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 Mitochondrial genome evolution of placozoans: gene rearrangements and repeat expansions

2020 ◽  
Author(s):  
Hideyuki Miyazawa ◽  
Hans-Jürgen Osigus ◽  
Sarah Rolfes ◽  
Kai Kamm ◽  
Bernd Schierwater ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gc Content ◽  
Distribution Patterns ◽  
Sister Group ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Inverted Repeats ◽  
Protein Coding ◽  
Group I ◽  
Phylogenomic Analyses

Abstract Placozoans, non-bilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNA are circular chromosomes of 32-43 kbp in size, which encode 12 protein-coding genes, 24 tRNAs, and 2 rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Since P. mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.

scholarly journals The Investigation of Perennial Sunflower Species (Helianthus L.) Mitochondrial Genomes

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 982
Author(s):  
Maksim Makarenko ◽  
Alexander Usatov ◽  
Tatiana Tatarinova ◽  
Kirill Azarin ◽  
Alexey Kovalevich ◽  
...  
Keyword(s):  
Low Frequency ◽  
Blind Spot ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Perennial Species ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gene Profiles ◽  
Helianthus Species ◽  
Reading Frames

The genus Helianthus is a diverse taxonomic group with approximately 50 species. Most sunflower genomic investigations are devoted to economically valuable species, e.g., H. annuus, while other Helianthus species, especially perennial, are predominantly a blind spot. In the current study, we have assembled the complete mitogenomes of two perennial species: H. grosseserratus (273,543 bp) and H. strumosus (281,055 bp). We analyzed their sequences and gene profiles in comparison to the available complete mitogenomes of H. annuus. Except for sdh4 and trnA-UGC, both perennial sunflower species had the same gene content and almost identical protein-coding sequences when compared with each other and with annual sunflowers (H. annuus). Common mitochondrial open reading frames (ORFs) (orf117, orf139, and orf334) in sunflowers and unique ORFs for H. grosseserratus (orf633) and H. strumosus (orf126, orf184, orf207) were identified. The maintenance of plastid-derived coding sequences in the mitogenomes of both annual and perennial sunflowers and the low frequency of nonsynonymous mutations point at an extremely low variability of mitochondrial DNA (mtDNA) coding sequences in the Helianthus genus.

The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi

2018 ◽  
Vol 64 (5) ◽  
pp. 339-348 ◽  
Author(s):  
Talal George Abboud ◽  
Abdullah Zubaer ◽  
Alvan Wai ◽  
Georg Hausner
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Open Reading Frames ◽  
Dutch Elm Disease ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Statistical Support ◽  
Size Variability ◽  
Reading Frames

Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.

scholarly journals Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Robin-Lee Troskie ◽  
Yohaann Jafrani ◽  
Tim R. Mercer ◽  
Adam D. Ewing ◽  
Geoffrey J. Faulkner ◽  
...  
Keyword(s):  
Cultured Cells ◽  
Open Reading Frames ◽  
Cdna Sequencing ◽  
Protein Coding ◽  
Dynamic Component ◽  
Gene Copies ◽  
Long Read ◽  
Normal Human ◽  
Reading Frames ◽  
Transcriptional Landscape

AbstractPseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes expressed in tissue-specific patterns. Some pseudogene transcripts have intact open reading frames and are translated in cultured cells, representing unannotated protein-coding genes. To assess the biological impact of noncoding pseudogenes, we CRISPR-Cas9 delete the nucleus-enriched pseudogene PDCL3P4 and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the human transcriptional landscape.

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 Disrupting upstream translation in mRNAs is associated with human disease

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David S. M. Lee ◽  
Joseph Park ◽  
Andrew Kromer ◽  
Aris Baras ◽  
Daniel J. Rader ◽  
...  
Keyword(s):  
Protein Expression ◽  
Biological Significance ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Stop Codons ◽  
Human Genes ◽  
Strong Negative Selection ◽  
Disease Associations ◽  
Reading Frames

AbstractRibosome-profiling has uncovered pervasive translation in non-canonical open reading frames, however the biological significance of this phenomenon remains unclear. Using genetic variation from 71,702 human genomes, we assess patterns of selection in translated upstream open reading frames (uORFs) in 5’UTRs. We show that uORF variants introducing new stop codons, or strengthening existing stop codons, are under strong negative selection comparable to protein-coding missense variants. Using these variants, we map and validate gene-disease associations in two independent biobanks containing exome sequencing from 10,900 and 32,268 individuals, respectively, and elucidate their impact on protein expression in human cells. Our results suggest translation disrupting mechanisms relating uORF variation to reduced protein expression, and demonstrate that translation at uORFs is genetically constrained in 50% of human genes.

