Upstream Open Reading Frames (uORFs) in the Apicomplexan Parasites Plasmodium falciparum and Toxoplasma gondii: Small yet Powerful Regulators of Translation

During their complex life cycles, the Apicomplexan parasites, Plasmodium falciparum and Toxoplasma gondii employ several genetic switches to regulate their gene expression. One such switch is mediated at the level of translation through upstream Open Reading Frames (uORFs). As uORFs are found in the upstream regions of a majority of genes in both the parasites, it is essential that their roles in translational regulation be appreciated to a greater extent. This review provides a comprehensive summary of studies that show uORF-mediated gene regulation in these parasites and highlights examples of clinically and physiologically relevant proteins that exhibit uORF-mediated regulation. In addition to these examples, several studies that use bioinformatics, transcriptomics, proteomics, and ribosome profiling also indicate the possibility of widespread translational regulation by uORFs. Further analysis of genome-wide datasets will reveal novel genes involved in key biological pathways such as cell-cycle progression, stress-response, and pathogenicity. The cumulative evidence from studies presented in this review suggests that uORFs will play crucial roles in regulating gene expression during clinical disease caused by these important human pathogens.

The role of upstream open reading frames in translation regulation in the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii

Parasitology ◽

10.1017/s0031182021000937 ◽

2021 ◽

pp. 1-45

Author(s):

Chhaminder Kaur ◽

Swati Patankar

Keyword(s):

Plasmodium Falciparum ◽

Toxoplasma Gondii ◽

Open Reading Frames ◽

Translation Regulation ◽

Apicomplexan Parasites ◽

Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells

Biomedicines ◽

10.3390/biomedicines9080911 ◽

2021 ◽

Vol 9 (8) ◽

pp. 911

Author(s):

Joana Silva ◽

Pedro Nina ◽

Luísa Romão

Keyword(s):

Translational Regulation ◽

Regulatory Elements ◽

Ribosome Profiling ◽

Leader Sequence ◽

Open Reading Frames ◽

Regulatory Function ◽

Coding Sequence ◽

Abc Protein ◽

ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.

uORF Shuffling Fine-Tunes Gene Expression at a Deep Level of the Process

Plants ◽

10.3390/plants9050608 ◽

2020 ◽

Vol 9 (5) ◽

pp. 608

Author(s):

Yukio Kurihara

Keyword(s):

Gene Expression ◽

Deep Level ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Protein Coding ◽

Polycistronic Mrna ◽

Fine Tune ◽

Insight Into ◽

Upstream open reading frames (uORFs) are present in the 5’ leader sequences (or 5’ untranslated regions) upstream of the protein-coding main ORFs (mORFs) in eukaryotic polycistronic mRNA. It is well known that a uORF negatively affects translation of the mORF. Emerging ribosome profiling approaches have revealed that uORFs themselves, as well as downstream mORFs, can be translated. However, it has also been revealed that plants can fine-tune gene expression by modulating uORF-mediated regulation in some situations. This article reviews several proposed mechanisms that enable genes to escape from uORF-mediated negative regulation and gives insight into the application of uORF-mediated regulation for precisely controlling gene expression.

A First Step towards Learning which uORFs Regulate Gene Expression

Journal of Integrative Bioinformatics ◽

10.1515/jib-2006-31 ◽

2006 ◽

Vol 3 (2) ◽

pp. 109-122 ◽

Cited By ~ 1

Author(s):

◽

Christopher H. Bryant ◽

Graham J.L. Kemp ◽

Marija Cvijovic

Keyword(s):

Gene Expression ◽

Inductive Logic ◽

Preliminary Evidence ◽

Open Reading Frames ◽

Yeast Saccharomyces Cerevisiae ◽

Regulate Gene Expression ◽

Integrative System ◽

Reading Frames ◽

Regulate Gene

Summary We have taken a first step towards learning which upstream Open Reading Frames (uORFs) regulate gene expression (i.e., which uORFs are functional) in the yeast Saccharomyces cerevisiae. We do this by integrating data from several resources and combining a bioinformatics tool, ORF Finder, with a machine learning technique, inductive logic programming (ILP). Here, we report the challenge of using ILP as part of this integrative system, in order to automatically generate a model that identifies functional uORFs. Our method makes searching for novel functional uORFs more efficient than random sampling. An attempt has been made to predict novel functional uORFs using our method. Some preliminary evidence that our model may be biologically meaningful is presented.

Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

10.1101/021501 ◽

2015 ◽

Cited By ~ 2

Author(s):

David E Weinberg ◽

Premal Shah ◽

Stephen W Eichhorn ◽

Jeffrey A Hussmann ◽

Joshua B Plotkin ◽

...

Keyword(s):

Translational Control ◽

Nucleotide Composition ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Untranslated Regions ◽

Coding Regions ◽

Genome Wide ◽

Improved Methods ◽

Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5′- untranslated regions. Collectively, our results reveal key features of translational control in yeast and provide a framework for executing and interpreting ribosome- profiling studies.

