scholarly journals Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hiro Takahashi ◽  
Shido Miyaki ◽  
Hitoshi Onouchi ◽  
Taichiro Motomura ◽  
Nobuo Idesako ◽  
...  
Keyword(s):  
Regulatory Peptides ◽  
Open Reading Frames ◽  
Dependent Manner ◽  
Wide Range ◽  
Eukaryotic Mrnas ◽  
Taxonomic Range ◽  
Upstream Open Reading Frames ◽  
Functional Peptides ◽  
Reading Frames ◽  
Animal Genomes

Abstract Upstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1517 (1373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.

scholarly journals Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes

2019 ◽  
Author(s):  
Hiro Takahashi ◽  
Shido Miyaki ◽  
Hitoshi Onouchi ◽  
Taichiro Motomura ◽  
Nobuo Idesako ◽  
...  
Keyword(s):  
Regulatory Peptides ◽  
Open Reading Frames ◽  
Dependent Manner ◽  
Wide Range ◽  
Eukaryotic Mrnas ◽  
Taxonomic Range ◽  
Upstream Open Reading Frames ◽  
Functional Peptides ◽  
Reading Frames ◽  
Animal Genomes

AbstractUpstream open reading frames (uORFs) are present in the 5’-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1,517 (1,373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.

scholarly journals DENR promotes translation reinitiation via ribosome recycling to drive expression of oncogenes including ATF4

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan Bohlen ◽  
Liza Harbrecht ◽  
Saioa Blanco ◽  
Katharina Clemm von Hohenberg ◽  
Kai Fenzl ◽  
...  
Keyword(s):  
Stress Response ◽  
Cancer Cells ◽  
Strong Correlation ◽  
Molecular Mechanisms ◽  
Open Reading Frames ◽  
Translation Efficiency ◽  
Dependent Manner ◽  
Translation Factors ◽  
Upstream Open Reading Frames ◽  
Reading Frames

Abstract Translation efficiency varies considerably between different mRNAs, thereby impacting protein expression. Translation of the stress response master-regulator ATF4 increases upon stress, but the molecular mechanisms are not well understood. We discover here that translation factors DENR, MCTS1 and eIF2D are required to induce ATF4 translation upon stress by promoting translation reinitiation in the ATF4 5′UTR. We find DENR and MCTS1 are only needed for reinitiation after upstream Open Reading Frames (uORFs) containing certain penultimate codons, perhaps because DENR•MCTS1 are needed to evict only certain tRNAs from post-termination 40S ribosomes. This provides a model for how DENR and MCTS1 promote translation reinitiation. Cancer cells, which are exposed to many stresses, require ATF4 for survival and proliferation. We find a strong correlation between DENR•MCTS1 expression and ATF4 activity across cancers. Furthermore, additional oncogenes including a-Raf, c-Raf and Cdk4 have long uORFs and are translated in a DENR•MCTS1 dependent manner.

scholarly journals Genome-wide identification of Arabidopsis non-AUG-initiated upstream ORFs with evolutionarily conserved regulatory sequences that control protein expression levels

2021 ◽  
Author(s):  
Yuta Hiragori ◽  
Hiro Takahashi ◽  
Noriya Hayashi ◽  
Shun Sasaki ◽  
Kodai Nakao ◽  
...  
Keyword(s):  
Regulatory Peptides ◽  
Inhibitory Effect ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Regulatory Sequences ◽  
Dependent Manner ◽  
Protein Coding ◽  
Genome Wide ◽  
Evolutionarily Conserved ◽  
Upstream Open Reading Frames

Upstream open reading frames (uORFs) are short ORFs found in the 5′-UTRs of many eukaryotic transcripts and can influence the translation of protein-coding main ORFs (mORFs). Recent genome-wide ribosome profiling studies have revealed that thousands of uORFs initiate translation at non-AUG start codons. However, the physiological significance of these non-AUG uORFs has so far been demonstrated for only a few of them. It is conceivable that physiologically important non-AUG uORFs are evolutionarily conserved across species. In this study, using a combination of bioinformatics and experimental approaches, we searched the Arabidopsis genome for non-AUG-initiated uORFs with conserved sequences that control the expression of the mORF-encoded proteins. As a result, we identified four novel regulatory non-AUG uORFs. Among these, two exerted repressive effects on mORF expression in an amino acid sequence-dependent manner. These two non-AUG uORFs are likely to encode regulatory peptides that cause ribosome stalling, thereby enhancing their repressive effects. In contrast, one of the identified regulatory non-AUG uORFs promoted mORF expression by alleviating the inhibitory effect of a downstream AUG-initiated uORF. These findings provide insights into the mechanisms that enable non-AUG uORFs to play regulatory roles despite their low translation initiation efficiencies.