scholarly journals Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear RNA byproducts

2021 ◽  
Author(s):  
Yanyi Jiang ◽  
Xiaofan Chen ◽  
Wei Zhang
Keyword(s):  
Open Reading Frames ◽  
Systematic Evaluation ◽  
Circular Rnas ◽  
Protein Coding ◽  
Rolling Circle ◽  
Functional Investigation ◽  
Overexpression System ◽  
Translation Signals ◽  
Coding Potential ◽  
Reading Frames

AbstractIn RNA field, the demarcation between coding and non-coding has been negotiated by the recent discovery of occasionally translated circular RNAs (circRNAs). Although absent of 5’ cap structure, circRNAs can be translated cap-independently. Complementary intron-mediated overexpression is one of the most utilized methodologies for circRNA research but not without bearing echoing skepticism for its poorly defined mechanism and latent coexistent side products. In this study, leveraging such circRNA overexpression system, we have interrogated the protein-coding potential of 30 human circRNAs containing infinite open reading frames in HEK293T cells. Surprisingly, pervasive translation signals are detected by immunoblotting. However, intensive mutagenesis reveals that numerous translation signals are generated independently of circRNA synthesis. We have developed a dual tag strategy to isolate translation noise and directly demonstrate that the fallacious translation signals originate from cryptically spliced linear transcripts. The concomitant linear RNA byproducts, presumably concatemers, can be translated to allow pseudo rolling circle translation signals, and can involve backsplicing junction (BSJ) to disqualify the BSJ-based evidence for circRNA translation. We also find non-AUG start codons may engage in the translation initiation of circRNAs. Taken together, our systematic evaluation sheds light on heterogeneous translational outputs from circRNA overexpression vector and comes with a caveat that ectopic overexpression technique necessitates extremely rigorous control setup in circRNA translation and functional investigation.

scholarly journals A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation

2020 ◽  
Vol 6 (21) ◽  
pp. eaaz2059 ◽  
Author(s):  
Liman Niu ◽  
Fangzhou Lou ◽  
Yang Sun ◽  
Libo Sun ◽  
Xiaojie Cai ◽  
...  
Keyword(s):  
Antigen Presentation ◽  
Inflammatory Diseases ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Histocompatibility Complex ◽  
Antigen Trafficking ◽  
Heat Shock Cognate Protein ◽  
Antigen Presenting ◽  
Cognate Protein ◽  
Reading Frames

Many annotated long noncoding RNAs (lncRNAs) harbor predicted short open reading frames (sORFs), but the coding capacities of these sORFs and the functions of the resulting micropeptides remain elusive. Here, we report that human lncRNA MIR155HG encodes a 17–amino acid micropeptide, which we termed miPEP155 (P155). MIR155HG is highly expressed by inflamed antigen-presenting cells, leading to the discovery that P155 interacts with the adenosine 5′-triphosphate binding domain of heat shock cognate protein 70 (HSC70), a chaperone required for antigen trafficking and presentation in dendritic cells (DCs). P155 modulates major histocompatibility complex class II–mediated antigen presentation and T cell priming by disrupting the HSC70-HSP90 machinery. Exogenously injected P155 improves two classical mouse models of DC-driven auto inflammation. Collectively, we demonstrate the endogenous existence of a micropeptide encoded by a transcript annotated as “non-protein coding” and characterize a micropeptide as a regulator of antigen presentation and a suppressor of inflammatory diseases.

scholarly journals When Long Noncoding Becomes Protein Coding

2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Corrine Corrina R. Hartford ◽  
Ashish Lal
Keyword(s):  
Cell Division ◽  
Cell Signaling ◽  
Transcription Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Small Proteins ◽  
Coding Potential ◽  
Reading Frames

ABSTRACT Recent advancements in genetic and proteomic technologies have revealed that more of the genome encodes proteins than originally thought possible. Specifically, some putative long noncoding RNAs (lncRNAs) have been misannotated as noncoding. Numerous lncRNAs have been found to contain short open reading frames (sORFs) which have been overlooked because of their small size. Many of these sORFs encode small proteins or micropeptides with fundamental biological importance. These micropeptides can aid in diverse processes, including cell division, transcription regulation, and cell signaling. Here we discuss strategies for establishing the coding potential of putative lncRNAs and describe various functions of known micropeptides.

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