The Functions of the Multiproduct and Rapidly Evolving dec-1 Eggshell Gene Are Conserved Between Evolutionarily Distant Species of Drosophila

Abstract The Drosophila dec-1 gene encodes multiple proteins that are required for female fertility and proper eggshell morphogenesis. Genetic and immunolocalization data suggest that the different DEC-1 proteins are functionally distinct. To identify regions within the proteins with potential biological significance, we cloned and sequenced the D. yakuba and D. virilis dec-1 homologs. Interspecies comparisons of the predicted translation products revealed rapidly evolving sequences punctuated by blocks of conserved amino acids. Despite extensive amino acid variability, the proteins produced by the different dec-1 homologs were functionally interchangeable. The introduction of transgenes containing either the D. yakuba or the D. virilis dec-1 open reading frames into a D. melanogaster DEC-1 protein null mutant was sufficient to restore female fertility and wild-type eggshell morphology. Normal expression and extracellular processing of the DEC-1 proteins was correlated with the phenotypic rescue. The nature of the conserved features highlighted by the evolutionary comparison and the molecular resemblance of some of these features to those found in other extracellular proteins suggests functional correlates for some of the multiple DEC-1 derivatives.

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Disrupting upstream translation in mRNAs is associated with human disease

Nature Communications ◽

10.1038/s41467-021-21812-1 ◽

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.

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Long antiparallel open reading frames are unlikely to be encoding essential proteins in prokaryotic genomes

10.1101/724807 ◽

2019 ◽

Author(s):

Denis Moshensky ◽

Andrei Alexeevski

Keyword(s):

Negative Selection ◽

Stop Codon ◽

Biological Significance ◽

Open Reading Frames ◽

Overlapping Genes ◽

Base Pairs ◽

Protein Coding ◽

Essential Proteins ◽

Prokaryotic Genomes ◽

Reading Frames

AbstractThe origin and evolution of genes that have common base pairs (overlapping genes) are of particular interest due to their influencing each other. Especially intriguing are gene pairs with long overlaps. In prokaryotes, co-directional overlaps longer than 60 bp were shown to be nonexistent except for some instances. A few antiparallel prokaryotic genes with long overlaps were described in the literature. We have analyzed putative long antiparallel overlapping genes to determine whether open reading frames (ORFs) located opposite to genes (antiparallel ORFs) can be protein-coding genes.We have confirmed that long antiparallel ORFs (AORFs) are observed reliably to be more frequent than expected. There are 10 472 000 AORFs in 929 analyzed genomes with overlap length more than 180 bp. Stop codons on the opposite to the coding strand are avoided in 2 898 cases with Benjamini-Hochberg threshold 0.01.Using Ka/Ks ratio calculations, we have revealed that long AORFs do not affect the type of selection acting on genes in a vast majority of cases. This observation indicates that long AORFs translations commonly are not under negative selection.The demonstrative example is 282 longer than 1 800 bp AORFs found opposite to extremely conserved dnaK genes. Translations of these AORFs were annotated “glutamate dehydrogenases” and were included into Pfam database as third protein family of glutamate dehydrogenases, PF10712. Ka/Ks analysis has demonstrated that if these translations correspond to proteins, they are not subjected by negative selection while dnaK genes are under strong stabilizing selection. Moreover, we have found other arguments against the hypothesis that these AORFs encode essential proteins, proteins indispensable for cellular machinery.However, some AORFs, in particular, dnaK related, have been found slightly resisting to synonymous changes in genes. It indicates the possibility of their translation. We speculate that translations of certain AORFs might have a functional role other than encoding essential proteins.Essential genes are unlikely to be encoded by AORFs in prokaryotic genomes. Nevertheless, some AORFs might have biological significance associated with their translations.Author summaryGenes that have common base pairs are called overlapping genes. We have examined the most intriguing case: if gene pairs encoded on opposite DNA strands exist in prokaryotes. An intersection length threshold 180 bp has been used. A few such pairs of genes were experimentally confirmed.We have detected all long antiparallel ORFs in 929 prokaryotic genomes and have found that the number of open reading frames, located opposite to annotated genes, is much more than expected according to statistical model. We have developed a measure of stop codon avoidance on the opposite strand. The lengths of found antiparallel ORFs with stop codon avoidance are typical for prokaryotic genes.Comparative genomics analysis shows that long antiparallel ORFs (AORFs) are unlikely to be essential protein-coding genes. We have analyzed distributions of features typical for essential proteins among formal translations of all long AORFs: prevalence of negative selection, non-uniformity of a conserved positions distribution in a multiple alignment of homologous proteins, the character of homologs distribution in phylogenetic tree of prokaryotes. All of them have not been observed for the majority of long AORFs. Particularly, the same results have been obtained for some experimentally confirmed AOGs.Thus, pairs of antiparallel overlapping essential genes are unlikely to exist. On the other hand, some antiparallel ORFs affect the evolution of genes opposite that they are located. Consequently, translations of some antiparallel ORFs might have yet unknown biological significance.

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Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins

Journal of Virology ◽

10.1128/jvi.02480-09 ◽

2010 ◽

Vol 84 (9) ◽

pp. 4330-4340 ◽

Cited By ~ 64

Author(s):

Ewan P. Plant ◽

Rasa Rakauskaitė ◽

Deborah R. Taylor ◽

Jonathan D. Dinman

Keyword(s):

Hepatitis Virus ◽

Biological Significance ◽

Open Reading Frames ◽

Nonstructural Proteins ◽

Virus Propagation ◽

Ribosomal Frameshifting ◽

Golden Mean ◽

Encoded Proteins ◽

Upstream Open Reading Frames ◽

Reading Frames

ABSTRACT In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed −1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the −1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a “golden mean” model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

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Detection and Analysis of C-to-U RNA Editing in Rice Mitochondria-Encoded ORFs

Plants ◽

10.3390/plants9101277 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1277

Author(s):

Peng Zheng ◽

Dongxin Wang ◽

Yuqing Huang ◽

Hao Chen ◽

Hao Du ◽

...

Keyword(s):

Rna Editing ◽

Sanger Sequencing ◽

Open Reading Frames ◽

Rna Modification ◽

Rna Seq ◽

Functional Consequence ◽

Precise Information ◽

Conserved Amino Acids ◽

Reading Frames ◽

Biological Context

Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA modification and is almost omnipresent in plant chloroplasts and mitochondria. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alterations needs to be investigated further. Here, by means of Sanger sequencing and publicly available RNA-seq data, we identified a total of 569 C-to-U editing sites in rice mitochondria-encoded open reading frames (ORFs), 85.41% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, based on the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 569 C-to-U RNA editing sites in their biological context. More precise information about C-to-U editing sites in rice mitochondria-encoded ORFs will facilitate our investigation on the function of C-to-U editing events in rice and also provide a valid benchmark from rice for the analysis of mitochondria C-to-U editing in other plant species.

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