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Bhattacharya A, Renault TT, Innis CA. The ribosome as a small-molecule sensor. Curr Opin Microbiol 2024; 77:102418. [PMID: 38159358 DOI: 10.1016/j.mib.2023.102418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Sensing small molecules is crucial for microorganisms to adapt their genetic programs to changes in their environment. Arrest peptides encoded by short regulatory open reading frames program the ribosomes that translate them to undergo translational arrest in response to specific metabolites. Ribosome stalling in turn controls the expression of downstream genes on the same messenger RNA by translational or transcriptional means. In this review, we present our current understanding of the mechanisms by which ribosomes translating arrest peptides sense different metabolites, such as antibiotics or amino acids, to control gene expression.
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Affiliation(s)
- Arunima Bhattacharya
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thibaud T Renault
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - C Axel Innis
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, F-33600 Pessac, France.
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2
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Gaikwad S, Ghobakhlou F, Zhang H, Hinnebusch AG. Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo. eLife 2024; 12:RP92916. [PMID: 38266075 PMCID: PMC10945734 DOI: 10.7554/elife.92916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S preinitiation complex (PIC) that attaches to the mRNA and scans the 5'-untranslated region (5' UTR) for an AUG start codon. Previous studies have implicated mammalian eIF2A in GTP-independent binding of Met-tRNAi to the 40S subunit and its recruitment to specialized mRNAs that do not require scanning, and in initiation at non-AUG start codons, when eIF2 function is attenuated by phosphorylation of its α-subunit during stress. The role of eIF2A in translation in vivo is poorly understood however, and it was unknown whether the conserved ortholog in budding yeast can functionally substitute for eIF2. We performed ribosome profiling of a yeast deletion mutant lacking eIF2A and isogenic wild-type (WT) cells in the presence or absence of eIF2α phosphorylation induced by starvation for amino acids isoleucine and valine. Whereas starvation of WT confers changes in translational efficiencies (TEs) of hundreds of mRNAs, the eIF2AΔ mutation conferred no significant TE reductions for any mRNAs in non-starved cells, and it reduced the TEs of only a small number of transcripts in starved cells containing phosphorylated eIF2α. We found no evidence that eliminating eIF2A altered the translation of mRNAs containing putative internal ribosome entry site (IRES) elements, or harboring uORFs initiated by AUG or near-cognate start codons, in non-starved or starved cells. Thus, very few mRNAs (possibly only one) appear to employ eIF2A for Met-tRNAi recruitment in yeast cells, even when eIF2 function is attenuated by stress.
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Affiliation(s)
- Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Fardin Ghobakhlou
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Hongen Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
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3
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Gaikwad S, Ghobakhlou F, Zhang H, Hinnebusch AG. Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561292. [PMID: 37986989 PMCID: PMC10659434 DOI: 10.1101/2023.10.06.561292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S preinitiation complex (PIC) that attaches to the mRNA and scans the 5'-untranslated region (5' UTR) for an AUG start codon. Previous studies have implicated mammalian eIF2A in GTP-independent binding of Met-tRNAi to the 40S subunit and its recruitment to specialized mRNAs that do not require scanning, and in initiation at non-AUG start codons, when eIF2 function is attenuated by phosphorylation of its α-subunit during stress. The role of eIF2A in translation in vivo is poorly understood however, and it was unknown whether the conserved ortholog in budding yeast can functionally substitute for eIF2. We performed ribosome profiling of a yeast deletion mutant lacking eIF2A and isogenic wild-type (WT) cells in the presence or absence of eIF2α phosphorylation induced by starvation for amino acids isoleucine and valine. Whereas starvation of WT confers changes in translational efficiencies (TEs) of hundreds of mRNAs, the eIF2AΔ mutation conferred no significant TE reductions for any mRNAs in non-starved cells, and it reduced the TEs of only a small number of transcripts in starved cells containing phosphorylated eIF2α. We found no evidence that eliminating eIF2A altered the translation of mRNAs containing putative IRES elements, or harboring uORFs initiated by AUG or near-cognate start codons, in non-starved or starved cells. Thus, very few mRNAs (possibly only one) appear to employ eIF2A for Met-tRNAi recruitment in yeast cells, even when eIF2 function is attenuated by stress.
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Affiliation(s)
- Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Fardin Ghobakhlou
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
- Current affiliations: Department of Microbiology, Infectiology & Immunology, Faculty of Medicine, University of Montreal, Canada, H3T 1J4
| | - Hongen Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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4
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Treichel AJ, Bazzini AA. Casting CRISPR-Cas13d to fish for microprotein functions in animal development. iScience 2022; 25:105547. [PMID: 36444300 PMCID: PMC9700322 DOI: 10.1016/j.isci.2022.105547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Protein coding genes were originally identified with sequence-based definitions that included a 100-codon cutoff to avoid annotating irrelevant open reading frames. However, many active proteins contain less than 100 amino acids. Indeed, functional genetics, ribosome profiling, and proteomic profiling have identified many short, translated open reading frames, including those with biologically active peptide products (microproteins). Yet, functions for most of these peptide products remain unknown. Because microproteins often act as key signals or fine-tune processes, animal development has already revealed functions for a handful of microproteins and provides an ideal context to uncover additional microprotein functions. However, many mRNAs during early development are maternally provided and hinder targeted mutagenesis approaches to characterize developmental microprotein functions. The recently established, RNA-targeting CRISPR-Cas13d system in zebrafish overcomes this barrier and produces potent knockdown of targeted mRNA, including maternally provided mRNA, and enables flexible, efficient interrogation of microprotein functions in animal development.
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Affiliation(s)
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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The dark proteome: translation from noncanonical open reading frames. Trends Cell Biol 2022; 32:243-258. [PMID: 34844857 PMCID: PMC8934435 DOI: 10.1016/j.tcb.2021.10.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023]
Abstract
Omics-based technologies have revolutionized our understanding of the coding potential of the genome. In particular, these studies revealed widespread unannotated open reading frames (ORFs) throughout genomes and that these regions have the potential to encode novel functional (micro-)proteins and/or hold regulatory roles. However, despite their genomic prevalence, relatively few of these noncanonical ORFs have been functionally characterized, likely in part due to their under-recognition by the broader scientific community. The few that have been investigated in detail have demonstrated their essentiality in critical and divergent biological processes. As such, here we aim to discuss recent advances in understanding the diversity of noncanonical ORFs and their roles, as well as detail biologically important examples within the context of the mammalian genome.
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Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs. Proc Natl Acad Sci U S A 2021; 118:2018899118. [PMID: 34593629 PMCID: PMC8501901 DOI: 10.1073/pnas.2018899118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 02/01/2023] Open
Abstract
Approximately 40% of human messenger RNAs (mRNAs) contain upstream open reading frames (uORFs) in their 5' untranslated regions. Some of these uORF sequences, thought to attenuate scanning ribosomes or lead to mRNA degradation, were recently shown to be translated, although the function of the encoded peptides remains unknown. Here, we show a uORF-encoded peptide that exhibits kinase inhibitory functions. This uORF, upstream of the protein kinase C-eta (PKC-η) main ORF, encodes a peptide (uPEP2) containing the typical PKC pseudosubstrate motif present in all PKCs that autoinhibits their kinase activity. We show that uPEP2 directly binds to and selectively inhibits the catalytic activity of novel PKCs but not of classical or atypical PKCs. The endogenous deletion of uORF2 or its overexpression in MCF-7 cells revealed that the endogenously translated uPEP2 reduces the protein levels of PKC-η and other novel PKCs and restricts cell proliferation. Functionally, treatment of breast cancer cells with uPEP2 diminished cell survival and their migration and synergized with chemotherapy by interfering with the response to DNA damage. Furthermore, in a xenograft of MDA-MB-231 breast cancer tumor in mice models, uPEP2 suppressed tumor progression, invasion, and metastasis. Tumor histology showed reduced proliferation, enhanced cell death, and lower protein expression levels of novel PKCs along with diminished phosphorylation of PKC substrates. Hence, our study demonstrates that uORFs may encode biologically active peptides beyond their role as translation regulators of their downstream ORFs. Together, we point to a unique function of a uORF-encoded peptide as a kinase inhibitor, pertinent to cancer therapy.
