1
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Luo S, Alwattar B, Li Q, Bora K, Blomfield AK, Lin J, Fulton A, Chen J, Agrawal PB. HBS1L deficiency causes retinal dystrophy in a child and in a mouse model associated with defective development of photoreceptor cells. Dis Model Mech 2024; 17:dmm050557. [PMID: 38966981 DOI: 10.1242/dmm.050557] [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] [Received: 10/19/2023] [Accepted: 06/21/2024] [Indexed: 07/06/2024] Open
Abstract
Inherited retinal diseases encompass a genetically diverse group of conditions caused by variants in genes critical to retinal function, including handful of ribosome-associated genes. This study focuses on the HBS1L gene, which encodes for the HBS1-like translational GTPase that is crucial for ribosomal rescue. We have reported a female child carrying biallelic HBS1L variants, manifesting with poor growth and neurodevelopmental delay. Here, we describe the ophthalmologic findings in the patient and in Hbs1ltm1a/tm1a hypomorph mice and describe the associated microscopic and molecular perturbations. The patient has impaired visual function, showing dampened amplitudes of a- and b-waves in both rod- and cone-mediated responses. Hbs1ltm1a/tm1a mice exhibited profound thinning of the entire retina, specifically of the outer photoreceptor layer, due to extensive photoreceptor cell apoptosis. Loss of Hbs1l resulted in comprehensive proteomic alterations by mass spectrometry analysis, with an increase in the levels of 169 proteins and a decrease in the levels of 480 proteins, including rhodopsin (Rho) and peripherin 2 (Prph2). Gene Ontology biological process and gene set enrichment analyses reveal that the downregulated proteins are primarily involved in phototransduction, cilium assembly and photoreceptor cell development. These findings underscore the importance of ribosomal rescue proteins in maintaining retinal health, particularly in photoreceptor cells.
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Affiliation(s)
- Shiyu Luo
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL 33136, USA
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bilal Alwattar
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Qifei Li
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL 33136, USA
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kiran Bora
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra K Blomfield
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jasmine Lin
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Fulton
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Chen
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL 33136, USA
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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2
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Chen KY, Park H, Subramaniam AR. Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control. Nucleic Acids Res 2024; 52:7171-7187. [PMID: 38647082 PMCID: PMC11229359 DOI: 10.1093/nar/gkae285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/28/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
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Affiliation(s)
- Katharine Y Chen
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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3
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Réthoré E, Pelletier S, Balliau T, Zivy M, Avelange-Macherel MH, Macherel D. Multi-scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy-transducing organelles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:300-331. [PMID: 38613336 DOI: 10.1111/tpj.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Much progress has been made in understanding the molecular mechanisms of plant adaptation to heat stress. However, the great diversity of models and stress conditions, and the fact that analyses are often limited to a small number of approaches, complicate the picture. We took advantage of a liquid culture system in which Arabidopsis seedlings are arrested in their development, thus avoiding interference with development and drought stress responses, to investigate through an integrative approach seedlings' global response to heat stress and acclimation. Seedlings perfectly tolerate a noxious heat shock (43°C) when subjected to a heat priming treatment at a lower temperature (38°C) the day before, displaying a thermotolerance comparable to that previously observed for Arabidopsis. A major effect of the pre-treatment was to partially protect energy metabolism under heat shock and favor its subsequent rapid recovery, which was correlated with the survival of seedlings. Rapid recovery of actin cytoskeleton and mitochondrial dynamics were another landmark of heat shock tolerance. The omics confirmed the role of the ubiquitous heat shock response actors but also revealed specific or overlapping responses to priming, heat shock, and their combination. Since only a few components or functions of chloroplast and mitochondria were highlighted in these analyses, the preservation and rapid recovery of their bioenergetic roles upon acute heat stress do not require extensive remodeling of the organelles. Protection of these organelles is rather integrated into the overall heat shock response, thus allowing them to provide the energy required to elaborate other cellular responses toward acclimation.
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Affiliation(s)
- Elise Réthoré
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Sandra Pelletier
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Thierry Balliau
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | - Michel Zivy
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | | | - David Macherel
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
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4
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Tseng YJ, Krans A, Malik I, Deng X, Yildirim E, Ovunc S, Tank EH, Jansen-West K, Kaufhold R, Gomez N, Sher R, Petrucelli L, Barmada S, Todd P. Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats. Nucleic Acids Res 2024; 52:5928-5949. [PMID: 38412259 PMCID: PMC11162809 DOI: 10.1093/nar/gkae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
A GGGGCC (G4C2) hexanucleotide repeat expansion in C9ORF72 causes amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), while a CGG trinucleotide repeat expansion in FMR1 leads to the neurodegenerative disorder Fragile X-associated tremor/ataxia syndrome (FXTAS). These GC-rich repeats form RNA secondary structures that support repeat-associated non-AUG (RAN) translation of toxic proteins that contribute to disease pathogenesis. Here we assessed whether these same repeats might trigger stalling and interfere with translational elongation. We find that depletion of ribosome-associated quality control (RQC) factors NEMF, LTN1 and ANKZF1 markedly boost RAN translation product accumulation from both G4C2 and CGG repeats while overexpression of these factors reduces RAN production in both reporter assays and C9ALS/FTD patient iPSC-derived neurons. We also detected partially made products from both G4C2 and CGG repeats whose abundance increased with RQC factor depletion. Repeat RNA sequence, rather than amino acid content, is central to the impact of RQC factor depletion on RAN translation-suggesting a role for RNA secondary structure in these processes. Together, these findings suggest that ribosomal stalling and RQC pathway activation during RAN translation inhibits the generation of toxic RAN products. We propose augmenting RQC activity as a therapeutic strategy in GC-rich repeat expansion disorders.