Tuning gene expression with synthetic upstream open reading frames

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1305590110 ◽

2013 ◽

Vol 110 (28) ◽

pp. 11284-11289 ◽

Cited By ~ 68

Author(s):

J. P. Ferreira ◽

K. W. Overton ◽

C. L. Wang

Keyword(s):

Gene Expression ◽

Open Reading Frames ◽

uORF-Tools – Workflow for the determination of translation-regulatory upstream open reading frames

10.1101/415018 ◽

2018 ◽

Cited By ~ 1

Author(s):

Anica Scholz ◽

Florian Eggenhofer ◽

Rick Gelhausen ◽

Björn Grüning ◽

Kathi Zarnack ◽

...

Keyword(s):

Ribosome Profiling ◽

Open Reading Frames ◽

Annotation File ◽

Inhibitory Effects ◽

Protein Coding ◽

Reading Frame ◽

Induced Changes ◽

AbstractRibosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding sequence of mRNAs. However, commonly reads are also found within the transcript leader sequence (TLS) (aka 5’ untranslated region) preceding the main open reading frame (ORF), indicating the translation of regulatory upstream ORFs (uORFs). Here, we present a workflow for the identification of translation-regulatory uORFs. Specifically, uORF-Tools identifies uORFs within a given dataset and generates a uORF annotation file. In addition, a comprehensive human uORF annotation file, based on 35 ribo-seq files, is provided, which can serve as an alternative input file for the workflow. To assess the translation-regulatory activity of the uORFs, stimulus-induced changes in the ratio of the RPFs residing in the main ORFs relative to those found in the associated uORFs are determined. The resulting output file allows for the easy identification of candidate uORFs, which have translation-inhibitory effects on their associated main ORFs. uORF-Tools is available as a free and open Snakemake workflow at https://github.com/Biochemistry1-FFM/uORF-Tools. It is easily installed and all necessary tools are provided in a version-controlled manner, which also ensures lasting usability. uORF-Tools is designed for intuitive use and requires only limited computing times and resources.

Autonomous functionality of an upstream open reading frame in polycistronic mammalian mRNAs

10.1101/325571 ◽

2018 ◽

Author(s):

Shohei Kitano ◽

Gabriel Pratt ◽

Keizo Takao ◽

Yasunori Aizawa

Keyword(s):

Brain Regions ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Upstream Open Reading Frame ◽

Translation Regulation ◽

Reading Frame ◽

Eukaryotic Translation ◽

Human And Mouse ◽

SUMMARYUpstream open reading frames (uORFs) are established as cis-acting elements for eukaryotic translation of annotated ORFs (anORFs) located on the same mRNAs. Here, we identified a mammalian uORF with functions that are independent from anORF translation regulation. Bioinformatics screening using ribosome profiling data of human and mouse brains yielded 308 neurologically vital genes from which anORF and uORFs are polycistronically translated in both species. Among them, Arhgef9 contains a uORF named SPICA, which is highly conserved among vertebrates and stably translated only in specific brain regions of mice. Disruption of SPICA translation by ATG-to-TAG substitutions did not perturb translation or function of its anORF product, collybistin. SPICA-null mice displayed abnormal maternal reproductive performance and enhanced anxiety-like behavior, characteristic of ARHGEF9-associated neurological disorders. This study demonstrates that mammalian uORFs can be independent genetic units, revising the prevailing dogma of the monocistronic gene in mammals, and even eukaryotes.

RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs

10.1101/223073 ◽

2017 ◽

Cited By ~ 1

Author(s):

Pierre Murat ◽

Giovanni Marsico ◽

Barbara Herdy ◽

Avazeh Ghanbarian ◽

Guillem Portella ◽

...

Keyword(s):

Secondary Structures ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Untranslated Regions ◽

Translation Regulation ◽

Physical Interaction ◽

Protein Coding ◽

Nucleotide Resolution ◽

ABSTRACTRNA secondary structures in the 5’ untranslated regions (UTRs) of mRNAs have been characterised as key determinants of translation initiation. However the role of non-canonical secondary structures, such as RNA G-quadruplexes (rG4s), in modulating translation of human mRNAs and the associated mechanisms remain largely unappreciated. Here we use a ribosome profiling strategy to investigate the translational landscape of human mRNAs with structured 5’ untranslated regions (5’-UTR). We found that inefficiently translated mRNAs, containing rG4-forming sequences in their 5’-UTRs, have an accumulation of ribosome footprints in their 5’-UTRs. We show that rG4-forming sequences are determinants of 5’-UTR translation, suggesting that the folding of rG4 structures thwarts the translation of protein coding sequences (CDS) by stimulating the translation of repressive upstream open reading frames (uORFs). To support our model, we demonstrate that depletion of two rG4s-specialised DEAH-box helicases, DHX36 and DHX9, shifts translation towards rG4-containing uORFs reducing the translation of selected transcripts comprising proto-oncogenes, transcription factors and epigenetic regulators. Transcriptome-wide identification of DHX9 binding sites using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) demonstrate that translation regulation is mediated through direct physical interaction between the helicase and its rG4 substrate. Our findings unveil a previously unknown role for non-canonical structures in governing 5’-UTR translation and suggest that the interaction of helicases with rG4s could be considered as a target for future therapeutic intervention.