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Rajendran E, Clark M, Goulart C, Steinhöfel B, Tjhin ET, Gross S, Smith NC, Kirk K, van Dooren GG. Substrate-mediated regulation of the arginine transporter of Toxoplasma gondii. PLoS Pathog 2021; 17:e1009816. [PMID: 34352043 PMCID: PMC8370653 DOI: 10.1371/journal.ppat.1009816] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/17/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
Intracellular parasites, such as the apicomplexan Toxoplasma gondii, are adept at scavenging nutrients from their host. However, there is little understanding of how parasites sense and respond to the changing nutrient environments they encounter during an infection. TgApiAT1, a member of the apicomplexan ApiAT family of amino acid transporters, is the major uptake route for the essential amino acid L-arginine (Arg) in T. gondii. Here, we show that the abundance of TgApiAT1, and hence the rate of uptake of Arg, is regulated by the availability of Arg in the parasite's external environment, increasing in response to decreased [Arg]. Using a luciferase-based 'biosensor' strain of T. gondii, we demonstrate that the expression of TgApiAT1 varies between different organs within the host, indicating that parasites are able to modulate TgApiAT1-dependent uptake of Arg as they encounter different nutrient environments in vivo. Finally, we show that Arg-dependent regulation of TgApiAT1 expression is post-transcriptional, mediated by an upstream open reading frame (uORF) in the TgApiAT1 transcript, and we provide evidence that the peptide encoded by this uORF is critical for mediating regulation. Together, our data reveal the mechanism by which an apicomplexan parasite responds to changes in the availability of a key nutrient.
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Affiliation(s)
- Esther Rajendran
- Research School of Biology, Australian National University, Canberra, Australia
| | - Morgan Clark
- Research School of Biology, Australian National University, Canberra, Australia
| | - Cibelly Goulart
- Research School of Biology, Australian National University, Canberra, Australia
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Birte Steinhöfel
- Research School of Biology, Australian National University, Canberra, Australia
| | - Erick T. Tjhin
- Research School of Biology, Australian National University, Canberra, Australia
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Simon Gross
- Research School of Biology, Australian National University, Canberra, Australia
| | - Nicholas C. Smith
- Research School of Biology, Australian National University, Canberra, Australia
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Kiaran Kirk
- Research School of Biology, Australian National University, Canberra, Australia
| | - Giel G. van Dooren
- Research School of Biology, Australian National University, Canberra, Australia
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Moro SG, Hermans C, Ruiz-Orera J, Albà MM. Impact of uORFs in mediating regulation of translation in stress conditions. BMC Mol Cell Biol 2021; 22:29. [PMID: 33992089 PMCID: PMC8126119 DOI: 10.1186/s12860-021-00363-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background A large fraction of genes contains upstream ORFs (uORFs) in the 5′ untranslated region (5’UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing premature dissociation of the two ribosomal units or ribosome stalling. However, it is currently unknown if most uORFs are inhibitory or if this activity is restricted to specific cases. Here we interrogate ribosome profiling data from three different stress experiments in yeast to gain novel insights into this question. Results By comparing ribosome occupancies in different conditions and experiments we obtain strong evidence that, in comparison to primary coding sequences (CDS), which undergo translational arrest during stress, the translation of uORFs is mostly unaffected by changes in the environment. As a result, the relative abundance of uORF-encoded peptides increases during stress. In general, the changes in the translational efficiency of regions containing uORFs do not seem to affect downstream translation. The exception are uORFs found in a subset of genes that are significantly up-regulated at the level of translation during stress; these uORFs tend to be translated at lower levels in stress conditions than in optimal growth conditions, facilitating the translation of the CDS during stress. We find new examples of uORF-mediated regulation of translation, including the Gcn4 functional homologue fil1 and ubi4 genes in S. pombe. Conclusion We find evidence that the relative amount of uORF-encoded peptides increases during stress. The increased translation of uORFs is however uncoupled from the general CDS translational repression observed during stress. In a subset of genes that encode proteins that need to be rapidly synthesized upon stress uORFs act as translational switches. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00363-9.
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Affiliation(s)
- Simone G Moro
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cedric Hermans
- Bioinformatics Knowledge Center, Howest University of Applied Sciences, Bruges, Belgium
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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Gaba A, Wang H, Fortune T, Qu X. Smart-ORF: a single-molecule method for accessing ribosome dynamics in both upstream and main open reading frames. Nucleic Acids Res 2021; 49:e26. [PMID: 33330921 PMCID: PMC7969011 DOI: 10.1093/nar/gkaa1185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 11/15/2022] Open
Abstract
Upstream open reading frame (uORF) translation disrupts scanning 43S flux on mRNA and modulates main open reading frame (mORF) translation efficiency. Current tools, however, have limited access to ribosome dynamics in both upstream and main ORFs of an mRNA. Here, we develop a new two-color in vitro fluorescence assay, Smart-ORF, that monitors individual uORF and mORF translation events in real-time with single-molecule resolution. We demonstrate the utility of Smart-ORF by applying it to uORF-encoded arginine attenuator peptide (AAP)-mediated translational regulation. The method enabled quantification of uORF and mORF initiation efficiencies, 80S dwell time, polysome formation, and the correlation between uORF and mORF translation dynamics. Smart-ORF revealed that AAP-mediated 80S stalling in the uORF stimulates the uORF initiation efficiency and promotes clustering of slower uORF-translating ribosomes. This technology provides a new tool that can reveal previously uncharacterized dynamics of uORF-containing mRNA translation.
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Affiliation(s)
- Anthony Gaba
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hongyun Wang
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Trinisia Fortune
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaohui Qu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Abstract
Bicistronic transcripts (operon-like transcripts) have occasionally been reported in eukaryotes, including unicellular yeasts, plants, and humans, despite the fact that they lack trans-splice mechanisms. However, the characteristics of eukaryotic bicistronic transcripts are poorly understood, except for those in nematodes. Here, we describe the genomic, transcriptomic, and ribosome profiling features of bicistronic transcripts in unicellular yeasts. By comparing the expression level of bicistronic transcripts with their monocistronic equivalents, we identify two main categories of bicistronic transcripts: highly and lowly expressed. These two categories exhibit quite different features. First, highly expressed bicistronic transcripts have higher conservation within and between strains and shorter intergenic spacers with higher GC content and less stable secondary structure. Second, genes in highly expressed bicistronic transcripts have lower translation efficiency, with the second gene showing statistically significant lower translation efficiency than the first. Finally, the genes found in these highly expressed bicistronic transcripts tend to be younger, with more recent origins. Together, these results suggest that bicistronic transcripts in yeast are heterogeneous. We further propose that at least some highly expressed bicistronic transcripts appear to play a role in modulating monocistronic translation.IMPORTANCE Operons, where a single mRNA transcript encodes multiple adjacent proteins, are a widespread feature of bacteria and archaea. In contrast, the genes of eukaryotes are generally considered monocistronic. However, a number of studies have revealed the presence of bicistronic transcripts in eukaryotes, including humans. The basic features of these transcripts are largely unknown in eukaryotes, especially in organisms lacking trans-splice mechanisms. Our analyses characterize bicistronic transcripts in one such eukaryotic group, yeasts. We show that highly expressed bicistronic transcripts have unusual features compared to lowly expressed bicistronic transcripts, with several features influencing translational modulation.
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Li G, Eriani G, Wang ED, Zhou XL. Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1645-1660. [PMID: 33515434 DOI: 10.1007/s11427-020-1838-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022]
Abstract
Mutations of the genes encoding aminoacyl-tRNA synthetases are highly associated with various central nervous system disorders. Recurrent mutations, including c.5A>G, p.D2G; c.1367C>T, p.S456L; c.1535G>A, p.R512Q and c.1846_1847del, p. Y616Lfs*6 of RARS1 gene, which encodes two forms of human cytoplasmic arginyl-tRNA synthetase (hArgRS), are linked to Pelizaeus-Merzbacher-like disease (PMLD) with unclear pathogenesis. Among these mutations, c.5A>G is the most extensively reported mutation, leading to a p.D2G mutation in the N-terminal extension of the long-form hArgRS. Here, we showed the detrimental effects of R512Q substitution and ΔC mutations on the structure and function of hArgRS, while the most frequent mutation c.5A>G, p.D2G acted in a different manner without impairing hArgRS activity. The nucleotide substitution c.5A>G reduced translation of hArgRS mRNA, and an upstream open reading frame contributed to the suppressed translation of the downstream main ORF. Taken together, our results elucidated distinct pathogenic mechanisms of various RARS1 mutations in PMLD.
