Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA311041 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacterial mRNAs are organized into operons consisting of discrete open reading frames (ORFs) in a single polycistronic mRNA. Individual ORFs on the mRNA are differentially translated, with rates varying as much as 100-fold. The signals controlling differential translation are poorly understood. Our genome-wide mRNA secondary structure analysis indicated that operonic mRNAs are comprised of ORF-wide units of secondary structure that vary across ORF boundaries such that adjacent ORFs on the same mRNA molecule are structurally distinct. ORF translation rate is strongly correlated with its mRNA structure in vivo, and correlation persists, albeit in a reduced form, with its structure when translation is inhibited and with that of in vitro refolded mRNA. These data suggests that intrinsic ORF mRNA structure encodes a rough blueprint for translation efficiency. This structure is then amplified by translation, in a self-reinforcing loop, to provide the structure that ultimately specifies the translation of each ORF.
2017-01-30 | GSE77617 | GEO
Project description:Translation of an mRNA in eukaryotes starts at AUG in most cases. Near-cognate codons (NCCs) such as UUG, ACG and AUU are also used as start sites at low levels in S. cerevisiae. Initiation from NCCs or AUGs in the 5’-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. Using reporter assays, we found that changes in growth temperature can affect translation from NCC start sites in yeast cells, suggesting the possibility that gene expression could be regulated by temperature by altering use of different uORF start codons. Using ribosome profiling, we provide evidence that growth temperature regulates the efficiency of translation of nearly 200 uORFs in S. cerevisiae. Of these uORFs, most that start with an AUG codon have increased translational efficiency at 37 ˚C relative to 30 ˚C and decreased efficiency at 20 ˚C. For translationally regulated uORFs starting with NCCs, we did not observe a general trend for the direction of regulation as a function of temperature, suggesting mRNA-specific features can determine the mode of temperature-dependent regulation. Consistent with this conclusion, the position of the uORFs in the 5’-leader relative to the 5’-cap and the start codon of the main ORF correlates with the direction of temperature-dependent regulation of uORF translation. We have identified several novel cases in which changes in uORF translation are inversely correlated with changes in the translational efficiency of the downstream main ORF. Our data suggest that translation of these mRNAs is subject to temperature-dependent, uORF-mediated regulation. Overall, our data suggest that alterations in the translation of specific uORFs by temperature can regulate gene expression in S. cerevisiae.
2019-10-28 | GSE137021 | GEO
Project description:Developmental regulation of Canonical and small ORF translation from mRNAs
| PRJNA615808 | ENA
Project description:Translational control is a key determinant of protein abundance, which in turns defines the physiology and pathology of human cells. Initiation of translation is highly regulated in eukaryotes and is considered as the rate-limiting step of protein synthesis. mRNA secondary structures in 5’ untranslated region (UTR) and associated helicases have been characterised as key determinants of translation initiation. Nevertheless the transcriptome-wide contribution of non-canonical secondary structures, such as RNA G-quadruplexes (rG4s), to the translation of human mRNAs remains largely unappreciated. Here we use a ribosome profiling strategy to investigate the translational landscape associated to rG4s-containing mRNAs and the contribution of two rG4s-specialised DExH-box helicases, DHX9 and DHX36, to translation initiation in human cells. We show that rG4-forming sequences in 5’-UTR is associated with decreased translation efficiency which correlate with an increased ribosome density within the 5’-UTRs. We found that rG4s contribute to the translation of upstream open reading frames, and as a consequence, thwart the translation of the associated protein coding sequences (CDS). Depletion of the DHX36 and DHX9 helicases demonstrated that the formation of the rG4 structural motif rather than its nucleotide sequence mediate translation initiation. Our findings unveil a role for non-canonical structures in defining alternative 5’ starts for human mRNAs translation initiation.
2018-04-30 | GSE105082 | GEO
Project description:This is a Random Forest algorithm-based machine learning model to predict lncRNAs from coding mRNAs in plant transcriptomic data. The model assigns 1 for coding sequences and 2 for long non-coding sequences. The prediction is performed using a combination of Open Reading Frame (ORF) based, Sequence-based and Codon-bias features. Users need to download the curated ONNX model and also need to convert the sequences into feature matrix as mentioned in PLIT paper (Deshpande et al. 2019) to make predictions on sequences from Zea Mays sequence data.
2023-05-22 | BIOMD0000001067 | BioModels
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE181503 | GEO
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE169161 | GEO
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE169168 | GEO
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE169166 | GEO
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE169163 | GEO