarly journals Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
S. R. Starkenburg ◽  
J. E. W. Polle ◽  
B. Hovde ◽  
H. E. Daligault ◽  
K. W. Davenport ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Green Alga ◽  
Industrial Production ◽  
Complete Mitochondrial Genome ◽  
Scenedesmus Obliquus ◽  
Nuclear Genome ◽  
Mitochondrial Genomes ◽  
Complete Chloroplast Genome ◽  
Draft Assembly

ABSTRACT The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

scholarly journals Becoming Archaea: Septic Shock, Warburg effect and loss of endosymbiotic relation-Billion year war of two genomes

2017 ◽  
Author(s):  
Vasanthakumar Natesan
Keyword(s):  
Septic Shock ◽  
Immune System ◽  
Mitochondrial Genome ◽  
Mitochondrial Respiration ◽  
Innate Immune System ◽  
Warburg Effect ◽  
Nuclear Genome ◽  
Eukaryotic Cell ◽  
Innate Immune ◽  
Molecular Pattern

Becoming Archaea: Septic Shock, Warburg effect and loss of endosymbiotic relation-Billion year war of two genomes.ABSTRACT : Septic shock is a major problem in medicine and carries high mortality rate. Irrespective of the advances in this field the underlying mechanism behind septic shock still remains a mystery. To understand septic shock we need to understand the evolution of eukaryotic cell and the billion year war between archaeal/nuclear genome and the bacterial/mitochondrial genome. The ancient infection of archaeal host by the bacteria (α-proteobacteria) resulted in the formation of eukaryotes and mitochondrial endosymbiont occurred >1.5 billion years ago and this extraordinary event is occurring from then on all the time till now resulted in formation of complex life forms. In this article I propose ‘Warburg common pathogenesis evolutionary model’, which has the potential to explain septic shock and most of the pathophysiological processes. I hypothesize that the bacterial/mitochondrial invasion of the eukaryote cell is supported by the mitochondrial system of the host eukaryotic cell and resisted by the innate immune system which is the archaeal part of the host eukaryotic cell, as archaea is the real host before it became eukaryote.Three major outcomes may result because of the bacterial /mitochondrial invasion related event,1) PAMP/DAMP via PRR eg.TLR4 over activates innate immune system which in turn inhibits the mitochondrial respiration and decreases the mitochondrial genome. Nuclear genome overpowers mitochondrial genome which results in the loss of the endosymbiotic relation between them, produces Warburg effect and the bacterial /mitochondrial invasion is successfully defeated. By Warburg effect, the eukaryotic host cell now returned to its original billion year old primitive form i.e. it became archaea like. This dedifferentiated state switching can be seen as the cells local survival strategy in response to injuries as the cells are now archaea like which has the ability to live in harsh environments. But returning to their primitive forms leads to disorder and ends in global collapse of the organ systems and organism which requires order in terms of differentiation which is maintained by the mitochondrial system in the eukaryotic cell and across the cells by intercellular mitochondrial transfer. Death of the organism may be due to the immortality pathway chosen by the cells locally. 2) Successful bacterial /mitochondrial invasion of the eukaryotic host will increase the mitochondrial genome and overpower the nuclear genome which may trigger apoptosis by degrading the nuclear genome and expelling it. 3) Partially successful invasion may result in the formation of cellular memory by increase in both OXPHOS and glycolysis. I propose that the treatment in septic shock should aim at activation of mitochondrial respiration thereby decreasing the aerobic glycolysis and changing the cell to its normal adult dynamic differentiation phenotype i.e all the drugs should be used as differentiation therapy. Adrenergic blockers and ascorbic acid may be the main treatment options, which are already used by some research groups. Abbrevations :, Oxidative phosphorylation (OXPHOS),Pathogen associated molecular pattern (PAMP), Danger associated molecular pattern(DAMP),Pattern recognition receptor(PRR),Toll like receptor (TLR).

scholarly journals Mitochondrial Fostering: The Mitochondrial Genome May Play a Role in Plant Orphan Gene Evolution

2020 ◽  
Vol 11 ◽  
Author(s):  
Seth O’Conner ◽  
Ling Li
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Gene Evolution ◽  
Nuclear Genome ◽  
Bioinformatic Analysis ◽  
Land Plants ◽  
Mitochondrial Genomes ◽  
Recombination Rates ◽  
Orphan Genes ◽  
Orphan Gene

Plant mitochondrial genomes exhibit unique evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a “Mitochondrial Fostering” theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologs in other lineages). Two approaches were used to test this theory: (1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that migrated to the nucleus) at the genome level, and (2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome of Arabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of this A. thaliana orphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between the amount of mitochondrial DNA transferred to the nuclear genome and the number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.

scholarly journals On the origin of mitochondria: a genomics perspective

2003 ◽  
Vol 358 (1429) ◽  
pp. 165-179 ◽  
Author(s):  
G. E. Andersson ◽  
Olof Karlberg ◽  
Björn Canbäck ◽  
Charles G. Kurland
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Nuclear Genome ◽  
Strong Relationship ◽  
Eukaryotic Cell ◽  
Mitochondrial Proteins ◽  
Origin And Evolution ◽  
Bacterial Genes

The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the α–proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with α–proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.

A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution

Genome ◽  
2013 ◽  
Vol 56 (4) ◽  
pp. 187-193 ◽  
Author(s):  
Mai Tsujimura ◽  
Naoki Mori ◽  
Hiroshi Yamagishi ◽  
Toru Terachi
Keyword(s):  
Mitochondrial Genome ◽  
Nuclear Genome ◽  
Mitochondrial Genomes ◽  
Chloroplast Microsatellite ◽  
Wheat Evolution ◽  
Closely Related Species ◽  
Genome Type ◽  
Sequence Characterized Amplified Region ◽  
Chloroplast Genomes ◽  
Different Types

In wheat (Triticum) and Aegilops, chloroplast and mitochondrial genomes have been studied for over three decades to clarify the phylogenetic relationships among species, and most of the maternal lineages of polyploid species have been clarified. Mitochondrial genomes of Emmer (tetraploid with nuclear genome AABB) and Dinkel (hexaploid with AABBDD) wheat are classified into two different types, VIIa and VIIb, by the presence–absence of the third largest HindIII fragment (named H3) in the mitochondrial DNA. Although the mitochondrial genome in the genera often provides useful information to clarify the phylogenetic relationship among closely related species, the phylogenetic significance of this dimorphism has yet not been clarified. In this study, to facilitate analysis using a large number of accessions, a sequence characterized amplified region (SCAR) marker that distinguishes the type VIIb mitochondrial genome from type VIIa was first developed. Mitochondrial genome type was determined for each of 30 accessions of wild and cultivated Emmer wheat and 25 accessions of Dinkel wheat. The mitochondrial genome type for each accession was compared with the plastogroup that had been determined using chloroplast microsatellite markers. Unexpectedly, the distribution of mitochondrial genome type was not in accordance with that of the plastogroups, suggesting occasional paternal leakage of either the mitochondrial or chloroplast genome during speciation and differentiation of Emmer and Dinkel wheat. An alternative possibility that substoichiometric shifting is involved in the observed dimorphism of the mitochondrial genome is also discussed.

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

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1306 ◽  
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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