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Affiliation(s)
- Guang Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, UPR9002 CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67084, Strasbourg, France
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
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12
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Pais P, Oliveira J, Almeida V, Yilmaz M, Monteiro PT, Teixeira MC. Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: Clues on host survival and probiotic activity based on promoter sequence variability. Genomics 2021; 113:530-539. [PMID: 33482324 DOI: 10.1016/j.ygeno.2020.11.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Although Saccharomyces cerevisiae and S. cerevisiae var. boulardii share more than 95% genome sequence homology, only S. cerevisiae var. boulardii displays probiotic activity. In this study, the transcriptomic differences exhibited by S. cerevisiae and S. cerevisiae var. boulardii in intestinal like medium were evaluated. S. cerevisiae was found to display stress response overexpression, consistent with higher ability of S. cerevisiae var. boulardii to survive within the human host, while S. cerevisiae var. boulardii exhibited transcriptional patterns associated with probiotic activity, suggesting increased acetate biosynthesis. Resorting to the creation of a S. cerevisiae var. boulardii genomic database within Yeastract+, a possible correlation between loss or gain of transcription factor binding sites in S. cerevisiae var. boulardii promoters and the transcriptomic pattern is discussed. This study suggests that S. cerevisiae var. boulardii probiotic activity, when compared to S. cerevisiae, relies, at least partially, on differential expression regulation, based on promoter variability.
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Affiliation(s)
- Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | | | - Vanda Almeida
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Melike Yilmaz
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Pedro T Monteiro
- Department of Computer Science and Engineering, Instituto Superior Técnico (IST), Universidade de Lisboa, Lisbon, Portugal; INESC-ID, Lisbon, Portugal.
| | - Miguel C Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal.
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Chew SY, Brown AJP, Lau BYC, Cheah YK, Ho KL, Sandai D, Yahaya H, Than LTL. Transcriptomic and proteomic profiling revealed reprogramming of carbon metabolism in acetate-grown human pathogen Candida glabrata. J Biomed Sci 2021; 28:1. [PMID: 33388061 PMCID: PMC7778802 DOI: 10.1186/s12929-020-00700-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 12/21/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Emergence of Candida glabrata, which causes potential life-threatening invasive candidiasis, has been widely associated with high morbidity and mortality. In order to cause disease in vivo, a robust and highly efficient metabolic adaptation is crucial for the survival of this fungal pathogen in human host. In fact, reprogramming of the carbon metabolism is believed to be indispensable for phagocytosed C. glabrata within glucose deprivation condition during infection. METHODS In this study, the metabolic responses of C. glabrata under acetate growth condition was explored using high-throughput transcriptomic and proteomic approaches. RESULTS Collectively, a total of 1482 transcripts (26.96%) and 242 proteins (24.69%) were significantly up- or down-regulated. Both transcriptome and proteome data revealed that the regulation of alternative carbon metabolism in C. glabrata resembled other fungal pathogens such as Candida albicans and Cryptococcus neoformans, with up-regulation of many proteins and transcripts from the glyoxylate cycle and gluconeogenesis, namely isocitrate lyase (ICL1), malate synthase (MLS1), phosphoenolpyruvate carboxykinase (PCK1) and fructose 1,6-biphosphatase (FBP1). In the absence of glucose, C. glabrata shifted its metabolism from glucose catabolism to anabolism of glucose intermediates from the available carbon source. This observation essentially suggests that the glyoxylate cycle and gluconeogenesis are potentially critical for the survival of phagocytosed C. glabrata within the glucose-deficient macrophages. CONCLUSION Here, we presented the first global metabolic responses of C. glabrata to alternative carbon source using transcriptomic and proteomic approaches. These findings implicated that reprogramming of the alternative carbon metabolism during glucose deprivation could enhance the survival and persistence of C. glabrata within the host.
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Affiliation(s)
- Shu Yih Chew
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Alistair J. P. Brown
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Benjamin Yii Chung Lau
- Proteomics and Metabolomics (PROMET) Group, Malaysian Palm Oil Board, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Yoke Kqueen Cheah
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Doblin Sandai
- Infectomics Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang Malaysia
| | - Hassan Yahaya
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Bayero University, Kano, Nigeria
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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14
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Dever TE, Ivanov IP, Sachs MS. Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation. Annu Rev Genet 2020; 54:237-264. [PMID: 32870728 DOI: 10.1146/annurev-genet-112618-043822] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize transcriptional and posttranscriptional mechanisms to alter gene expression in response to environmental cues. Gene-specific controls, including changing the translation of specific messenger RNAs (mRNAs), provide a rapid means to respond precisely to different conditions. Upstream open reading frames (uORFs) are known to control the translation of mRNAs. Recent studies in bacteria and eukaryotes have revealed the functions of evolutionarily conserved uORF-encoded peptides. Some of these uORF-encoded nascent peptides enable responses to specific metabolites to modulate the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their mRNAs. In this review, we highlight several examples of conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to specific metabolites in bacteria, fungi, mammals, and plants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Ivaylo P Ivanov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA;
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15
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Zhou F, Zhang H, Kulkarni SD, Lorsch JR, Hinnebusch AG. eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide. RNA (NEW YORK, N.Y.) 2020; 26:419-438. [PMID: 31915290 PMCID: PMC7075259 DOI: 10.1261/rna.073536.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/06/2020] [Indexed: 05/22/2023]
Abstract
The translation preinitiation complex (PIC) scans the mRNA for an AUG codon in a favorable context. Previous findings suggest that the factor eIF1 discriminates against non-AUG start codons by impeding full accommodation of Met-tRNAi in the P site of the 40S ribosomal subunit, necessitating eIF1 dissociation for start codon selection. Consistent with this, yeast eIF1 substitutions that weaken its binding to the PIC increase initiation at UUG codons on a mutant his4 mRNA and particular synthetic mRNA reporters; and also at the AUG start codon of the mRNA for eIF1 itself owing to its poor Kozak context. It was not known however whether such eIF1 mutants increase initiation at suboptimal start codons genome-wide. By ribosome profiling, we show that the eIF1-L96P variant confers increased translation of numerous upstream open reading frames (uORFs) initiating with either near-cognate codons (NCCs) or AUGs in poor context. The increased uORF translation is frequently associated with the reduced translation of the downstream main coding sequences (CDS). Initiation is also elevated at certain NCCs initiating amino-terminal extensions, including those that direct mitochondrial localization of the GRS1 and ALA1 products, and at a small set of main CDS AUG codons with especially poor context, including that of eIF1 itself. Thus, eIF1 acts throughout the yeast translatome to discriminate against NCC start codons and AUGs in poor context; and impairing this function enhances the repressive effects of uORFs on CDS translation and alters the ratios of protein isoforms translated from near-cognate versus AUG start codons.
