scholarly journals The 5'- and 3'-untranslated regions of ornithine decarboxylase mRNA affect the translational efficiency.

1990 ◽  
Vol 265 (20) ◽  
pp. 11810-11816
Author(s):  
A Grens ◽  
I E Scheffler
Keyword(s):  
Ornithine Decarboxylase ◽  
Untranslated Regions ◽  
Translational Efficiency

scholarly journals Co-operation of the 5′ and 3′ untranslated regions of ornithine decarboxylase mRNA and inhibitory role of its 3′ untranslated region in regulating the translational efficiency of hybrid RNA species via cellular factor(s)

1997 ◽  
Vol 326 (2) ◽  
pp. 361-367 ◽  
Author(s):  
Erna C. LORENZINI ◽  
Immo E. SCHEFFLER
Keyword(s):  
Ornithine Decarboxylase ◽  
Untranslated Region ◽  
Expression Vectors ◽  
Serum Starvation ◽  
Translational Efficiency ◽  
Cellular Factor ◽  
Mrna Species ◽  
Inhibitory Role ◽  
Partial Release

The 5′ untranslated region (UTR) has an inhibitory role in the translatability of ornithine decarboxylase (ODC) mRNA and of hybrid mRNA species, whereas the ODC 3′ UTR causes a partial release of this inhibition. We designed experiments to explore whether the co-operation between ODC 5′ UTR and 3′ UTR in the translational regulation is due to a direct interaction of those sequences or whether it is mediated by their interaction with cellular factor(s). We stably transfected Chinese hamster ovary (CHO)-K1 cells and transiently transfected COS-1 cells with expression vectors carrying different chimaeric DNAs having the luciferase (LUC) coding sequence as reporter gene, the ODC 5′ UTR or the ODC 3′ UTR, or both, in the appropriate positions. We compared the results obtained by assaying the LUC activities of both transfected cell lines with each chimaeric DNA with those observed by translating the hybrid RNAs in a translation system in vitro. When the ODC 3′ UTR was present, we observed a partial release of the translation inhibition owing to the ODC 5′ UTR only in vivo. The releasing effect was restored in vitro by the addition of cytoplasmic extracts from wild-type CHO-K1 or COS-1 cells, prepared 2 and 8 h after their release from serum starvation. We also observed a partial inhibition of the translatability of the hybrid RNA owing to the presence of the ODC 3′ UTR itself; the translational efficiency could be rescued by cell extract from 8 h serum-stimulated cells. The co-operation between the ODC-UTRs might be mediated by factors expressed by cells during particular phases of the cell cycle. Excess copies of the ODC-UTRs, expressed in trans, could compete in binding limited amounts of such regulatory factors and remove them from interaction with the endogenous ODC mRNA. This phenomenon should be reflected by modifications of the kinetics of ODC and/or LUC activities during serum stimulation. The overexpression of the ODC 3′ UTR determined an increase in both endogenous ODC activity and LUC activity. Moreover, in the transfectants expressing the hybrid RNA species bearing the ODC 3′ UTR the basal ODC activity is higher than that observed in control cells. We suggest that excess copies of the ODC 3′ UTR mis-regulate the endogenous ODC translatability, probably by tying up regulatory molecules expressed by cells in limited amounts and sequestering them from the ODC mRNA species they should interact with.

scholarly journals ­ Functional Characterization of 5’ UTR Cis-Acting Sequence Elements That Modulate Translational Efficiency in P. Falciparum and Humans

2021 ◽  
Author(s):  
Valentina E. Garcia ◽  
Rebekah Dial ◽  
Joseph L DeRisi
Keyword(s):  
Translational Regulation ◽  
Base Composition ◽  
Functional Characterization ◽  
Gc Content ◽  
Untranslated Regions ◽  
Model Organisms ◽  
Translational Efficiency ◽  
Regulatory Sequences ◽  
The Impact

Abstract BackgroundThe eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common antimalarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5’ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency. MethodsHere, we deployed in vitro translation to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5’ untranslated regions, were characterized. ResultsThe density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5’ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had nonadditive effects. The base composition of the 5’ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. ConclusionWhile translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context.

scholarly journals Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

2022 ◽  
Vol 21 (1) ◽  
Author(s):  
Valentina E. Garcia ◽  
Rebekah Dial ◽  
Joseph L. DeRisi
Keyword(s):  
Plasmodium Falciparum ◽  
Translational Regulation ◽  
Base Composition ◽  
Functional Characterization ◽  
In Vitro Translation ◽  
Untranslated Regions ◽  
Model Organisms ◽  
Translational Efficiency ◽  
Regulatory Sequences ◽  
The Impact

Abstract Background The eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common anti-malarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5′ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency. Methods Here, in vitro translation is deployed to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5′ untranslated regions, were characterized. Results The density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5′ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had non-additive effects. The base composition of the 5′ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. Conclusions While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context.

scholarly journals Importance of the 3′ untranslated region of ornithine decarboxylase mRNA in the translational regulation of the enzyme

2001 ◽  
Vol 356 (2) ◽  
pp. 627-634 ◽  
Author(s):  
Eva LÖVKVIST WALLSTRÖM ◽  
Koichi TAKAO ◽  
Anna WENDT ◽  
Cristina VARGIU ◽  
Hong YIN ◽  
...  
Keyword(s):  
Feedback Control ◽  
Ornithine Decarboxylase ◽  
Translational Control ◽  
Translational Regulation ◽  
Chinese Hamster Ovary Cells ◽  
Chinese Hamster ◽  
Specific Effect ◽  
Untranslated Regions ◽  
Ovary Cells ◽  
Stable Transfectants

