RNA editing of a conserved reading frame in plant mitochondria increases its similarity to two overlapping reading frames in Escherichia coli

1994 ◽  
Vol 242 (1) ◽  
pp. 65-72 ◽  
Author(s):  
Sabine Sünkel ◽  
Axel Brennicke ◽  
Volker Knoop
Keyword(s):  
Escherichia Coli ◽  
Rna Editing ◽  
Plant Mitochondria ◽  
Reading Frame ◽  
Overlapping Reading Frames ◽  
Reading Frames

scholarly journals Automatic simulation of RNA editing in plants for the identification of novel putative Open Reading Frames

2017 ◽  
Author(s):  
Fabio Fassetti ◽  
Claudia Giallombardo ◽  
Ofelia Leone ◽  
Luigi Palopoli ◽  
Simona E Rombo ◽  
...  
Keyword(s):  
Rna Editing ◽  
Dna Sequences ◽  
Information Transfer ◽  
Plant Mitochondria ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Novel Proteins ◽  
Gene Search ◽  
Novel Strategy

In plant mitochondria an essential mechanism for gene expression is RNA editing, often influencing the synthesis of functional proteins. RNA editing alters the linearity of genetic information transfer, intro- ducing differences between RNAs and their coding DNA sequences that hind both experimental and computational research of genes. Thus common software tools for gene search, successfully exploited to find canonic genes, often can fail in discovering genes encrypted in the genome of plants. In this work we propose a novel strategy useful to intercept candidate coding sequences resulting from some possible editing substitutions on the start and stop codons of a given input organism DNA. Our method is based on the simulation of the RNA editing mechanism, in order to generate candidate Open Reading Frame (ORF) sequences that could code for some, yet unknown, proteins. Results obtained on the mtDNA of Oryza sativa are promising, since we identified ORF sequences trascripted in Oriza, that do not cor- respond to already known proteins in this organism. Part of the corresponding amino acid sequences present high homologies with proteins already discovered in other organisms, the remaining ones could represent novel proteins not yet discovered in Oryza.

scholarly journals The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons

1986 ◽  
Vol 6 (1) ◽  
pp. 168-182
Author(s):  
D D Loeb ◽  
R W Padgett ◽  
S C Hardies ◽  
W R Shehee ◽  
M B Comer ◽  
...  
Keyword(s):  
Mouse Genome ◽  
Large Open Reading Frame ◽  
Protein Coding ◽  
Coding Sequences ◽  
Reading Frame ◽  
Reverse Transcriptases ◽  
Multiple Copies ◽  
Overlapping Reading Frames ◽  
Coding Capacity ◽  
Reading Frames

The complete nucleotide sequence of a 6,851-base pair (bp) member of the L1Md repetitive family from a selected random isolate of the BALB/c mouse genome is reported here. Five kilobases of the element contains two overlapping reading frames of 1,137 and 3,900 bp. The entire 3,900-bp frame and the 3' 600 bp of the 1,137-bp frame, when compared with a composite consensus primate L1 sequence, show a ratio of replacement to silent site differences characteristic of protein coding sequences. This more closely defines the protein coding capacity of this repetitive family, which was previously shown to possess a large open reading frame of undetermined extent. The relative organization of the 1,137- and 3,900-bp reading frames, which overlap by 14 bp, bears resemblance to protein-coding, mobile genetic elements. Homology can be found between the amino acid sequence of the 3,900-bp frame and selected domains of several reverse transcriptases. The 5' ends of the two L1Md elements described in this report have multiple copies, 4 2/3 copies and 1 2/3 copy, of a 208-bp direct tandem repeat. The sequence of this 208-bp element differs from the sequence of a previously defined 5' end for an L1Md element, indicating that there are at least two different 5' end motifs for L1Md.

scholarly journals Clustering and visualizing the distribution of overlapping reading frames in virus genomes

2021 ◽  
Author(s):  
Laura Munoz-Baena ◽  
Art Poon
Keyword(s):  
Purifying Selection ◽  
Protein Coding ◽  
Virus Family ◽  
Reading Frame ◽  
New Genes ◽  
Overlapping Reading Frames ◽  
Genome Level ◽  
Dsdna Viruses ◽  
Virus Genomes ◽  
Reading Frames

Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated reading frames in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in dsDNA viruses. However, the longest overlaps involve no shift in reading frame (+0), increasing the selective burden of the same nucleotide positions within codons, instead of exposing additional sites to purifying selection. Next, we develop a new graph-based representation of the distribution of OvRFs among the reading frames of genomes in a given virus family. In the absence of an unambiguous partition of reading frames by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent reading frames are adjacent in one or more genomes, and (2) that the reading frames overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.