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Affiliation(s)
- Fujun Zhou
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hongen Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shardul D Kulkarni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jon R Lorsch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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16
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Behura SK, Kelleher AM, Spencer TE. Regulation of uterine genes during the peri‐implantation period, and its relationship to the maternal brain in gestating mice. Mol Reprod Dev 2020; 87:482-492. [DOI: 10.1002/mrd.23338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/11/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Susanta K. Behura
- Division of Animal SciencesUniversity of MissouriColumbia Missouri
- Institute for Data Science and InformaticsUniversity of MissouriColumbia Missouri
| | | | - Thomas E. Spencer
- Division of Animal SciencesUniversity of MissouriColumbia Missouri
- Department of Obstetrics, Gynecology and Women's HealthUniversity of MissouriColumbia Missouri
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17
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Wang Y, Yang C, Liu X, Zheng J, Zhang F, Wang D, Xue Y, Li X, Shen S, Shao L, Yang Y, Liu L, Ma J, Liu Y. Transcription factor AP-4 (TFAP4)-upstream ORF coding 66 aa inhibits the malignant behaviors of glioma cells by suppressing the TFAP4/long noncoding RNA 00520/microRNA-520f-3p feedback loop. Cancer Sci 2020; 111:891-906. [PMID: 31943575 PMCID: PMC7060482 DOI: 10.1111/cas.14308] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 02/06/2023] Open
Abstract
Upstream ORF (uORF) is a translational initiation element located in the 5′UTR of eukaryotic mRNAs. Studies have found that uORFs play an important regulatory role in many diseases. Based on The Cancer Genome Atlas database, the results of our experiments and previous research evidence, we investigated transcription factor AP‐4 (TFAP4) and its uORF, LIM and SH3 protein 1 (LASP1), long noncoding RNA 00520 (LINC00520), and microRNA (miR)‐520f‐3p as candidates involved in glioma malignancy, which is a poorly understood process. Both TFAP4‐66aa‐uORF and miR‐520f‐3p were downregulated, and TFAP4, LASP1, and LINC00520 were highly expressed in glioma tissues and cells. TFAP4‐66aa‐uORF or miR‐520f‐3p overexpression or TFAP4, LASP1, or LINC00520 knockdown inhibited glioma cell proliferation, migration, and invasion, but promoted apoptosis. TFAP4‐66aa‐uORF inhibited the translation of TFAP4 by binding to the TFAP4 mRNA. MicroRNA‐520f‐3p inhibited TFAP4 expression by binding to its 3′UTR. However, LINC00520 could promote the expression of TFAP4 by competitively binding to miR‐520f‐3p. In addition, TFAP4 transcriptionally activated LASP1 and LINC00520 expression by binding to their promoter regions, forming a positive feedback loop of TFAP4/LINC00520/miR‐520f‐3p. Our findings together indicated that TFAP4‐66aa‐uORF inhibited the TFAP4/LINC00520/miR‐520f‐3p feedback loop by directly inhibiting TFAP4 expression, subsequently leading to inhibition of glioma malignancy. This provides a basis for developing new therapeutic approaches for glioma treatment.
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Affiliation(s)
- Yipeng Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Fangfang Zhang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Xiaozhi Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Shuyuan Shen
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Lianqi Shao
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Yang Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Libo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Jun Ma
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
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18
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Kulkarni SD, Zhou F, Sen ND, Zhang H, Hinnebusch AG, Lorsch JR. Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae. BMC Biol 2019; 17:101. [PMID: 31810458 PMCID: PMC6898956 DOI: 10.1186/s12915-019-0718-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/01/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Translation of an mRNA in eukaryotes starts at an AUG codon in most cases, but near-cognate codons (NCCs) such as UUG, ACG, and AUU can also be used as start sites at low levels in Saccharomyces 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. RESULTS 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. CONCLUSIONS Our data suggest that alterations in the translation of specific uORFs by temperature can regulate gene expression in S. cerevisiae.
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Affiliation(s)
- Shardul D Kulkarni
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Neelam Dabas Sen
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Present Address: School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Hongen Zhang
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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19
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Function and Evolution of Upstream ORFs in Eukaryotes. Trends Biochem Sci 2019; 44:782-794. [PMID: 31003826 DOI: 10.1016/j.tibs.2019.03.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 12/18/2022]
Abstract
There is growing interest in the role of translational regulation in cellular homeostasis during organismal development. Translation initiation is the rate-limiting step in mRNA translation and is central to translational regulation. Upstream open reading frames (uORFs) are regulatory elements that are prevalent in eukaryotic mRNAs. uORFs modulate the translation initiation rate of downstream coding sequences (CDSs) by sequestering ribosomes. Over the past several years, genome-wide studies have revealed the widespread regulatory functions of uORFs in different species in different biological contexts. Here, we review the current understanding of uORF-mediated translational regulation from the perspective of functional and evolutionary genomics and address remaining gaps that deserve further study.
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20
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Scheidler CM, Kick LM, Schneider S. Ribosomal Peptides and Small Proteins on the Rise. Chembiochem 2019; 20:1479-1486. [PMID: 30648812 DOI: 10.1002/cbic.201800715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 11/05/2022]
Abstract
Genetically encoded and ribosomally synthesised peptides and small proteins act as important regulators in fundamental cellular processes, including gene expression, development, signalling and metabolism. Moreover, they also play a crucial role in eukaryotic and prokaryotic defence against microorganisms. Extremely diverse in size and structure, they are often subject to extensive post-translational modification. Recent technological advances are now allowing the analysis of the whole cellular transcriptome and proteome, revealing the presence of hundreds of long-overlooked alternative and short open reading frames (short ORFs, or sORFs) in mRNA and supposedly noncoding RNAs. However, in many instances the biological roles of their translational products remain to be elucidated. Here we provide an overview on the intriguing structural and functional diversity of ribosomally synthesised peptides and newly discovered peptides and small proteins.
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Affiliation(s)
- Christopher M Scheidler
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Leonhard M Kick
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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21
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Khitun A, Ness TJ, Slavoff SA. Small open reading frames and cellular stress responses. Mol Omics 2019; 15:108-116. [PMID: 30810554 DOI: 10.1039/c8mo00283e] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small open reading frames (smORFs) encoding polypeptides of less than 100 amino acids in eukaryotes (50 amino acids in prokaryotes) were historically excluded from genome annotation. However, recent advances in genomics, ribosome footprinting, and proteomics have revealed thousands of translated smORFs in genomes spanning evolutionary space. These smORFs can encode functional polypeptides, or act as cis-translational regulators. Herein we review evidence that some smORF-encoded polypeptides (SEPs) participate in stress responses in both prokaryotes and eukaryotes, and that some upstream ORFs (uORFs) regulate stress-responsive translation of downstream cistrons in eukaryotic cells. These studies provide insight into a regulated subclass of smORFs and suggest that at least some SEPs may participate in maintenance of cellular homeostasis under stress.
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Affiliation(s)
- Alexandra Khitun
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Travis J Ness
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Sarah A Slavoff
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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22
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Magnesium-sensitive upstream ORF controls PRL phosphatase expression to mediate energy metabolism. Proc Natl Acad Sci U S A 2019; 116:2925-2934. [PMID: 30718434 DOI: 10.1073/pnas.1815361116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Phosphatases of regenerating liver (PRL-1, PRL-2, and PRL-3, also known as PTP4A1, PTP4A2, and PTP4A3) control magnesium homeostasis through an association with the CNNM magnesium transport regulators. Although high PRL levels have been linked to cancer progression, regulation of their expression is poorly understood. Here we show that modulating intracellular magnesium levels correlates with a rapid change of PRL expression by a mechanism involving its 5'UTR mRNA region. Mutations or CRISPR-Cas9 targeting of the conserved upstream ORF present in the mRNA leader derepress PRL protein synthesis and attenuate the translational response to magnesium levels. Mechanistically, magnesium depletion reduces intracellular ATP but up-regulates PRL protein expression via activation of the AMPK/mTORC2 pathway, which controls cellular energy status. Hence, altered PRL-2 expression leads to metabolic reprogramming of the cells. These findings uncover a magnesium-sensitive mechanism controlling PRL expression, which plays a role in cellular bioenergetics.
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23
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Crawford RA, Pavitt GD. Translational regulation in response to stress in Saccharomyces cerevisiae. Yeast 2018; 36:5-21. [PMID: 30019452 PMCID: PMC6492140 DOI: 10.1002/yea.3349] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/08/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae must dynamically alter the composition of its proteome in order to respond to diverse stresses. The reprogramming of gene expression during stress typically involves initial global repression of protein synthesis, accompanied by the activation of stress‐responsive mRNAs through both translational and transcriptional responses. The ability of specific mRNAs to counter the global translational repression is therefore crucial to the overall response to stress. Here we summarize the major repressive mechanisms and discuss mechanisms of translational activation in response to different stresses in S. cerevisiae. Taken together, a wide range of studies indicate that multiple elements act in concert to bring about appropriate translational responses. These include regulatory elements within mRNAs, altered mRNA interactions with RNA‐binding proteins and the specialization of ribosomes that each contribute towards regulating protein expression to suit the changing environmental conditions.
