scholarly journals Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Kazuyoshi Kitazaki ◽  
Tomohiko Kubo
Keyword(s):  
Mitochondrial Genome ◽  
Current Knowledge ◽  
Open Reading Frames ◽  
Plant Mitochondrial Genome ◽  
Unknown Mechanism ◽  
Evolutionary Mechanism ◽  
Copy Numbers ◽  
Intergenic Regions ◽  
Genome Alteration ◽  
Reading Frames

The angiosperm mitochondrial genome is the largest and least gene-dense among the eukaryotes, because its intergenic regions are expanded. There seems to be no functional constraint on the size of the intergenic regions; angiosperms maintain the large mitochondrial genome size by a currently unknown mechanism. After a brief description of the angiosperm mitochondrial genome, this review focuses on our current knowledge of the mechanisms that control the maintenance and alteration of the genome. In both processes, the control of homologous recombination is crucial in terms of site and frequency. The copy numbers of various types of mitochondrial DNA molecules may also be controlled, especially during transmission of the mitochondrial genome from one generation to the next. An important characteristic of angiosperm mitochondria is that they contain polypeptides that are translated from open reading frames created as byproducts of genome alteration and that are generally nonfunctional. Such polypeptides have potential to evolve into functional ones responsible for mitochondrially encoded traits such as cytoplasmic male sterility or may be remnants of the former functional polypeptides.

scholarly journals Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 777-788 ◽  
Author(s):  
Carole H Sellem ◽  
Yves d'Aubenton-Carafa ◽  
Michèle Rossignol ◽  
Léon Belcour
Keyword(s):  
Mitochondrial Genome ◽  
Open Reading Frames ◽  
Nucleotide Substitutions ◽  
Sequence Comparisons ◽  
Modular Evolution ◽  
Group I ◽  
Sequence Variations ◽  
Type Strains ◽  
Reading Frames ◽  
Adjacent Exon

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

scholarly journals The complete mitochondrial genome of the lipid-producing yeast Rhodotorula toruloides

2020 ◽  
Vol 20 (6) ◽  
Author(s):  
Renhui Zhou ◽  
Zhiwei Zhu ◽  
Sufang Zhang ◽  
Zongbao Kent Zhao
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Open Reading Frames ◽  
Circular Dna ◽  
Transfer Rnas ◽  
Fundamental Information ◽  
Significant Genetic Divergence ◽  
Reading Frames

ABSTRACT Mitochondria are semi-autonomous organelles with their own genome and crucial to cellular material and energy metabolism. Here, we report the complete mitochondrial genome of a lipid-producing basidiomycetous yeast Rhodotorula toruloides NP11. The mitochondrial genome of R. toruloides NP11 was assembled into a circular DNA molecule of 125937bp, encoding 15 proteins, 28 transfer RNAs, 2 ribosomal RNA subunits and 10 open reading frames with unknown function. The G + C content (41%) of the mitochondrial genome is substantially lower than that of the nuclear genome (62%) of R. toruloides NP11. Further reanalysis of the transcriptome data confirmed the transcription of four mitochondrial genes. The comparison of the mitochondrial genomes of R. toruloides NP11 and NBRC0880 revealed a significant genetic divergence. These data can complement our understanding of the genetic background of R. toruloides and provide fundamental information for further genetic engineering of this strain.

scholarly journals Identifying small proteins by ribosome profiling with stalled initiation complexes

2019 ◽  
Author(s):  
Jeremy Weaver ◽  
Fuad Mohammad ◽  
Allen R. Buskirk ◽  
Gisela Storz
Keyword(s):  
Amino Acids ◽  
Model Organism ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Genomic Context ◽  
True Prevalence ◽  
New Genes ◽  
Small Proteins ◽  
Intergenic Regions ◽  
Reading Frames

ABSTRACTSmall proteins consisting of 50 or fewer amino acids have been identified as regulators of larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the true prevalence of small proteins remains unknown because conventional annotation pipelines usually exclude small open reading frames (smORFs). We previously identified several dozen small proteins in the model organism Escherichia coli using theoretical bioinformatic approaches based on sequence conservation and matches to canonical ribosome binding sites. Here, we present an empirical approach for discovering new proteins, taking advantage of recent advances in ribosome profiling in which antibiotics are used to trap newly-initiated 70S ribosomes at start codons. This approach led to the identification of many novel initiation sites in intergenic regions in E. coli. We tagged 41 smORFs on the chromosome and detected protein synthesis for all but three. The corresponding genes are not only intergenic, but are also found antisense to other genes, in operons, and overlapping other open reading frames (ORFs), some impacting the translation of larger downstream genes. These results demonstrate the utility of this method for identifying new genes, regardless of their genomic context.IMPORTANCEProteins comprised of 50 or fewer amino acids have been shown to interact with and modulate the function of larger proteins in a range of organisms. Despite the possible importance of small proteins, the true prevalence and capabilities of these regulators remain unknown as the small size of the proteins places serious limitations on their identification, purification and characterization. Here, we present a ribosome profiling approach with stalled initiation complexes that led to the identification of 38 new small proteins.