scholarly journals Cell-line specific RNA editing patterns in Trypanosoma brucei suggest a unique mechanism to generate protein variation in a system intolerant to genetic mutations

2019 ◽  
Vol 48 (3) ◽  
pp. 1479-1493
Author(s):  
Laura E Kirby ◽  
Donna Koslowsky
Keyword(s):  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Dual Coding ◽  
Reading Frame ◽  
Guide Rnas ◽  
Insertion And Deletion ◽  
Editing Domain ◽  
Ribosomal Protein S12 ◽  
Reading Frames ◽  
Unique Mechanism

Abstract Trypanosoma brucei possesses a highly complex RNA editing system that uses guide RNAs to direct the insertion and deletion of uridines in mitochondrial mRNAs. These changes extensively alter the target mRNAs and can more than double them in length. Recently, analyses showed that several of the edited genes possess the capacity to encode two different protein products. The overlapped reading frames can be accessed through alternative RNA editing that shifts the translated reading frame. In this study, we analyzed the editing patterns of three putative dual-coding genes, ribosomal protein S12 (RPS12), the 5′ editing domain of NADH dehydrogenase subunit 7 (ND7 5′), and C-rich region 3 (CR3). We found evidence that alternatively 5′-edited ND7 5′ and CR3 transcripts are present in the transcriptome, providing evidence for the use of dual ORFs in these transcripts. Moreover, we found that CR3 has a complex set of editing pathways that vary substantially between cell lines. These findings suggest that alternative editing can work to introduce genetic variation in a system that selects against nucleotide mutations.

scholarly journals Automatic simulation of RNA editing in plants for the identification of novel putative Open Reading Frames

2017 ◽  
Author(s):  
Fabio Fassetti ◽  
Claudia Giallombardo ◽  
Ofelia Leone ◽  
Luigi Palopoli ◽  
Simona E Rombo ◽  
...  
Keyword(s):  
Rna Editing ◽  
Dna Sequences ◽  
Information Transfer ◽  
Plant Mitochondria ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Novel Proteins ◽  
Gene Search ◽  
Novel Strategy

In plant mitochondria an essential mechanism for gene expression is RNA editing, often influencing the synthesis of functional proteins. RNA editing alters the linearity of genetic information transfer, intro- ducing differences between RNAs and their coding DNA sequences that hind both experimental and computational research of genes. Thus common software tools for gene search, successfully exploited to find canonic genes, often can fail in discovering genes encrypted in the genome of plants. In this work we propose a novel strategy useful to intercept candidate coding sequences resulting from some possible editing substitutions on the start and stop codons of a given input organism DNA. Our method is based on the simulation of the RNA editing mechanism, in order to generate candidate Open Reading Frame (ORF) sequences that could code for some, yet unknown, proteins. Results obtained on the mtDNA of Oryza sativa are promising, since we identified ORF sequences trascripted in Oriza, that do not cor- respond to already known proteins in this organism. Part of the corresponding amino acid sequences present high homologies with proteins already discovered in other organisms, the remaining ones could represent novel proteins not yet discovered in Oryza.

scholarly journals The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons.

1986 ◽  
Vol 6 (1) ◽  
pp. 168-182 ◽  
Author(s):  
D D Loeb ◽  
R W Padgett ◽  
S C Hardies ◽  
W R Shehee ◽  
M B Comer ◽  
...  
Keyword(s):  
Mouse Genome ◽  
Large Open Reading Frame ◽  
Protein Coding ◽  
Coding Sequences ◽  
Reading Frame ◽  
Reverse Transcriptases ◽  
Multiple Copies ◽  
Overlapping Reading Frames ◽  
Coding Capacity ◽  
Reading Frames

The complete nucleotide sequence of a 6,851-base pair (bp) member of the L1Md repetitive family from a selected random isolate of the BALB/c mouse genome is reported here. Five kilobases of the element contains two overlapping reading frames of 1,137 and 3,900 bp. The entire 3,900-bp frame and the 3' 600 bp of the 1,137-bp frame, when compared with a composite consensus primate L1 sequence, show a ratio of replacement to silent site differences characteristic of protein coding sequences. This more closely defines the protein coding capacity of this repetitive family, which was previously shown to possess a large open reading frame of undetermined extent. The relative organization of the 1,137- and 3,900-bp reading frames, which overlap by 14 bp, bears resemblance to protein-coding, mobile genetic elements. Homology can be found between the amino acid sequence of the 3,900-bp frame and selected domains of several reverse transcriptases. The 5' ends of the two L1Md elements described in this report have multiple copies, 4 2/3 copies and 1 2/3 copy, of a 208-bp direct tandem repeat. The sequence of this 208-bp element differs from the sequence of a previously defined 5' end for an L1Md element, indicating that there are at least two different 5' end motifs for L1Md.

