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The role of upstream open reading frames in translation regulation in the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii. Parasitology 2021; 148:1277-1287. [PMID: 34099078 PMCID: PMC8383288 DOI: 10.1017/s0031182021000937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During their complex life cycles, the Apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii employ several layers of regulation of their gene expression. One such layer 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 transcripts 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 genes, including var2csa in P. falciparum, and ApiAT1 in T. gondii, 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 these genome-wide datasets, taking into account uORFs associated with each gene, 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.
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Robert F, Pelletier J. Exploring the Impact of Single-Nucleotide Polymorphisms on Translation. Front Genet 2018; 9:507. [PMID: 30425729 PMCID: PMC6218417 DOI: 10.3389/fgene.2018.00507] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/10/2018] [Indexed: 01/08/2023] Open
Abstract
Over the past 15 years, sequencing of the human genome and The Cancer Genome Atlas (TCGA) project have led to comprehensive lists of single-nucleotide polymorphisms (SNPs) and gene mutations across a large number of human samples. However, our ability to predict the functional impact of SNPs and mutations on gene expression is still in its infancy. Here, we provide key examples to help understand how mutations present in genes can affect translational output.
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Affiliation(s)
- Francis Robert
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC, Canada.,Department of Oncology, McGill University, Montreal, QC, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
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Jones L, Goode L, Davila E, Brown A, McCarthy DM, Sharma N, Bhide PG, Armata IA. Translational effects and coding potential of an upstream open reading frame associated with DOPA Responsive Dystonia. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1171-1182. [PMID: 28366877 DOI: 10.1016/j.bbadis.2017.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/17/2017] [Accepted: 03/29/2017] [Indexed: 01/08/2023]
Abstract
Upstream open reading frames (uORFs) have emerged as major post-transcriptional regulatory elements in eukaryotic species. In general, uORFs are initiated by a translation start codon within the 5' untranslated region of a gene (upstream ATG; uATG), and they are negatively correlated with translational efficiency. In addition to their translational regulatory role, some uORFs can code for biologically active short peptides. The importance of uATGs/uORFs is further underscored by human diseases associated with single nucleotide polymorphisms (SNPs), which disrupt existing uORFs or introduce novel uORFs. Although several functional proteins translated from naturally occurring uORFs have been described, the coding potential of uORFs created by SNPs has been ignored because of the a priori assumption that these proteins are short-lived with no likely impact on protein homeostasis. Thus, studies on SNP-created uORFs are limited to their translational effects, leaving unexplored the potential cellular consequences of a SNP/uORF-encoded protein. Here, we investigate functionality of a uATG/uORF introduced by a +142C>T SNP within the GCH1 gene and associated with a familial form of DOPA Responsive Dystonia. We report that the +142C>T SNP represses GCH1 translation, and introduces a short, frame shifted uORF that encodes a 73-amino acid peptide. This peptide is localized within the nucleus and compromises cell viability upon proteasome inhibition. Our work extends the list of uATG/uORF associated diseases and advances research on peptides translated from SNP-introduced uORFs, a neglected component of the proteome.
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Affiliation(s)
- Lataisia Jones
- Center for Brain Repair and Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Lacy Goode
- Center for Brain Repair and Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Eduardo Davila
- Center for Brain Repair and Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Amber Brown
- Center for Brain Repair and Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Deirdre M McCarthy
- Center for Brain Repair and Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Pradeep G Bhide
- Center for Brain Repair and Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA.
| | - Ioanna A Armata
- Center for Brain Repair and Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA.
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