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Affiliation(s)
- Robert A Crawford
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
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24
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Erpf PE, Fraser JA. The Long History of the Diverse Roles of Short ORFs: sPEPs in Fungi. Proteomics 2018; 18:e1700219. [PMID: 29465163 DOI: 10.1002/pmic.201700219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/30/2018] [Indexed: 12/30/2022]
Abstract
Since the completion of the genome sequence of the model eukaryote Saccharomyces cerevisiae, there have been significant advancements in the field of genome annotation, in no small part due to the availability of datasets that make large-scale comparative analyses possible. As a result, since its completion there has been a significant change in annotated ORF size distribution in this first eukaryotic genome, especially in short ORFs (sORFs) predicted to encode polypeptides less than 150 amino acids in length. Due to their small size and the difficulties associated with their study, it is only relatively recently that these genomic features and the sORF-encoded peptides (sPEPs) they encode have become a focus of many researchers. Yet while this class of peptides may seem new and exciting, the study of this part of the proteome is nothing new in S. cerevisiae, a species where the biological importance of sPEPs has been elegantly illustrated over the past 30 years. Here the authors showcase a range of different sORFs found in S. cerevisiae and the diverse biological roles of their encoded sPEPs, and provide an insight into the sORFs found in other fungal species, particularly those pathogenic to humans.
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Affiliation(s)
- Paige E Erpf
- Australian Infectious Diseases Research Centre, St Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - James A Fraser
- Australian Infectious Diseases Research Centre, St Lucia, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
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25
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Martin-Marcos P, Zhou F, Karunasiri C, Zhang F, Dong J, Nanda J, Kulkarni SD, Sen ND, Tamame M, Zeschnigk M, Lorsch JR, Hinnebusch AG. eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast. eLife 2017; 6:31250. [PMID: 29206102 PMCID: PMC5756025 DOI: 10.7554/elife.31250] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/04/2017] [Indexed: 11/13/2022] Open
Abstract
The translation pre-initiation complex (PIC) scans the mRNA for an AUG codon in favorable context, and AUG recognition stabilizes a closed PIC conformation. The unstructured N-terminal tail (NTT) of yeast eIF1A deploys five basic residues to contact tRNAi, mRNA, or 18S rRNA exclusively in the closed state. Interestingly, EIF1AX mutations altering the human eIF1A NTT are associated with uveal melanoma (UM). We found that substituting all five basic residues, and seven UM-associated substitutions, in yeast eIF1A suppresses initiation at near-cognate UUG codons and AUGs in poor context. Ribosome profiling of NTT substitution R13P reveals heightened discrimination against unfavorable AUG context genome-wide. Both R13P and K16D substitutions destabilize the closed complex at UUG codons in reconstituted PICs. Thus, electrostatic interactions involving the eIF1A NTT stabilize the closed conformation and promote utilization of suboptimal start codons. We predict UM-associated mutations alter human gene expression by increasing discrimination against poor initiation sites.
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Affiliation(s)
- Pilar Martin-Marcos
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States.,Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Charm Karunasiri
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Fan Zhang
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Jinsheng Dong
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Jagpreet Nanda
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Shardul D Kulkarni
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Neelam Dabas Sen
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Michael Zeschnigk
- Institute of Human Genetics, University Duisburg-Essen, Essen, Germany.,Eye Cancer Research Group, Faculty of Medicine, University Duisburg-Essen, Essen, Germany
| | - Jon R Lorsch
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, United States
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26
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Cuperus JT, Groves B, Kuchina A, Rosenberg AB, Jojic N, Fields S, Seelig G. Deep learning of the regulatory grammar of yeast 5' untranslated regions from 500,000 random sequences. Genome Res 2017; 27:2015-2024. [PMID: 29097404 PMCID: PMC5741052 DOI: 10.1101/gr.224964.117] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/18/2017] [Indexed: 11/25/2022]
Abstract
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting our limited understanding of cis-regulatory grammar and hampering the design of engineered genes for synthetic biology applications. Here, we generate a model that predicts the protein expression of the 5′ untranslated region (UTR) of mRNAs in the yeast Saccharomyces cerevisiae. We constructed a library of half a million 50-nucleotide-long random 5′ UTRs and assayed their activity in a massively parallel growth selection experiment. The resulting data allow us to quantify the impact on protein expression of Kozak sequence composition, upstream open reading frames (uORFs), and secondary structure. We trained a convolutional neural network (CNN) on the random library and showed that it performs well at predicting the protein expression of both a held-out set of the random 5′ UTRs as well as native S. cerevisiae 5′ UTRs. The model additionally was used to computationally evolve highly active 5′ UTRs. We confirmed experimentally that the great majority of the evolved sequences led to higher protein expression rates than the starting sequences, demonstrating the predictive power of this model.
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Affiliation(s)
- Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Anna Kuchina
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Alexander B Rosenberg
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
| | | | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.,Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA.,Department of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, USA
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27
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Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae. Genetics 2017; 203:65-107. [PMID: 27183566 DOI: 10.1534/genetics.115.186221] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/24/2016] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.
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28
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Hinnebusch AG, Ivanov IP, Sonenberg N. Translational control by 5'-untranslated regions of eukaryotic mRNAs. Science 2016; 352:1413-6. [PMID: 27313038 DOI: 10.1126/science.aad9868] [Citation(s) in RCA: 672] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The eukaryotic 5' untranslated region (UTR) is critical for ribosome recruitment to the messenger RNA (mRNA) and start codon choice and plays a major role in the control of translation efficiency and shaping the cellular proteome. The ribosomal initiation complex is assembled on the mRNA via a cap-dependent or cap-independent mechanism. We describe various mechanisms controlling ribosome scanning and initiation codon selection by 5' upstream open reading frames, translation initiation factors, and primary and secondary structures of the 5'UTR, including particular sequence motifs. We also discuss translational control via phosphorylation of eukaryotic initiation factor 2, which is implicated in learning and memory, neurodegenerative diseases, and cancer.
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Affiliation(s)
- Alan G Hinnebusch
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivaylo P Ivanov
- Group on Cell Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.
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29
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Olexiouk V, Menschaert G. Identification of Small Novel Coding Sequences, a Proteogenomics Endeavor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:49-64. [PMID: 27686805 DOI: 10.1007/978-3-319-42316-6_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The identification of small proteins and peptides has consistently proven to be challenging. However, technological advances as well as multi-omics endeavors facilitate the identification of novel small coding sequences, leading to new insights. Specifically, the application of next generation sequencing technologies (NGS), providing accurate and sample specific transcriptome / translatome information, into the proteomics field led to more comprehensive results and new discoveries. This book chapter focuses on the inclusion of RNA-Seq and RIBO-Seq also known as ribosome profiling, an RNA-Seq based technique sequencing the +/- 30 bp long fragments captured by translating ribosomes. We emphasize the identification of micropeptides and neo-antigens, two distinct classes of small translation products, triggering our current understanding of biology. RNA-Seq is capable of capturing sample specific genomic variations, enabling focused neo-antigen identification. RIBO-Seq can identify translation events in small open reading frames which are considered to be non-coding, leading to the discovery of micropeptides. The identification of small translation products requires the integration of multi-omics data, stressing the importance of proteogenomics in this novel research area.
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Affiliation(s)
- Volodimir Olexiouk
- Lab of Bioinformatics and Computational Genomics (BioBix), Faculty of Bioscience Engineering, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Building A, Ghent, 9000, Belgium.
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics (BioBix), Faculty of Bioscience Engineering, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Building A, Ghent, 9000, Belgium
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30
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Fiebig M, Kelly S, Gluenz E. Comparative Life Cycle Transcriptomics Revises Leishmania mexicana Genome Annotation and Links a Chromosome Duplication with Parasitism of Vertebrates. PLoS Pathog 2015; 11:e1005186. [PMID: 26452044 PMCID: PMC4599935 DOI: 10.1371/journal.ppat.1005186] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/03/2015] [Indexed: 02/07/2023] Open
Abstract
Leishmania spp. are protozoan parasites that have two principal life cycle stages: the motile promastigote forms that live in the alimentary tract of the sandfly and the amastigote forms, which are adapted to survive and replicate in the harsh conditions of the phagolysosome of mammalian macrophages. Here, we used Illumina sequencing of poly-A selected RNA to characterise and compare the transcriptomes of L. mexicana promastigotes, axenic amastigotes and intracellular amastigotes. These data allowed the production of the first transcriptome evidence-based annotation of gene models for this species, including genome-wide mapping of trans-splice sites and poly-A addition sites. The revised genome annotation encompassed 9,169 protein-coding genes including 936 novel genes as well as modifications to previously existing gene models. Comparative analysis of gene expression across promastigote and amastigote forms revealed that 3,832 genes are differentially expressed between promastigotes and intracellular amastigotes. A large proportion of genes that were downregulated during differentiation to amastigotes were associated with the function of the motile flagellum. In contrast, those genes that were upregulated included cell surface proteins, transporters, peptidases and many uncharacterized genes, including 293 of the 936 novel genes. Genome-wide distribution analysis of the differentially expressed genes revealed that the tetraploid chromosome 30 is highly enriched for genes that were upregulated in amastigotes, providing the first evidence of a link between this whole chromosome duplication event and adaptation to the vertebrate host in this group. Peptide evidence for 42 proteins encoded by novel transcripts supports the idea of an as yet uncharacterised set of small proteins in Leishmania spp. with possible implications for host-pathogen interactions.