scholarly journals Mitochondrial Dual-coding Genes in Trypanosoma brucei

2017 ◽  
Author(s):  
Laura E. Kirby ◽  
Donna Koslowsky
Keyword(s):  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Genetic Drift ◽  
Mitochondrial Genes ◽  
Open Reading Frame ◽  
Dual Coding ◽  
Mutational Bias ◽  
Reading Frame ◽  
African Trypanosomes ◽  
Reading Frames

AbstractTrypanosoma brucei is transmitted between mammalian hosts by the tsetse fly. In the mammal, they are exclusively extracellular, continuously replicating within the bloodstream. During this stage, the mitochondrion lacks a functional electron transport chain (ETC). Successful transition to the fly, requires activation of the ETC and ATP synthesis via oxidative phosphorylation. This life cycle leads to a major problem: in the bloodstream, the mitochondrial genes are not under selection and are subject to genetic drift that endangers their integrity. Exacerbating this, T. brucei undergoes repeated population bottlenecks as they evade the host immune system that would create additional forces of genetic drift. These parasites possess several unique genetic features, including RNA editing of mitochondrial transcripts. RNA editing creates open reading frames by the guided insertion and deletion of U-residues within the mRNA. A major question in the field has been why this metabolically expensive system of RNA editing would evolve and persist. Here, we show that many of the edited mRNAs can alter the choice of start codon and the open reading frame by alternative editing of the 5’ end. Analyses of mutational bias indicate that six of the mitochondrial genes may be dual-coding and that RNA editing allows access to both reading frames. We hypothesize that dual-coding genes can protect genetic information by essentially hiding a non-selected gene within one that remains under selection. Thus, the complex RNA editing system found in the mitochondria of trypanosomes provides a unique molecular strategy to combat genetic drift in non-selective conditions.Author SummaryIn African trypanosomes, many of the mitochondrial mRNAs require extensive RNA editing before they can be translated. During this process, each edited transcript can undergo hundreds of cleavage/ligation events as U-residues are inserted or deleted to generate a translatable open reading frame. A major paradox has been why this incredibly metabolically expensive process would evolve and persist. In this work, we show that many of the mitochondrial genes in trypanosomes are dual-coding, utilizing different reading frames to potentially produce two very different proteins. Access to both reading frames is made possible by alternative editing of the 5’ end of the transcript. We hypothesize that dual-coding genes may work to protect the mitochondrial genes from mutations during growth in the mammalian host, when many of the mitochondrial genes are not being used. Thus, the complex RNA editing system may be maintained because it provides a unique molecular strategy to combat genetic drift.

scholarly journals Analyses of the 5-prime Ends of Escherichia coli ORFs

2021 ◽  
Author(s):  
James F Curran ◽  
Michael Ward
Keyword(s):  
Escherichia Coli ◽  
Nearest Neighbor ◽  
Initiation Site ◽  
Translational Efficiency ◽  
Translational Initiation ◽  
Reading Frame ◽  
Internal Sequence ◽  
Prime Ends ◽  
Selection For ◽  
Reading Frames

Sequence biases at 5-prime ends of coding sequences differ from those of the remainder of ORFs, reflecting differences in function. Internal sequence biases promote translational efficiency by several mechanisms including correlating codon usage and tRNA concentration. However, the early region may also facilitate translational initiation, establishment of the reading frame, and polypeptide processing. Here we examine the beginnings of the ORFs of an Escherichia coli K12 reference genome. The results extend previous observations of A-richness to include an overabundance of the AAA triplet in all reading frames, consistent with the hypothesis that the beginnings of ORFs contribute to initiation site accessibility. Results are also consistent with the idea that the first two amino acids are under selection because they facilitate solvation of the amino-terminus at the end of the ribosomal exit channel. Moreover, serine is highly overrepresented as the second amino acid, possibly because it can facilitate removal of the terminal formylmethionine. Non-AUG initiation codons are known to be less efficient than AUG at directing initiation, presumably because of relatively weak base pairing to the initiator-tRNA. But non-UAG initiation codons are not followed by unusual 3-prime nearest neighbor codons. Moreover, the four NUG initiation codons do not differ in their propensity to frameshift in an assay known to be sensitive to base pair strength. Altogether, these data suggest that the 5-prime ends of ORFs are under selection for several functions, and that initiation codon identity may not critical beyond its role in initiation.

scholarly journals Organelle Genetics in Plants

2021 ◽  
Vol 22 (4) ◽  
pp. 2104
Author(s):  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Rna Editing ◽  
Posttranscriptional Regulation ◽  
Genome Engineering ◽  
Plant Mitochondria ◽  
Plastid Dna ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Organelle Genetics ◽  
Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

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