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Affiliation(s)
- Yi-Ju Tseng
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI 48109, USA
| | - Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284 Telangana, India
| | - Xiexiong Deng
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Evrim Yildirim
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sinem Ovunc
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth M H Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Ross Kaufhold
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicolas B Gomez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roger Sher
- Department of Neurobiology and Behavior & Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI 48109, USA
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5
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Hwang HJ, Kim YK. Molecular mechanisms of circular RNA translation. Exp Mol Med 2024; 56:1272-1280. [PMID: 38871818 PMCID: PMC11263353 DOI: 10.1038/s12276-024-01220-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs without a 5' cap structure and a 3' poly(A) tail typically present in linear mRNAs of eukaryotic cells. CircRNAs are predominantly generated through a back-splicing process within the nucleus. CircRNAs have long been considered non-coding RNAs seemingly devoid of protein-coding potential. However, many recent studies have challenged this idea and have provided substantial evidence that a subset of circRNAs can associate with polysomes and indeed be translated. Therefore, in this review, we primarily highlight the 5' cap-independent internal initiation of translation that occurs on circular RNAs. Several molecular features of circRNAs, including the internal ribosome entry site, N6-methyladenosine modification, and the exon junction complex deposited around the back-splicing junction after back-splicing event, play pivotal roles in their efficient internal translation. We also propose a possible relationship between the translatability of circRNAs and their stability, with a focus on nonsense-mediated mRNA decay and nonstop decay, both of which are well-characterized mRNA surveillance mechanisms. An in-depth understanding of circRNA translation will reshape and expand our current knowledge of proteomics.
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Affiliation(s)
- Hyun Jung Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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6
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Blake LA, Watkins L, Liu Y, Inoue T, Wu B. A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies. Nat Commun 2024; 15:2720. [PMID: 38548718 PMCID: PMC10979015 DOI: 10.1038/s41467-024-46943-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
RNA decay is vital for regulating mRNA abundance and gene expression. Existing technologies lack the spatiotemporal precision or transcript specificity to capture the stochastic and transient decay process. We devise a general strategy to inducibly recruit protein factors to modulate target RNA metabolism. Specifically, we introduce a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNAs within minutes. The fast and synchronous induction enables direct visualization of mRNA decay dynamics in cells. Applying RIDR to endogenous ACTB mRNA reveals rapid formation and dissolution of RNA granules in pre-existing P-bodies. Time-resolved RNA distribution measurements demonstrate rapid RNA decay inside P-bodies, which is further supported by knocking down P-body constituent proteins. Light and oxidative stress modulate P-body behavior, potentially reconciling the contradictory literature about P-body function. This study reveals compartmentalized RNA decay kinetics, establishing RIDR as a pivotal tool for exploring the spatiotemporal RNA metabolism in cells.
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Affiliation(s)
- Lauren A Blake
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leslie Watkins
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yang Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Takanari Inoue
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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7
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Peng G, Liu M, Luo Z, Deng S, Wang Q, Wang M, Chen H, Xiao Y, Zhang Y, Hong H, Zhu L, Liu Z, Zhou L, Wang Y, Zhuang C, Zhou H. An E3 ubiquitin ligase CSIT2 controls critical sterility-inducing temperature of thermo-sensitive genic male sterile rice. THE NEW PHYTOLOGIST 2024; 241:2059-2074. [PMID: 38197218 DOI: 10.1111/nph.19520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 12/08/2023] [Indexed: 01/11/2024]
Abstract
Thermo-sensitive genic male sterile (TGMS) lines are the core of two-line hybrid rice (Oryza sativa). However, elevated or unstable critical sterility-inducing temperatures (CSITs) of TGMS lines are bottlenecks that restrict the development of two-line hybrid rice. However, the genes and molecular mechanisms controlling CSIT remain unknown. Here, we report the CRITICAL STERILITY-INDUCING TEMPERATURE 2 (CSIT2) that encodes a really interesting new gene (RING) type E3 ligase, controlling the CSIT of thermo-sensitive male sterility 5 (tms5)-based TGMS lines through ribosome-associated protein quality control (RQC). CSIT2 binds to the large and small ribosomal subunits and ubiquitinates 80S ribosomes for dissociation, and may also ubiquitinate misfolded proteins for degradation. Mutation of CSIT2 inhibits the possible damage to ubiquitin system and protein translation, which allows more proteins such as catalases to accumulate for anther development and inhibits abnormal accumulation of reactive oxygen species (ROS) and premature programmed cell death (PCD) in anthers, partly rescuing male sterility and raised the CSIT of tms5-based TGMS lines. These findings reveal a mechanism controlling CSIT and provide a strategy for solving the elevated or unstable CSITs of tms5-based TGMS lines in two-line hybrid rice.
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Affiliation(s)
- Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Minglong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Shuangfan Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinghua Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huiqiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yueping Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yongjie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Haona Hong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lingyan Zhou
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yingxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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8
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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol Syst Biol 2024; 20:276-290. [PMID: 38273160 PMCID: PMC10912769 DOI: 10.1038/s44320-024-00013-0] [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] [Received: 11/27/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
- Department of Cell Biology, Duke University Medical Center, Durham, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, USA
- Department of Neurobiology, Duke University Medical Center, Durham, USA
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, USA.