Analysis of plant mRNA upstream open reading frames

2005 ◽  
Vol 2 (1) ◽  
pp. 59-66
Author(s):  
Jin Yong-Feng ◽  
Jin Hui-Qing ◽  
Zhou Ping ◽  
Bian Teng-Fei
Keyword(s):  
Plant Species ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Translation Efficiency ◽  
Consensus Sequences ◽  
Codon Context ◽  
Eukaryotic Mrnas ◽  
Upstream Open Reading Frames ◽  
Regulatory Functions ◽  
Reading Frames

AbstractUpstream open reading frames (uORFs) in 5′-untranslated regions (5′-UTRs) of eukaryotic mRNAs play an important role in translation efficiency. Computational analysis of the upstream ATG (uATG) and uORFs of 5′-UTRs of plant mRNAs, adopted from the nucleotide sequence databank, was carried out. Statistical analysis revealed that up to 18% of 5′-UTRs contain uATG, which is much higher than the earlier estimate. Among them, about 50% of the genes have one uATG and nearly 20% of them have two uATGs. About 85% of uORFs are non-overlapping. Thirty per cent of uORF peptides comprise 1–5 aa, and about 80% of uORFs fall in the range of below 20 aa. Sequences flanking the uATG codon differ strikingly from the functional initiation codon and the uATG triplet is more frequently located in a non-optimal context. Consensus sequences of the ATG codon context of mRNA with and without uATG are similar, whereas the ATG codon context of mRNA without uATG is more frequently located in an optimal context than is mRNA with uATG. Most mRNAs with uATGs are possibly related to regulatory functions. In addition, most mRNA uORFs have no similarity between plant species whereas sequences of a few uORFs are highly conserved. For example, mRNA uORFs encoding S-adenosyl-l-methionine decarboxylase (AdoMetDC) share 75–100% homology between plant species, which is much more conserved than AdoMetDC protein.

scholarly journals Impacts of uORF codon identity and position on translation regulation

2019 ◽  
Vol 47 (17) ◽  
pp. 9358-9367 ◽  
Author(s):  
Yizhu Lin ◽  
Gemma E May ◽  
Hunter Kready ◽  
Lauren Nazzaro ◽  
Mao Mao ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Open Reading Frames ◽  
Translation Regulation ◽  
Coding Region ◽  
Wide Range ◽  
Range Of Functions ◽  
Functional Peptides ◽  
Regulatory Functions ◽  
The Impact ◽  
Reading Frames

Abstract Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5′ mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a minority of uORFs encode conserved functional peptides, the coding regions of most uORFs are not conserved. Thus, the importance of uORF coding sequences on their regulatory functions remains largely unknown. We investigated the impact of an uORF coding region on gene regulation by assaying the functions of thousands of variants in the yeast YAP1 uORF. Varying uORF codons resulted in a wide range of functions, including repressing and enhancing expression of the downstream ORF. The presence of rare codons resulted in the most inhibitory YAP1 uORF variants. Inhibitory functions of such uORFs were abrogated by overexpression of complementary tRNA. Finally, regression analysis of our results indicated that both codon identity and position impact uORF function. Our results support a model in which a uORF coding sequence impacts its regulatory functions by altering the speed of uORF translation.

scholarly journals Conserved Peptide Upstream Open Reading Frames Act Via Ribosome Stalling to Regulate Translation in Response to Environmental Signals.

2021 ◽  
Author(s):  
Barry Causier ◽  
Tayah Hopes ◽  
Mary McKay ◽  
Zachary Paling ◽  
Brendan Davies
Keyword(s):  
Growth And Development ◽  
Open Reading Frames ◽  
Peptide Sequence ◽  
Dependent Manner ◽  
Environmental Signals ◽  
Ribosome Stalling ◽  
Mrna Transcripts ◽  
Upstream Open Reading Frames ◽  
Fine Tune ◽  
Reading Frames

The regulation of protein synthesis plays a key role in growth and development in all organisms. Upstream open reading frames (uORFs) are commonly found in eukaryotic mRNA transcripts and typically inhibit translation of downstream ORFs, in part by stalling ribosomes. Conserved peptide uORFs (CPuORFs) are a rare subset of uORFs, some of which conditionally regulate translation. Here we identify three Arabidopsis CPuORFs that specifically regulate translation of any downstream ORF, in response to the agriculturally significant environmental signals, heat shock and water limitation. Mechanistically, we provide evidence that CPuORF translation causes ribosome stalling, in a peptide sequence-dependent manner, attenuating translation of downstream ORFs. We propose a model in which plant CPuORFs are not simply on/off switches for translation, but rather act conditionally, along a continuum, to fine-tune translation dynamically.

scholarly journals Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA

2019 ◽  
Author(s):  
Hiro Takahashi ◽  
Noriya Hayashi ◽  
Yui Yamashita ◽  
Satoshi Naito ◽  
Anna Takahashi ◽  
...  
Keyword(s):  
Plant Species ◽  
Regulatory Peptides ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Cis Acting ◽  
Genome Wide ◽  
Eukaryotic Mrnas ◽  
Regulatory Effects ◽  
Functional Peptides ◽  
Taxonomic Groups

AbstractBackgroundUpstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.ResultsTo efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 88 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved in wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.ConclusionsThis study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.

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