Translational regulation of ornithine decarboxylase (ODC), which catalyses the first step in the biosynthesis of polyamines, appears to be an important mechanism in the strong feedback control as well as in the hypotonic induction of the enzyme. However, the exact mechanisms are not yet understood. The ODC mRNA has long 5′ and 3′ untranslated regions (UTRs) which may be involved in the translational control of the enzyme. In the present study we have used a series of stable transfectants of Chinese Hamster ovary cells expressing ODC mRNAs with various truncations in the 5′ and 3′ UTRs to investigate the importance of these regions. It is demonstrated that neither the 5′ UTR nor the 3′ UTR appears to be involved in the polyamine-mediated feedback control of ODC synthesis. The hypotonic induction of ODC, on the other hand, was shown to be highly dependent on the presence of the 3′ UTR, but not on the 5′ UTR, of ODC mRNA. Cells expressing ODC mRNAs lacking the 3′ UTR showed no, or only a very slight, induction of ODC whether the 5′ UTR was present or not, whereas the cell lines expressing ODC mRNAs containing the 3′ UTR (with or without the 5′ UTR) markedly induced ODC after a hypotonic shock. The present finding of a role for the ODC mRNA 3′ UTR in the hypotonic induction of ODC is the first demonstration of a specific effect of the 3′ UTR in the regulation of ODC.

scholarly journals Effects of mRNA Untranslated Regions on Translational Efficiency of NMDA Receptor Subunits

Neurosignals ◽  
2004 ◽  
Vol 13 (4) ◽  
pp. 194-206 ◽  
Author(s):  
Antonius M.J. VanDongen ◽  
Hendrika M.A. VanDongen
Keyword(s):  
Nmda Receptor ◽  
Untranslated Regions ◽  
Translational Efficiency ◽  
Nmda Receptor Subunits

scholarly journals Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation

mSystems ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Jan Karlsen ◽  
Johannes Asplund-Samuelsson ◽  
Quentin Thomas ◽  
Michael Jahn ◽  
Elton P. Hudson
Keyword(s):  
Gene Regulation ◽  
Stress Response ◽  
Translational Control ◽  
Carbon Starvation ◽  
Ribosome Profiling ◽  
Untranslated Regions ◽  
Translational Efficiency ◽  
Data Set ◽  
Stress Response Genes ◽  
Regulation Strategies

ABSTRACT Cyanobacteria experience both rapid and periodic fluctuations in light and inorganic carbon (Ci) and have evolved regulatory mechanisms to respond to these, including extensive posttranscriptional gene regulation. We report the first genome-wide ribosome profiling data set for cyanobacteria, where ribosome occupancy on mRNA is quantified with codon-level precision. We measured the transcriptome and translatome of Synechocystis during autotrophic growth before (high carbon [HC] condition) and 24 h after removing CO2 from the feedgas (low carbon [LC] condition). Ribosome occupancy patterns in the 5′ untranslated region suggest that ribosomes can assemble there and slide to the Shine-Dalgarno site, where they pause. At LC, total translation was reduced by 80% and ribosome pausing was increased at stop and start codons and in untranslated regions, which may be a sequestration mechanism to inactivate ribosomes in response to rapid Ci depletion. Several stress response genes, such as thioredoxin M (sll1057), a putative endonuclease (slr0915), protease HtrA (slr1204), and heat shock protein HspA (sll1514) showed marked increases in translational efficiency at LC, indicating translational control in response to Ci depletion. Ribosome pause scores within open reading frames were mostly constant, though several ribosomal proteins had significantly altered pause score distributions at LC, which might indicate translational regulation of ribosome biosynthesis in response to Ci depletion. We show that ribosome profiling is a powerful tool to decipher dynamic gene regulation strategies in cyanobacteria. IMPORTANCE Ribosome profiling accesses the translational step of gene expression via deep sequencing of ribosome-protected mRNA footprints. Pairing of ribosome profiling and transcriptomics data provides a translational efficiency for each gene. Here, the translatome and transcriptome of the model cyanobacterium Synechocystis were compared under carbon-replete and carbon starvation conditions. The latter may be experienced when cyanobacteria are cultivated in poorly mixed bioreactors or engineered to be product-secreting cell factories. A small fraction of genes (<200), including stress response genes, showed changes in translational efficiency during carbon starvation, indicating condition-dependent translation-level regulation. We observed ribosome occupancy in untranslated regions, possibly due to an alternative translation initiation mechanism in Synechocystis. The higher proportion of ribosomes residing in untranslated regions during carbon starvation may be a mechanism to quickly inactivate superfluous ribosomes. This work provides the first ribosome profiling data for cyanobacteria and reveals new regulation strategies for coping with nutrient limitation.

scholarly journals Functional characterization of 5’ UTR cis-acting sequence elements that modulate translational efficiency in P. falciparum and humans

2021 ◽  
Author(s):  
Valentina E. Garcia ◽  
Rebekah Dial ◽  
Joseph L. DeRisi
Keyword(s):  
Translational Regulation ◽  
Base Composition ◽  
Functional Characterization ◽  
Protein Translation ◽  
Untranslated Regions ◽  
Translational Efficiency ◽  
Regulatory Sequences ◽  
Termination Status ◽  
The Impact

AbstractThe eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually and drug resistance to common antimalarials confounds eradication efforts. Protein translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. Translation initiation drives translational efficiency and is regulated by both cis and trans acting factors. P. falciparum mRNAs feature unusual 5’ untranslated regions suggesting that cis-acting sequences could play a significant role in determining translational efficiency. Here, we deployed in vitro translation to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream start site, in addition to the base composition of the 5’ untranslated regions, were characterized. Within 130 nucleotide 5’ untranslated regions, upstream start sites were generally repressive but exhibited a nonadditive effect when combined, while the base composition of the two mRNAs demonstrated a more subtle role in regulating translational efficacy. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discreet cis-acting features.

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