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9
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Monem PC, Arribere JA. A ubiquitin language communicates ribosomal distress. Semin Cell Dev Biol 2024; 154:131-137. [PMID: 36963992 PMCID: PMC10878831 DOI: 10.1016/j.semcdb.2023.03.009] [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] [Received: 04/15/2022] [Revised: 02/10/2023] [Accepted: 03/16/2023] [Indexed: 03/26/2023]
Abstract
Cells entrust ribosomes with the critical task of identifying problematic mRNAs and facilitating their degradation. Ribosomes must communicate when they encounter and stall on an aberrant mRNA, lest they expose the cell to toxic and disease-causing proteins, or they jeopardize ribosome homeostasis and cellular translation. In recent years, ribosomal ubiquitination has emerged as a central signaling step in this process, and proteomic studies across labs and experimental systems show a myriad of ubiquitination sites throughout the ribosome. Work from many labs zeroed in on ubiquitination in one region of the small ribosomal subunit as being functionally significant, with the balance and exact ubiquitination sites determined by stall type, E3 ubiquitin ligases, and deubiquitinases. This review discusses the current literature surrounding ribosomal ubiquitination during translational stress and considers its role in committing translational complexes to decay.
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Affiliation(s)
- Parissa C Monem
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Joshua A Arribere
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA.
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10
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Popper B, Bürkle M, Ciccopiedi G, Marchioretto M, Forné I, Imhof A, Straub T, Viero G, Götz M, Schieweck R. Ribosome inactivation regulates translation elongation in neurons. J Biol Chem 2024; 300:105648. [PMID: 38219816 PMCID: PMC10869266 DOI: 10.1016/j.jbc.2024.105648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/10/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
Cellular plasticity is crucial for adapting to ever-changing stimuli. As a result, cells consistently reshape their translatome, and, consequently, their proteome. The control of translational activity has been thoroughly examined at the stage of translation initiation. However, the regulation of ribosome speed in cells is widely unknown. In this study, we utilized a timed ribosome runoff approach, along with proteomics and transmission electron microscopy, to investigate global translation kinetics in cells. We found that ribosome speeds vary among various cell types, such as astrocytes, induced pluripotent human stem cells, human neural stem cells, and human and rat neurons. Of all cell types studied, mature cortical neurons exhibit the highest rate of translation. This finding is particularly remarkable because mature cortical neurons express the eukaryotic elongation factor 2 (eEF2) at lower levels than other cell types. Neurons solve this conundrum by inactivating a fraction of their ribosomes. As a result, the increase in eEF2 levels leads to a reduction of inactive ribosomes and an enhancement of active ones. Processes that alter the demand for active ribosomes, like neuronal excitation, cause increased inactivation of redundant ribosomes in an eEF2-dependent manner. Our data suggest a novel regulatory mechanism in which neurons dynamically inactivate ribosomes to facilitate translational remodeling. These findings have important implications for developmental brain disorders characterized by, among other things, aberrant translation.
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Affiliation(s)
- Bastian Popper
- Core Facility Animal Models, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Martina Bürkle
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Giuliana Ciccopiedi
- Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Marta Marchioretto
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Ignasi Forné
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Tobias Straub
- Bioinformatics Core Facility, Department of Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Gabriella Viero
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Magdalena Götz
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany; SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Rico Schieweck
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy.
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11
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Wang L, Li H, Lei Z, Jeong DH, Cho J. The CARBON CATABOLITE REPRESSION 4A-mediated RNA deadenylation pathway acts on the transposon RNAs that are not regulated by small RNAs. THE NEW PHYTOLOGIST 2024; 241:1636-1645. [PMID: 38009859 DOI: 10.1111/nph.19435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Transposable elements (TEs) are mobile genetic elements that can impair the host genome stability and integrity. It has been well documented that activated transposons in plants are suppressed by small interfering (si) RNAs. However, transposon repression by the cytoplasmic RNA surveillance system is unknown. Here, we show that mRNA deadenylation is critical for controlling transposons in Arabidopsis. Trimming of poly(A) tail is a rate-limiting step that precedes the RNA decay and is primarily mediated by the CARBON CATABOLITE REPRESSION 4 (CCR4)-NEGATIVE ON TATA-LESS (NOT) complex. We found that the loss of CCR4a leads to strong derepression and mobilization of TEs in Arabidopsis. Intriguingly, CCR4a regulates a largely distinct set of TEs from those controlled by RNA-dependent RNA Polymerase 6 (RDR6), a key enzyme that produces cytoplasmic siRNAs. This indicates that the cytoplasmic RNA quality control mechanism targets the TEs that are poorly recognized by the previously well-characterized RDR6-mediated pathway, and thereby augments the host genome stability. Our study suggests a hitherto unknown mechanism for transposon repression mediated by RNA deadenylation and unveils a complex nature of the host's strategy to maintain the genome integrity.
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Affiliation(s)
- Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Zhen Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Dong-Hoon Jeong
- Department of Life Science, Hallym University, Chuncheon, 24252, Korea
- Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Korea
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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12
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Lyons EF, Devanneaux LC, Muller RY, Freitas AV, Meacham ZA, McSharry MV, Trinh VN, Rogers AJ, Ingolia NT, Lareau LF. Codon optimality modulates protein output by tuning translation initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568910. [PMID: 38076849 PMCID: PMC10705293 DOI: 10.1101/2023.11.27.568910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The impact of synonymous codon choice on protein output has important implications for understanding endogenous gene expression and design of synthetic mRNAs. Previously, we used a neural network model to design a series of synonymous fluorescent reporters whose protein output in yeast spanned a seven-fold range corresponding to their predicted translation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability, but rather, that an active mechanism further decreases the number of proteins made per mRNA. We combine simulations and careful experiments on fluorescent reporters to argue that translation initiation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen to discover factors modulating the output from non-optimal transcripts, we identify a set of translation initiation factors including multiple subunits of eIF3 whose depletion restored protein output of a non-optimal reporter. Our results show that codon usage can directly limit protein production, across the full range of endogenous variability in codon usage, by limiting translation initiation.