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Affiliation(s)
- Michael Fiebig
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom
- * E-mail: (SK); (EG)
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
- * E-mail: (SK); (EG)
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31
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Wethmar K. The regulatory potential of upstream open reading frames in eukaryotic gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:765-78. [DOI: 10.1002/wrna.1245] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Klaus Wethmar
- Max-Delbrueck-Center for Molecular Medicine; Berlin Germany
- Helios Klinikum Berlin-Buch; Berlin Germany
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32
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Gandin V, Topisirovic I. Co-translational mechanisms of quality control of newly synthesized polypeptides. ACTA ACUST UNITED AC 2014; 2:e28109. [PMID: 26779401 PMCID: PMC4705825 DOI: 10.4161/trla.28109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 12/30/2013] [Accepted: 02/04/2014] [Indexed: 01/23/2023]
Abstract
During protein synthesis, nascent polypeptides emerge from ribosomes to fold into functional proteins. Misfolding of newly synthesized polypeptides (NSPs) at this stage leads to their aggregation. These misfolded NSPs must be expediently cleared to circumvent the deleterious effects of protein aggregation on cell physiology. To this end, a sizable portion of NSPs are ubiquitinated and rapidly degraded by the proteasome. This suggests the existence of co-translational mechanisms that play a pivotal role in the quality control of NSPs. It is generally thought that ribosomes play a central role in this process. During mRNA translation, ribosomes sense errors that lead to the accumulation of aberrant polypeptides, and serve as a hub for protein complexes that are required for optimal folding and/or proteasome-dependent degradation of misfolded polypeptides. In this review, we discuss recent findings that shed light on the molecular underpinnings of the co-translational quality control of NSPs.
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Affiliation(s)
- Valentina Gandin
- Lady Davis Institute for Medical Research; Sir Mortimer B. Davis-Jewish General Hospital; Montréal, QC Canada; Department of Oncology; McGill University; Montréal, QC Canada
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research; Sir Mortimer B. Davis-Jewish General Hospital; Montréal, QC Canada; Department of Oncology; McGill University; Montréal, QC Canada
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33
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Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 2014; 15:193-204. [PMID: 24514441 DOI: 10.1038/nrg3520] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Short open reading frames (sORFs) are a common feature of all genomes, but their coding potential has mostly been disregarded, partly because of the difficulty in determining whether these sequences are translated. Recent innovations in computing, proteomics and high-throughput analyses of translation start sites have begun to address this challenge and have identified hundreds of putative coding sORFs. The translation of some of these has been confirmed, although the contribution of their peptide products to cellular functions remains largely unknown. This Review examines this hitherto overlooked component of the proteome and considers potential roles for sORF-encoded peptides.
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34
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Carlsson M, Gustavsson M, Hu GZ, Murén E, Ronne H. A Ham1p-dependent mechanism and modulation of the pyrimidine biosynthetic pathway can both confer resistance to 5-fluorouracil in yeast. PLoS One 2013; 8:e52094. [PMID: 24124444 PMCID: PMC3792807 DOI: 10.1371/journal.pone.0052094] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 11/09/2012] [Indexed: 12/13/2022] Open
Abstract
5-Fluorouracil (5-FU) is an anticancer drug and pyrimidine analogue. A problem in 5-FU therapy is acquired resistance to the drug. To find out more about the mechanisms of resistance, we screened a plasmid library in yeast for genes that confer 5-FU resistance when overexpressed. We cloned five genes: CPA1, CPA2, HMS1, HAM1 and YJL055W. CPA1 and CPA2 encode a carbamoyl phosphate synthase involved in arginine biosynthesis and HMS1 a helix-loop-helix transcription factor. Our results suggest that CPA1, CPA2, and HMS1 confer 5-FU resistance by stimulating pyrimidine biosynthesis. Thus, they are unable to confer 5-FU resistance in a ura2 mutant, and inhibit the uptake and incorporation into RNA of both uracil and 5-FU. In contrast, HAM1 and YJL055W confer 5-FU resistance in a ura2 mutant, and selectively inhibit incorporation into RNA of 5-FU but not uracil. HAM1 is the strongest resistance gene, but it partially depends on YJL055W for its function. This suggests that HAM1 and YJL055W function together in mediating resistance to 5-FU. Ham1p encodes an inosine triphosphate pyrophosphatase that has been implicated in resistance to purine analogues. Our results suggest that Ham1p could have a broader specificity that includes 5-FUTP and other pyrimidine analogoue triphosphates.
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Affiliation(s)
- Mattias Carlsson
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marie Gustavsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Guo-Zhen Hu
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Eva Murén
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hans Ronne
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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35
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Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci U S A 2013; 110:E2792-801. [PMID: 23832786 DOI: 10.1073/pnas.1222534110] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The 5'-untranslated region (5'-UTR) of mRNAs contains elements that affect expression, yet the rules by which these regions exert their effect are poorly understood. Here, we studied the impact of 5'-UTR sequences on protein levels in yeast, by constructing a large-scale library of mutants that differ only in the 10 bp preceding the translational start site of a fluorescent reporter. Using a high-throughput sequencing strategy, we obtained highly accurate measurements of protein abundance for over 2,000 unique sequence variants. The resulting pool spanned an approximately sevenfold range of protein levels, demonstrating the powerful consequences of sequence manipulations of even 1-10 nucleotides immediately upstream of the start codon. We devised computational models that predicted over 70% of the measured expression variability in held-out sequence variants. Notably, a combined model of the most prominent features successfully explained protein abundance in an additional, independently constructed library, whose nucleotide composition differed greatly from the library used to parameterize the model. Our analysis reveals the dominant contribution of the start codon context at positions -3 to -1, mRNA secondary structure, and out-of-frame upstream AUGs (uAUGs) to phenotypic diversity, thereby advancing our understanding of how protein levels are modulated by 5'-UTR sequences, and paving the way toward predictably tuning protein expression through manipulations of 5'-UTRs.
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36
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Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 2012; 9:59-64. [PMID: 23160002 PMCID: PMC3625679 DOI: 10.1038/nchembio.1120] [Citation(s) in RCA: 440] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 10/16/2012] [Indexed: 11/24/2022]
Abstract
The amount of the transcriptome that is translated into polypeptides is of fundamental importance. We developed a peptidomic strategy to detect short ORF (sORF)-encoded polypeptides (SEPs) in human cells. We identified 90 SEPs, 86 of which are novel, the largest number of human SEPs ever reported. SEP abundances range from 10-1000 molecules per cell, identical to known proteins. SEPs arise from sORFs in non-coding RNAs as well as multi-cistronic mRNAs, and many SEPs initiate with non-AUG start codons, indicating that non-canonical translation may be more widespread in mammals than previously thought. In addition, coding sORFs are present in a small fraction (8/1866) of long intergenic non-coding RNAs (lincRNAs). Together, these results provide the strongest evidence to date that the human proteome is more complex than previously appreciated.
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Affiliation(s)
- Sarah A Slavoff
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
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37
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Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics 2012; 190:885-929. [PMID: 22419079 DOI: 10.1534/genetics.111.133306] [Citation(s) in RCA: 348] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ever since the beginning of biochemical analysis, yeast has been a pioneering model for studying the regulation of eukaryotic metabolism. During the last three decades, the combination of powerful yeast genetics and genome-wide approaches has led to a more integrated view of metabolic regulation. Multiple layers of regulation, from suprapathway control to individual gene responses, have been discovered. Constitutive and dedicated systems that are critical in sensing of the intra- and extracellular environment have been identified, and there is a growing awareness of their involvement in the highly regulated intracellular compartmentalization of proteins and metabolites. This review focuses on recent developments in the field of amino acid, nucleotide, and phosphate metabolism and provides illustrative examples of how yeast cells combine a variety of mechanisms to achieve coordinated regulation of multiple metabolic pathways. Importantly, common schemes have emerged, which reveal mechanisms conserved among various pathways, such as those involved in metabolite sensing and transcriptional regulation by noncoding RNAs or by metabolic intermediates. Thanks to the remarkable sophistication offered by the yeast experimental system, a picture of the intimate connections between the metabolomic and the transcriptome is becoming clear.