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

PeerJ ◽  
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.

scholarly journals NpdR, a Repressor Involved in 2,4,6-Trinitrophenol Degradation in Rhodococcus opacus HL PM-1

2004 ◽  
Vol 186 (1) ◽  
pp. 98-103 ◽  
Author(s):  
Dang P. Nga ◽  
Josef Altenbuchner ◽  
Gesche S. Heiss
Keyword(s):  
Wild Type Strain ◽  
Picric Acid ◽  
Open Reading Frames ◽  
Rhodococcus Opacus ◽  
Promoter Probe ◽  
Hydrogenation Reactions ◽  
Intergenic Regions ◽  
In The Wild ◽  
Promoter Probe Vector ◽  
Reading Frames

ABSTRACT Rhodococcus opacus HL PM-1 utilizes 2,4,6-trinitrophenol (picric acid) as a sole nitrogen source. The initial attack on picric acid occurs through two hydrogenation reactions. Hydride transferase II (encoded by npdI) and hydride transferase I (encoded by npdC) are responsible for the hydride transfers. Database searches with the npd genes have indicated the presence of a putative transcriptional regulator, npdR. Here, the npdR gene was expressed in Escherichia coli, and the protein was purified and shown to form a complex with intergenic regions between open reading frames A and B and between npdH and npdI within the npd gene cluster. A change in DNA-NpdR complex formation occurred in the presence of 2,4-dinitrophenol, picric acid, 2-chloro-4,6-dinitrophenol, and 2-methyl-4,6-dinitrophenol. By constructing a promoter-probe vector, we demonstrated that both intergenic regions caused the expression of reporter gene xylE. Hence, both of these regions contain promoters. A deletion mutant of R. opacus HL PM-1 was constructed in which part of npdR was deleted. The expression of npdI and npdC was induced by 2,4-dinitrophenol in the wild-type strain, while in the mutant these genes were constitutively expressed. Hence, NpdR is a repressor involved in picric acid degradation.

scholarly journals Heteroplasmy and repeat expansion in the plant-like mitochondrial genome of a bivalve mollusc

2020 ◽  
Author(s):  
Andrew D Calcino ◽  
Christian Baranyi ◽  
Andreas Wanninger
Keyword(s):  
Mitochondrial Genome ◽  
Error Correction ◽  
Plant Mitochondria ◽  
Bivalve Mollusc ◽  
Open Reading Frames ◽  
Quagga Mussel ◽  
Gene Repertoire ◽  
Repeat Content ◽  
Repeat Expansions ◽  
Reading Frames

Background: Animal mitochondrial genomes are typically circular, 14-20 kb in length, maternally inherited, contain 13 coding genes, two ribosomal genes and are homoplasmic. In contrast, plant mitogenomes display frequent gene rearrangements, often contain greatly expanded repetitive regions, encode various open reading frames of unknown function and may be heteroplasmic due to differential repeat expansions between molecules. Error correction by recombination is common in plant mitochondria and has been proposed as the driver behind the rearrangements and repeat expansions that are often observed. In contrast, most animal mitochondria never or only very seldomly recombine and their utilisation of other repair mechanisms for mitochondrial genome error correction is a potential driver of their non-coding DNA reduction. Results: Using PacBio long reads for genome assembly and structural variant detection, we identify evidence of heteroplasmy in the form of variable repeat lengths within two blocks of repetitive DNA within the expanded 46 kb mitochondrial genome of the bivalve mollusc, quagga mussel, Dreissena rostriformis. The quagga mussel also has a greatly expanded repertoire of coding genes in comparison to most animals which includes an additional nine open reading frames (ORFs) encoding predicted transmembrane peptides of unknown orthology. Conclusions: The genome size, repeat content and coding gene repertoire of the quagga mussel mitogenome closely resemble those of plants and the identification of repeat-associated heteroplasmy is consistent with the utilisation of plant-like recombination-based error correction mechanisms. Given the frequency of mitochondrial repeat expansions within the Bivalvia, recombination may be an underappreciated mechanism for mitogenomic error correction within this and other animal lineages.

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