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Affiliation(s)
| | | | | | | | | | | | - Van N Trinh
- Department of Bioengineering, University of California, Berkeley
| | | | | | - Liana F Lareau
- Department of Molecular and Cell Biology
- California Institute for Quantitative Biosciences
- Department of Bioengineering, University of California, Berkeley
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13
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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540322. [PMID: 37214951 PMCID: PMC10197686 DOI: 10.1101/2023.05.11.540322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, United States
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, United States
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
- Department of Cell Biology, Duke University Medical Center, Durham, United States
- Duke Regeneration Center, Duke University Medical Center, Durham, United States
- Department of Neurobiology, Duke University Medical Center, Durham, United States
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, United States
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, United States
- Helen Diller Family Comprehensive Cancer Center, San Francisco, United States
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14
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Wu K, Fu Y, Ren Y, Liu L, Zhang X, Ruan M. Turnip crinkle virus-encoded suppressor of RNA silencing suppresses mRNA decay by interacting with Arabidopsis XRN4. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:744-755. [PMID: 37522642 DOI: 10.1111/tpj.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
Plant cells employ intricate defense mechanisms, including mRNA decay pathways, to counter viral infections. Among the RNA quality control (RQC) mechanisms, nonsense-mediated decay (NMD), no-go decay (NGD), and nonstop decay (NSD) pathways play critical roles in recognizing and cleaving aberrant mRNA molecules. Turnip crinkle virus (TCV) is a plant virus that triggers mRNA decay pathways, but it has also evolved strategies to evade this antiviral defense. In this study, we investigated the activation of mRNA decay during TCV infection and its impact on TCV RNA accumulation. We found that TCV infection induced the upregulation of essential mRNA decay factors, indicating their involvement in antiviral defense and the capsid protein (CP) of TCV, a well-characterized viral suppressor of RNA silencing (VSR), also compromised the mRNA decay-based antiviral defense by targeting AtXRN4. This interference with mRNA decay was supported by the observation that TCV CP stabilized a reporter transcript with a long 3' untranslated region (UTR). Moreover, TCV CP suppressed the decay of known NMD target transcripts, further emphasizing its ability to modulate host RNA control mechanisms. Importantly, TCV CP physically interacted with AtXRN4, providing insight into the mechanism of viral interference with mRNA decay. Overall, our findings reveal an alternative strategy employed by TCV, wherein the viral coat protein suppresses the mRNA decay pathway to facilitate viral infection.
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Affiliation(s)
- Kunxin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agriculture Resources, Haikou, 571101, China
| | - Yan Fu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agriculture Resources, Haikou, 571101, China
| | - Yanli Ren
- School of Biological and Geographical Sciences, Yili Normal University, Yili, 835000, China
| | - Linyu Liu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agriculture Resources, Haikou, 571101, China
- School of Biological and Geographical Sciences, Yili Normal University, Yili, 835000, China
| | - Xiuchun Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agriculture Resources, Haikou, 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572025, China
| | - Mengbin Ruan
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agriculture Resources, Haikou, 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, 572025, China
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15
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Alagar Boopathy LR, Beadle E, Garcia-Bueno Rico A, Vera M. Proteostasis regulation through ribosome quality control and no-go-decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1809. [PMID: 37488089 DOI: 10.1002/wrna.1809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/14/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Abstract
Cell functionality relies on the existing pool of proteins and their folding into functional conformations. This is achieved through the regulation of protein synthesis, which requires error-free mRNAs and ribosomes. Ribosomes are quality control hubs for mRNAs and proteins. Problems during translation elongation slow down the decoding rate, leading to ribosome halting and the eventual collision with the next ribosome. Collided ribosomes form a specific disome structure recognized and solved by ribosome quality control (RQC) mechanisms. RQC pathways orchestrate the degradation of the problematic mRNA by no-go decay and the truncated nascent peptide, the repression of translation initiation, and the recycling of the stalled ribosomes. All these events maintain protein homeostasis and return valuable ribosomes to translation. As such, cell homeostasis and function are maintained at the mRNA level by preventing the production of aberrant or unnecessary proteins. It is becoming evident that the crosstalk between RQC and the protein homeostasis network is vital for cell function, as the absence of RQC components leads to the activation of stress response and neurodegenerative diseases. Here, we review the molecular events of RQC discovered through well-designed stalling reporters. Given the impact of RQC in proteostasis, we discuss the relevance of identifying endogenous mRNA regulated by RQC and their preservation in stress conditions. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms Translation > Regulation.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
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16
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Krempl C, Lazzaretti D, Sprangers R. A structural biology view on the enzymes involved in eukaryotic mRNA turnover. Biol Chem 2023; 404:1101-1121. [PMID: 37709756 DOI: 10.1515/hsz-2023-0182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023]
Abstract