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38
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Molecular mechanism of scanning and start codon selection in eukaryotes. Microbiol Mol Biol Rev 2012; 75:434-67, first page of table of contents. [PMID: 21885680 DOI: 10.1128/mmbr.00008-11] [Citation(s) in RCA: 281] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5' end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNAiMet) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an "open" conformation of the 40S subunit with Met-tRNAiMet bound in a low-affinity state conducive to scanning and in triggering rearrangement into a "closed" conformation incompatible with scanning, which features Met-tRNAiMet more tightly bound to the "P" site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded "landing pad" for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.
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39
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Nascent polypeptide sequences that influence ribosome function. Curr Opin Microbiol 2011; 14:160-6. [PMID: 21342782 DOI: 10.1016/j.mib.2011.01.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 01/28/2011] [Indexed: 11/23/2022]
Abstract
Ribosomes catalyze protein synthesis using transfer RNAs and auxiliary proteins. Historically, ribosomes have been considered nonspecific translational machines, having no regulatory functions. However, a new class of regulatory mechanisms has been discovered that is based on interactions occurring within the ribosomal peptide exit tunnel that result in ribosome stalling during translation of an appropriate mRNA segment. These discoveries reveal an unexpectedly dynamic role ribosomes play in regulating their own activity. By using nascent leader peptides in combination with bound specific amino acids or antibiotics, ribosome functions can be altered significantly resulting in regulated expression of downstream coding regions. This review summarizes relevant findings in recent articles and outlines our current understanding of nascent peptide-induced ribosome stalling in regulating gene expression.
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40
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Spevak CC, Ivanov IP, Sachs MS. Sequence requirements for ribosome stalling by the arginine attenuator peptide. J Biol Chem 2010; 285:40933-42. [PMID: 20884617 DOI: 10.1074/jbc.m110.164152] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 5' regions of eukaryotic mRNAs often contain upstream open reading frames (uORFs). The Neurospora crassa arg-2 uORF encodes the 24-residue arginine attenuator peptide (AAP). This regulatory uORF-encoded peptide, which is evolutionarily conserved in fungal transcripts specifying an arginine biosynthetic enzyme, functions as a nascent peptide within the ribosomal tunnel and negatively regulates gene expression. The nascent AAP causes ribosomes to stall at the uORF stop codon in response to arginine, thus, blocking ribosomes from reaching the ARG-2 initiation codon. Here scanning mutagenesis with alanine and proline was performed to systematically determine which AAP residues were important for conferring regulation. Changing many of the most highly conserved residues (Asp-12, Tyr-13, Lys-14, and Trp-19) abolished regulatory function. The minimal functional domain of the AAP was determined by positioning AAP sequences internally within a large polypeptide. Pulse-chase analyses revealed that residues 9-20 of the AAP composed the minimal domain that was sufficient to confer regulatory function. An extensive analysis of predicted fungal AAPs revealed that the minimal functional domain of the N. crassa AAP corresponded closely to the region that was most highly conserved among the fungi. We also observed that the tripeptide RGD could function similarly to arginine in triggering AAP-mediated ribosome stalling. These studies provide a better understanding of the elements required for a nascent peptide and a small regulatory molecule to control translational processes.
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Affiliation(s)
- Christina C Spevak
- Department of Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA
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41
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Zuercher J, Neidhardt J, Magyar I, Labs S, Moore AT, Tanner FC, Waseem N, Schorderet DF, Munier FL, Bhattacharya S, Berger W, Kloeckener-Gruissem B. Alterations of the 5'untranslated region of SLC16A12 lead to age-related cataract. Invest Ophthalmol Vis Sci 2010; 51:3354-61. [PMID: 20181839 PMCID: PMC2904002 DOI: 10.1167/iovs.10-5193] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 02/04/2010] [Accepted: 02/09/2010] [Indexed: 11/24/2022] Open
Abstract
PURPOSE. Knowledge of genetic factors predisposing to age-related cataract is very limited. The aim of this study was to identify DNA sequences that either lead to or predispose for this disease. METHODS. The candidate gene SLC16A12, which encodes a solute carrier of the monocarboxylate transporter family, was sequenced in 484 patients with cataract (134 with juvenile cataract, 350 with age-related cataract) and 190 control subjects. Expression studies included luciferase reporter assay and RT-PCR experiments. RESULTS. One patient with age-related cataract showed a novel heterozygous mutation (c.-17A>G) in the 5'untranslated region (5'UTR). This mutation is in cis with the minor G-allele of the single nucleotide polymorphism (SNP) rs3740030 (c.-42T/G), also within the 5'UTR. Using a luciferase reporter assay system, a construct with the patient's haplotype caused a significant upregulation of luciferase activity. In comparison, the SNP G-allele alone promoted less activity, but that amount was still significantly higher than the amount of the common T-allele. Analysis of SLC16A12 transcripts in surrogate tissue demonstrated striking allele-specific differences causing 5'UTR heterogeneity with respect to sequence and quantity. These differences in gene expression were mirrored in an allele-specific predisposition to age-related cataract, as determined in a Swiss population (odds ratio approximately 2.2; confidence intervals, 1.23-4.3). CONCLUSIONS. The monocarboxylate transporter SLC16A12 may contribute to age-related cataract. Sequences within the 5'UTR modulate translational efficiency with pathogenic consequences.
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Affiliation(s)
- Jurian Zuercher
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - John Neidhardt
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Istvan Magyar
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Stephan Labs
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anthony T. Moore
- Moorfields Eye Hospital London, London, United Kingdom
- UCL-Institute of Ophthalmology, London, United Kingdom
| | - Felix C. Tanner
- the Department of Cardiology, Cardiovascular Center, University of Zurich, Zurich, Switzerland
| | | | - Daniel F. Schorderet
- IRO-Institute for Research in Ophthalmology, EPFL-École polytechnique fédérale of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Francis L. Munier
- Jules Gonin Eye Hospital, Faculté de Biologie et Médecine de L'Université de Lausanne, Switzerland; and
| | | | - Wolfgang Berger
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Barbara Kloeckener-Gruissem
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- the Department of Biology, ETH Zurich, Zurich, Switzerland
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42
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Tian C, Kasiborski B, Koul R, Lammers PJ, Bücking H, Shachar-Hill Y. Regulation of the nitrogen transfer pathway in the arbuscular mycorrhizal symbiosis: gene characterization and the coordination of expression with nitrogen flux. PLANT PHYSIOLOGY 2010; 153:1175-87. [PMID: 20448102 PMCID: PMC2899933 DOI: 10.1104/pp.110.156430] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 05/05/2010] [Indexed: 05/19/2023]
Abstract
The arbuscular mycorrhiza (AM) brings together the roots of over 80% of land plant species and fungi of the phylum Glomeromycota and greatly benefits plants through improved uptake of mineral nutrients. AM fungi can take up both nitrate and ammonium from the soil and transfer nitrogen (N) to host roots in nutritionally substantial quantities. The current model of N handling in the AM symbiosis includes the synthesis of arginine in the extraradical mycelium and the transfer of arginine to the intraradical mycelium, where it is broken down to release N for transfer to the host plant. To understand the mechanisms and regulation of N transfer from the fungus to the plant, 11 fungal genes putatively involved in the pathway were identified from Glomus intraradices, and for six of them the full-length coding sequence was functionally characterized by yeast complementation. Two glutamine synthetase isoforms were found to have different substrate affinities and expression patterns, suggesting different roles in N assimilation. The spatial and temporal expression of plant and fungal N metabolism genes were followed after nitrate was added to the extraradical mycelium under N-limited growth conditions using hairy root cultures. In parallel experiments with (15)N, the levels and labeling of free amino acids were measured to follow transport and metabolism. The gene expression pattern and profiling of metabolites involved in the N pathway support the idea that the rapid uptake, translocation, and transfer of N by the fungus successively trigger metabolic gene expression responses in the extraradical mycelium, intraradical mycelium, and host plant.