The cellular environment contains numerous ribonucleases that are dedicated to process mRNA transcripts that have been targeted for degradation. Here, we review the three dimensional structures of the ribonuclease complexes (Pan2-Pan3, Ccr4-Not, Xrn1, exosome) and the mRNA decapping enzymes (Dcp2, DcpS) that are involved in mRNA turnover. Structures of major parts of these proteins have been experimentally determined. These enzymes and factors do not act in isolation, but are embedded in interaction networks which regulate enzyme activity and ensure that the appropriate substrates are recruited. The structural details of the higher order complexes that form can, in part, be accurately deduced from known structural data of sub-complexes. Interestingly, many of the ribonuclease and decapping enzymes have been observed in structurally different conformations. Together with experimental data, this highlights that structural changes are often important for enzyme function. We conclude that the known structural data of mRNA decay factors provide important functional insights, but that static structural data needs to be complemented with information regarding protein motions to complete the picture of how transcripts are turned over. In addition, we highlight multiple aspects that influence mRNA turnover rates, but that have not been structurally characterized so far.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Lazzaretti
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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17
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Luo S, Alwattar B, Li Q, Bora K, Blomfield AK, Lin J, Fulton A, Chen J, Agrawal PB. Genetic deficiency of ribosomal rescue factor HBS1L causes retinal dystrophy associated with Pelota and EDF1 depletion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562924. [PMID: 37905068 PMCID: PMC10614867 DOI: 10.1101/2023.10.18.562924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Inherited retinal diseases (IRDs) encompass a genetically diverse group of conditions in which mutations in genes critical to retinal function lead to progressive loss of photoreceptor cells and subsequent visual impairment. A handful of ribosome-associated genes have been implicated in retinal disorders alongside neurological phenotypes. This study focuses on the HBS1L gene, encoding HBS1 Like Translational GTPase which has been recognized as a critical ribosomal rescue factor. Previously, we have reported a female child carrying biallelic HBS1L mutations, manifesting growth restriction, developmental delay, and hypotonia. In this study, we describe her ophthalmologic findings, compare them with the Hbs1ltm1a/tm1a hypomorph mouse model, and evaluate the underlying microscopic and molecular perturbations. The patient was noted to have impaired visual function observed by electroretinogram (ERG), with dampened amplitudes of a- and b-waves in both rod- and cone-mediated responses. Hbs1ltm1a/tm1a mice exhibited profound retinal thinning of the entire retina, specifically of the outer retinal photoreceptor layer, detected using in vivo imaging of optical coherence tomography (OCT) and retinal cross sections. TUNEL assay revealed retinal degeneration due to extensive photoreceptor cell apoptosis. Loss of HBS1L resulted in comprehensive proteomic alterations in mass spectrometry analysis, with169 proteins increased and 480 proteins decreased including many critical IRD-related proteins. GO biological process and GSEA analyses reveal that these downregulated proteins are primarily involved in photoreceptor cell development, cilium assembly, phototransduction, and aerobic respiration. Furthermore, apart from the diminished level of PELO, a known partner protein, HBS1L depletion was accompanied by reduction in translation machinery associated 7 homolog (Tma7), and Endothelial differentiation-related factor 1(Edf1) proteins, the latter of which coordinates cellular responses to ribosome collisions. This novel connection between HBS1L and ribosome collision sensor (EDF1) further highlights the intricate mechanisms underpinning ribosomal rescue and quality control that are essential to maintain homeostasis of key proteins of retinal health, such as rhodopsin.
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Affiliation(s)
- Shiyu Luo
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children’s Hospital, Jackson Health System, Miami, FL 33136, USA
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Bilal Alwattar
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School; Boston, MA 02115, USA
| | - Qifei Li
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children’s Hospital, Jackson Health System, Miami, FL 33136, USA
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Kiran Bora
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School; Boston, MA 02115, USA
| | - Alexandra K. Blomfield
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School; Boston, MA 02115, USA
| | - Jasmine Lin
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Anne Fulton
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School; Boston, MA 02115, USA
| | - Jing Chen
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School; Boston, MA 02115, USA
| | - Pankaj B. Agrawal
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children’s Hospital, Jackson Health System, Miami, FL 33136, USA
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston, MA 02115, USA
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18
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EL-Seedy A, Pellerin L, Page G, Ladeveze V. Identification of Intron Retention in the Slc16a3 Gene Transcript Encoding the Transporter MCT4 in the Brain of Aged and Alzheimer-Disease Model (APPswePS1dE9) Mice. Genes (Basel) 2023; 14:1949. [PMID: 37895298 PMCID: PMC10606527 DOI: 10.3390/genes14101949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
The monocarboxylate transporter 4 (MCT4; Slc16a3) is expressed in the central nervous system, notably by astrocytes. It is implicated in lactate release and the regulation of glycolytic flux. Whether its expression varies during normal and/or pathological aging is unclear. As the presence of its mature transcript in the brain of young and old mice was determined, an unexpectedly longer RT-PCR fragment was detected in the mouse frontal cortex and hippocampus at 12 vs. 3 months of age. Cultured astrocytes expressed the expected 516 base pair (bp) fragment but treatment with IL-1β to mimic inflammation as can occur during aging led to the additional expression of a 928 bp fragment like that seen in aged mice. In contrast, cultured pericytes (a component of the blood-brain barrier) only exhibited the 516 bp fragment. Intriguingly, cultured endothelial cells constitutively expressed both fragments. When RT-PCR was performed on brain subregions of an Alzheimer mouse model (APPswePS1dE9), no fragment was detected at 3 months, while only the 928 bp fragment was present at 12 months. Sequencing of MCT4 RT-PCR products revealed the presence of a remaining intron between exon 2 and 3, giving rise to the longer fragment detected by RT-PCR. These results unravel the existence of intron retention for the MCT4 gene in the central nervous system. Such alternative splicing appears to increase with age in the brain and might be prominent in neurodegenerative diseases such as Alzheimer's disease. Hence, further studies in vitro and in vivo of intron 2 retention in the Slc16a3 gene transcript are required for adequate characterization concerning the biological roles of Slc16a3 isoforms in the context of aging and Alzheimer's disease pathology.
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Affiliation(s)
- Ayman EL-Seedy
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Alexandria University, Aflaton Street, El-Shatby, Alexandria 21545, Egypt;
- Neurovascular Unit and Cognitive Disorders (NEUVACOD), Faculty of Pharmacy (GP), Faculty of Fundamental and Applied Science (VL), University of Poitiers, Pôle Biologie Santé, 86073 Poitiers, France;
| | - Luc Pellerin
- IRMETIST, INSERM, Faculty of Medicine, University of Poitiers (U1313), CHU de Poitiers, 86021 Poitiers, France;
| | - Guylène Page
- Neurovascular Unit and Cognitive Disorders (NEUVACOD), Faculty of Pharmacy (GP), Faculty of Fundamental and Applied Science (VL), University of Poitiers, Pôle Biologie Santé, 86073 Poitiers, France;
| | - Veronique Ladeveze
- Neurovascular Unit and Cognitive Disorders (NEUVACOD), Faculty of Pharmacy (GP), Faculty of Fundamental and Applied Science (VL), University of Poitiers, Pôle Biologie Santé, 86073 Poitiers, France;
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19
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Monaghan L, Longman D, Cáceres JF. Translation-coupled mRNA quality control mechanisms. EMBO J 2023; 42:e114378. [PMID: 37605642 PMCID: PMC10548175 DOI: 10.15252/embj.2023114378] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
mRNA surveillance pathways are essential for accurate gene expression and to maintain translation homeostasis, ensuring the production of fully functional proteins. Future insights into mRNA quality control pathways will enable us to understand how cellular mRNA levels are controlled, how defective or unwanted mRNAs can be eliminated, and how dysregulation of these can contribute to human disease. Here we review translation-coupled mRNA quality control mechanisms, including the non-stop and no-go mRNA decay pathways, describing their mechanisms, shared trans-acting factors, and differences. We also describe advances in our understanding of the nonsense-mediated mRNA decay (NMD) pathway, highlighting recent mechanistic findings, the discovery of novel factors, as well as the role of NMD in cellular physiology and its impact on human disease.
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Affiliation(s)
- Laura Monaghan
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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20
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Chen KY, Park H, Subramaniam AR. Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559793. [PMID: 37808677 PMCID: PMC10557687 DOI: 10.1101/2023.09.27.559793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
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Affiliation(s)
- Katharine Y. Chen
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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21
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Latallo MJ, Wang S, Dong D, Nelson B, Livingston NM, Wu R, Zhao N, Stasevich TJ, Bassik MC, Sun S, Wu B. Single-molecule imaging reveals distinct elongation and frameshifting dynamics between frames of expanded RNA repeats in C9ORF72-ALS/FTD. Nat Commun 2023; 14:5581. [PMID: 37696852 PMCID: PMC10495369 DOI: 10.1038/s41467-023-41339-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
C9ORF72 hexanucleotide repeat expansion is the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism is the accumulation of toxic dipeptide repeat (DPR) proteins like poly-GA, GP and GR, produced by the noncanonical translation of the expanded RNA repeats. However, how different DPRs are synthesized remains elusive. Here, we use single-molecule imaging techniques to directly measure the translation dynamics of different DPRs. Besides initiation, translation elongation rates vary drastically between different frames, with GP slower than GA and GR the slowest. We directly visualize frameshift events using a two-color single-molecule translation assay. The repeat expansion enhances frameshifting, but the overall frequency is low. There is a higher chance of GR-to-GA shift than in the reversed direction. Finally, the ribosome-associated protein quality control (RQC) factors ZNF598 and Pelota modulate the translation dynamics, and the repeat RNA sequence is important for invoking the RQC pathway. This study reveals that multiple translation steps modulate the final DPR production. Understanding repeat RNA translation is critically important to decipher the DPR-mediated pathogenesis and identify potential therapeutic targets in C9ORF72-ALS/FTD.
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Affiliation(s)
- Malgorzata J Latallo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shaopeng Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Daoyuan Dong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Blake Nelson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nathan M Livingston
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ning Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shuying Sun
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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22
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Sahinbegovic H, Vdovin A, Snaurova R, Durech M, Nezval J, Sobotka J, Hajek R, Jelinek T, Simicek M. Length-Dependent Translation Efficiency of ER-Destined Proteins. Curr Issues Mol Biol 2023; 45:6717-6727. [PMID: 37623244 PMCID: PMC10453119 DOI: 10.3390/cimb45080425] [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] [Received: 07/12/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Gene expression is a fundamental process that enables cells to produce specific proteins in a timely and spatially dependent manner. In eukaryotic cells, the complex organization of the cell body requires precise control of protein synthesis and localization. Certain mRNAs encode proteins with an N-terminal signal sequences that direct the translation apparatus toward a specific organelle. Here, we focus on the mechanisms governing the translation of mRNAs, which encode proteins with an endoplasmic reticulum (ER) signal in human cells. The binding of a signal-recognition particle (SRP) to the translation machinery halts protein synthesis until the mRNA-ribosome complex reaches the ER membrane. The commonly accepted model suggests that mRNA that encodes a protein that contains an ER signal peptide continuously repeats the cycle of SRP binding followed by association and dissociation with the ER. In contrast to the current view, we show that the long mRNAs remain on the ER while being translated. On the other hand, due to low ribosome occupancy, the short mRNAs continue the cycle, always facing a translation pause. Ultimately, this leads to a significant drop in the translation efficiency of small, ER-targeted proteins. The proposed mechanism advances our understanding of selective protein synthesis in eukaryotic cells and provides new avenues to enhance protein production in biotechnological settings.