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Affiliation(s)
- Chunjie Tian
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA.
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Clark PL, Ugrinov KG. Measuring cotranslational folding of nascent polypeptide chains on ribosomes. Methods Enzymol 2009; 466:567-90. [PMID: 21609877 DOI: 10.1016/s0076-6879(09)66024-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein folding has been studied extensively in vitro, but much less is known about how folding proceeds in vivo. A particular distinction of folding in vivo is that folding begins while the nascent polypeptide chain is still undergoing synthesis by the ribosome. Studies of cotranslational protein folding are inherently much more complex than classical in vitro protein folding studies, and historically there have been few methods available to produce the quantities of pure material required for biophysical studies of the nascent chain, or assays to specifically interrogate its conformation. However, the past few years have produced dramatic methodological advances, which now place cotranslational folding studies within reach of more biochemists, enabling a detailed comparison of the earliest stages of protein folding on the ribosome to the wealth of information available for the refolding of full-length polypeptide chains in vitro.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Hood HM, Neafsey DE, Galagan J, Sachs MS. Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol 2009; 63:385-409. [PMID: 19514854 DOI: 10.1146/annurev.micro.62.081307.162835] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Upstream open reading frames (uORFs) are frequently present in the 5'-leader regions of fungal mRNAs. They can affect translation by controlling the ability of ribosomes that scan from the mRNA 5' end to reach the downstream genic reading frame. The translation of uORFs can also affect mRNA stability. For several genes, including Saccharomyces cerevisiae GCN4, S. cerevisiae CPA1, and Neurospora crassa arg-2, regulation by uORFs controls expression in response to specific physiological signals. The roles of many uORFs that are identified by genome-level approaches, as have been initiated for Saccharomyces, Aspergillus, and Cryptococcus species, remain to be determined. Some uORFs may have regulatory roles, while others may exist to insulate the genic reading frame from the negative impacts of upstream translation start sites in the mRNA 5' leader.
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Affiliation(s)
- Heather M Hood
- Department of Science and Engineering, Oregon Health & Science University, Beaverton, Oregon 97006, USA
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Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008; 320:1344-9. [PMID: 18451266 DOI: 10.1126/science.1158441] [Citation(s) in RCA: 1753] [Impact Index Per Article: 109.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.
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Affiliation(s)
- Ugrappa Nagalakshmi
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs. Methods Mol Biol 2008; 419:231-42. [PMID: 18369987 DOI: 10.1007/978-1-59745-033-1_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The number and distribution of ribosomes on a transcript provide useful information in ascertaining the efficiency of translation. Herein we describe a direct method to determine the association of ribosomes with specific regions of an mRNA. The method, termed Ribosome Density Mapping (RDM), includes cleavage of ribosomes-associated mRNAs with RNase H and complementary oligodeoxynucleotide followed by separation of the cleavage products on a sucrose gradient. The gradient is then fractionated and the sedimentation position of each mRNA fragment is determined by northern analysis. Although developed for yeast mRNAs, RDM is likely to be applicable to various other systems.
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Hayden CA, Jorgensen RA. Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes. BMC Biol 2007; 5:32. [PMID: 17663791 PMCID: PMC2075485 DOI: 10.1186/1741-7007-5-32] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 07/30/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upstream open reading frames (uORFs) can mediate translational control over the largest, or major ORF (mORF) in response to starvation, polyamine concentrations, and sucrose concentrations. One plant uORF with conserved peptide sequences has been shown to exert this control in an amino acid sequence-dependent manner but generally it is not clear what kinds of genes are regulated, or how extensively this mechanism is invoked in a given genome. RESULTS By comparing full-length cDNA sequences from Arabidopsis and rice we identified 26 distinct homology groups of conserved peptide uORFs, only three of which have been reported previously. Pairwise Ka/Ks analysis showed that purifying selection had acted on nearly all conserved peptide uORFs and their associated mORFs. Functions of predicted mORF proteins could be inferred for 16 homology groups and many of these proteins appear to have a regulatory function, including 6 transcription factors, 5 signal transduction factors, 3 developmental signal molecules, a homolog of translation initiation factor eIF5, and a RING finger protein. Transcription factors are clearly overrepresented in this data set when compared to the frequency calculated for the entire genome (p = 1.2 x 10(-7)). Duplicate gene pairs arising from a whole genome duplication (ohnologs) with a conserved uORF are much more likely to have been retained in Arabidopsis (Arabidopsis thaliana) than are ohnologs of other genes (39% vs 14% of ancestral genes, p = 5 x 10(-3)). Two uORF groups were found in animals, indicating an ancient origin of these putative regulatory elements. CONCLUSION Conservation of uORF amino acid sequence, association with homologous mORFs over long evolutionary time periods, preferential retention after whole genome duplications, and preferential association with mORFs coding for transcription factors suggest that the conserved peptide uORFs identified in this study are strong candidates for translational controllers of regulatory genes.
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Affiliation(s)
- Celine A Hayden
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA
| | - Richard A Jorgensen
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA
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Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 2006; 25:117-24. [PMID: 17187058 DOI: 10.1038/nbt1270] [Citation(s) in RCA: 858] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Accepted: 10/26/2006] [Indexed: 11/09/2022]
Abstract
We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about approximately 5,600 ( approximately 540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms.
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Affiliation(s)
- Peng Lu
- Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 2500 Speedway, University of Texas, Austin, Texas 78712, USA
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Nishida H. Detection and characterization of fungal-specific proteins in Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2006; 70:2646-52. [PMID: 17090923 DOI: 10.1271/bbb.60251] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this study, I searched for fungal-specific proteins in the genome of the budding yeast Saccharomyces cerevisiae, inferred from a comparison of amino acid sequences. I used the GTOP (Genomes to Protein structures and functions) database of the DDBJ (DNA Data Bank of Japan), which consists of 21 genomes from Archaea, 203 genomes from Bacteria, and 50 genomes from Eucarya (including 18 fungal genomes). Among 5,874 proteins of S. cerevisiae, 1,551 have homologs only in Eucarya, and 504 of the 1,551 have homologs only in fungi. To find fungal-specific proteins, homologs of the homologs have been searched repeatedly. As a result, 132 of the 504 are characterized as fungal-specific proteins. The genes encoding the 132 fungal-specific proteins are not included in the list of essential genes for viability in the S. cerevisiae genome deletion project. Among the 132 proteins, 99 are S. cerevisiae-specific, and no protein that is distributed among 10 or more of the 18 fungal species exists. In addition, most of the fungal-specific proteins are very small and functionally unknown. My results show that the fungal-specific proteins have short evolutionary histories, suggesting that S. cerevisiae produces novel proteins and that ancestral fungi also produced small proteins most of which have disappeared or have been combined with other proteins during fungal evolution.
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Affiliation(s)
- Hiromi Nishida
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunyo-ku, Tokyo, Japan.
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Hood HM, Spevak CC, Sachs MS. Evolutionary changes in the fungal carbamoyl-phosphate synthetase small subunit gene and its associated upstream open reading frame. Fungal Genet Biol 2006; 44:93-104. [PMID: 16979358 DOI: 10.1016/j.fgb.2006.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2006] [Revised: 07/11/2006] [Accepted: 07/19/2006] [Indexed: 11/28/2022]
Abstract
The Neurospora crassa arg-2 and the Saccharomyces cerevisiae ortholog CPA1 encode the arginine-specific carbamoyl-phosphate synthetase (CPS-A) small subunit. Arginine decreases synthesis of this subunit through the action of a 5' upstream open reading frame in the mRNA that encodes a cis-regulatory element, the arginine attenuator peptide (AAP), which stalls ribosomes in response to arginine. We performed a comparative analysis of the genomic structure and predicted peptide sequence of the AAP and CPS-A small subunit across many fungi. Differences at the genomic level included variation in intron number and position within the AAP and CPS-A coding regions and differences in known regulatory motifs. Although differences exist in AAP sequence, there were three absolutely conserved amino acid residues in the predicted peptide, including an aspartic acid crucial for arginine-dependent regulation of arg-2 and CPA1. A diverged Basidiomycete AAP was shown to retain function as an Arg-specific negative regulator of translation.
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Affiliation(s)
- Heather M Hood
- Department of Environmental and Biomolecular Systems, Oregon Health & Science University, Beaverton, OR 97006-8921, USA
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