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Affiliation(s)
- Hana Sahinbegovic
- Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
- Faculty of Science, Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Alexander Vdovin
- Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
- Faculty of Science, Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Renata Snaurova
- Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
- Faculty of Science, Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Michal Durech
- Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
| | - Jakub Nezval
- Faculty of Science, Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Jiri Sobotka
- Laboratory of Medical Genetics, SPADIA LAB a.s., 700 30 Ostrava, Czech Republic
| | - Roman Hajek
- Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
| | - Tomas Jelinek
- Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
| | - Michal Simicek
- Faculty of Medicine, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
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23
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Alagar Boopathy L, Beadle E, Xiao A, Garcia-Bueno Rico A, Alecki C, Garcia de-Andres I, Edelmeier K, Lazzari L, Amiri M, Vera M. The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome. Nucleic Acids Res 2023; 51:6370-6388. [PMID: 37158240 PMCID: PMC10325905 DOI: 10.1093/nar/gkad338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
Cells survive harsh environmental conditions by potently upregulating molecular chaperones such as heat shock proteins (HSPs), particularly the inducible members of the HSP70 family. The life cycle of HSP70 mRNA in the cytoplasm is unique-it is translated during stress when most cellular mRNA translation is repressed and rapidly degraded upon recovery. Contrary to its 5' untranslated region's role in maximizing translation, we discovered that the HSP70 coding sequence (CDS) suppresses its translation via the ribosome quality control (RQC) mechanism. The CDS of the most inducible Saccharomyces cerevisiae HSP70 gene, SSA4, is uniquely enriched with low-frequency codons that promote ribosome stalling during heat stress. Stalled ribosomes are recognized by the RQC components Asc1p and Hel2p and two novel RQC components, the ribosomal proteins Rps28Ap and Rps19Bp. Surprisingly, RQC does not signal SSA4 mRNA degradation via No-Go-Decay. Instead, Asc1p destabilizes SSA4 mRNA during recovery from heat stress by a mechanism independent of ribosome binding and SSA4 codon optimality. Therefore, Asc1p operates in two pathways that converge to regulate the SSA4 mRNA life cycle during stress and recovery. Our research identifies Asc1p as a critical regulator of the stress response and RQC as the mechanism tuning HSP70 synthesis.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Alan RuoChen Xiao
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Celia Alecki
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Kyla Edelmeier
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Luca Lazzari
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Mehdi Amiri
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Maria Vera
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
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24
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Abstract
Messenger RNA (mRNA) stability and translational efficiency are two crucial aspects of the post-transcriptional process that profoundly impact protein production in a cell. While it is widely known that ribosomes produce proteins, studies during the past decade have surprisingly revealed that ribosomes also control mRNA stability in a codon-dependent manner, a process referred to as codon optimality. Therefore, codons, the three-nucleotide words read by the ribosome, have a potent effect on mRNA stability and provide cis-regulatory information that extends beyond the amino acids they encode. While the codon optimality molecular mechanism is still unclear, the translation elongation rate appears to trigger mRNA decay. Thus, transfer RNAs emerge as potential master gene regulators affecting mRNA stability. Furthermore, while few factors related to codon optimality have been identified in yeast, the orthologous genes in vertebrates do not necessary share the same functions. Here, we discuss codon optimality findings and gene regulation layers related to codon composition in different eukaryotic species.
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Affiliation(s)
- Qiushuang Wu
- Stowers Institute for Medical Research, Kansas City, Missouri, USA;
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, Missouri, USA;
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
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25
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Tseng YJ, Malik I, Deng X, Krans A, Jansen-West K, Tank EM, Gomez NB, Sher R, Petrucelli L, Barmada SJ, Todd PK. Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544135. [PMID: 37333274 PMCID: PMC10274811 DOI: 10.1101/2023.06.07.544135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A GGGGCC (G4C2) hexanucleotide repeat expansion in C9ORF72 causes amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), while a CGG trinucleotide repeat expansion in FMR1 leads to the neurodegenerative disorder Fragile X-associated tremor/ataxia syndrome (FXTAS). These GC-rich repeats form RNA secondary structures that support repeat-associated non-AUG (RAN) translation of toxic proteins that contribute to disease pathogenesis. Here we assessed whether these same repeats might trigger stalling and interfere with translational elongation. We find that depletion of ribosome-associated quality control (RQC) factors NEMF, LTN1, and ANKZF1 markedly boost RAN translation product accumulation from both G4C2 and CGG repeats while overexpression of these factors reduces RAN production in both reporter cell lines and C9ALS/FTD patient iPSC-derived neurons. We also detected partially made products from both G4C2 and CGG repeats whose abundance increased with RQC factor depletion. Repeat RNA sequence, rather than amino acid content, is central to the impact of RQC factor depletion on RAN translation - suggesting a role for RNA secondary structure in these processes. Together, these findings suggest that ribosomal stalling and RQC pathway activation during RAN translation elongation inhibits the generation of toxic RAN products. We propose augmenting RQC activity as a therapeutic strategy in GC-rich repeat expansion disorders.
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Affiliation(s)
- Yi-Ju Tseng
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiexiong Deng
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, 48109, USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Nicolas B. Gomez
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Roger Sher
- Department of Neurobiology and Behavior & Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY, 11794, USA
| | | | - Sami J. Barmada
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter K. Todd
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, 48109, USA
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26
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Kim YJ. Crosstalk between RNA silencing and RNA quality control in plants. BMB Rep 2023; 56:321-325. [PMID: 37156633 PMCID: PMC10315563 DOI: 10.5483/bmbrep.2023-0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2024] Open
Abstract
RNAs are pivotal molecules acting as messengers of genetic information and regulatory molecules for cellular development and survival. From birth to death, RNAs face constant cellular decision for the precise control of cellular function and activity. Most eukaryotic cells employ conserved machineries for RNA decay including RNA silencing and RNA quality control (RQC). In plants, RQC monitors endogenous RNAs and degrades aberrant and dysfunctional species, whereas RNA silencing promotes RNA degradation to repress the expression of selected endogenous RNAs or exogenous RNA derived from transgenes and virus. Interestingly, emerging evidences have indicated that RQC and RNA silencing interact with each by sharing target RNAs and regulatory components. Such interaction should be tightly organized for proper cellular survival. However, it is still elusive that how each machinery specifically recognizes target RNAs. In this review, we summarize recent advances on RNA silencing and RQC pathway and discuss potential mechanisms underlying the interaction between the two machineries. [BMB Reports 2023; 56(6): 321-325].
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Affiliation(s)
- Yun Ju Kim
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
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27
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Wang X, Li Y, Yan X, Yang Q, Zhang B, Zhang Y, Yuan X, Jiang C, Chen D, Liu Q, Liu T, Mi W, Yu Y, Dong C. Recognition of an Ala-rich C-degron by the E3 ligase Pirh2. Nat Commun 2023; 14:2474. [PMID: 37120596 PMCID: PMC10148881 DOI: 10.1038/s41467-023-38173-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
The ribosome-associated quality-control (RQC) pathway degrades aberrant nascent polypeptides arising from ribosome stalling during translation. In mammals, the E3 ligase Pirh2 mediates the degradation of aberrant nascent polypeptides by targeting the C-terminal polyalanine degrons (polyAla/C-degrons). Here, we present the crystal structure of Pirh2 bound to the polyAla/C-degron, which shows that the N-terminal domain and the RING domain of Pirh2 form a narrow groove encapsulating the alanine residues of the polyAla/C-degron. Affinity measurements in vitro and global protein stability assays in cells further demonstrate that Pirh2 recognizes a C-terminal A/S-X-A-A motif for substrate degradation. Taken together, our study provides the molecular basis underlying polyAla/C-degron recognition by Pirh2 and expands the substrate recognition spectrum of Pirh2.
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Affiliation(s)
- Xiaolu Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Tianjin Medical University, 300070, Tianjin, China
| | - Yao Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Xiaojie Yan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Qing Yang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Bing Zhang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Ying Zhang
- Department of Immunology, Tianjin Institute of Immunology, Tianjin Medical University, 300070, Tianjin, China
| | - Xinxin Yuan
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China
| | - Chenhao Jiang
- Department of Immunology, Tianjin Institute of Immunology, Tianjin Medical University, 300070, Tianjin, China
| | - Dongxing Chen
- Department of Medicinal Chemistry, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, 300070, Tianjin, China
| | - Quanyan Liu
- Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Tong Liu
- Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, 300211, Tianjin, China
| | - Wenyi Mi
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
- Department of Immunology, Tianjin Institute of Immunology, Tianjin Medical University, 300070, Tianjin, China
| | - Ying Yu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Tianjin Medical University, 300070, Tianjin, China.
| | - Cheng Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, China.
- Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital, 300052, Tianjin, China.
- Department of Cardiology, Tianjin Institute of Cardiology, Second Hospital of Tianjin Medical University, 300211, Tianjin, China.
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28
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Blake LA, Liu Y, Inoue T, Wu B. A Rapid Inducible RNA Decay system reveals fast mRNA decay in P-bodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538452. [PMID: 37162943 PMCID: PMC10168379 DOI: 10.1101/2023.04.26.538452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNA decay plays a crucial role in regulating mRNA abundance and gene expression. Modulation of RNA degradation is imperative to investigate an RNA's function. However, information regarding where and how RNA decay occurs remains scarce, partially because existing technologies fail to initiate RNA decay with the spatiotemporal precision or transcript specificity required to capture this stochastic and transient process. Here, we devised a general method that employs inducible tethering of regulatory protein factors to target RNAs and modulate their metabolism. Specifically, we established a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNA within minutes. The fast and synchronous induction enabled direct visualization of mRNA decay dynamics in cells with spatiotemporal precision previously unattainable. When applying RIDR to endogenous ACTB mRNA, we observed rapid formation and disappearance of RNA granules, which coincided with pre-existing processing bodies (P-bodies). We measured the time-resolved RNA distribution in P-bodies and cytoplasm after induction, and compared different models of P-body function. We determined that mRNAs rapidly decayed in P-bodies upon induction. Additionally, we validated the functional role of P-bodies by knocking down specific a P-body constituent protein and RNA degradation enzyme. This study determined compartmentalized RNA decay kinetics for the first time. Together, RIDR provides a valuable and generalizable tool to study the spatial and temporal RNA metabolism in cells.
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29
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Ge L, Cao B, Qiao R, Cui H, Li S, Shan H, Gong P, Zhang M, Li H, Wang A, Zhou X, Li F. SUMOylation-modified Pelota-Hbs1 RNA surveillance complex restricts the infection of potyvirids in plants. MOLECULAR PLANT 2023; 16:632-642. [PMID: 36597359 DOI: 10.1016/j.molp.2022.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/12/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
RNA quality control nonsense-mediated decay is involved in viral restriction in both plants and animals. However, it is not known whether two other RNA quality control pathways, nonstop decay and no-go decay, are capable of restricting viruses in plants. Here, we show that the evolutionarily conserved Pelota-Hbs1 complex negatively regulates infection of plant viruses in the family Potyviridae (termed potyvirids), the largest group of plant RNA viruses that accounts for more than half of the viral crop damage worldwide. Pelota enables the recognition of the functional G1-2A6-7 motif in the P3 cistron, which is conserved in almost all potyvirids. This allows Pelota to target the virus and act as a viral restriction factor. Furthermore, Pelota interacts with the SUMO E2-conjugating enzyme SCE1 and is SUMOylated in planta. Blocking Pelota SUMOylation disrupts the ability to recruit Hbs1 and inhibits viral RNA degradation. These findings reveal the functional importance of Pelota SUMOylation during the infection of potyvirids in plants.
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Affiliation(s)
- Linhao Ge
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Buwei Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Qiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongguang Cui
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and College of Plant Protection, Hainan University, Haikou, Hainan, China
| | - Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongying Shan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pan Gong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingzhen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hao Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada; Department of Biology, Western University, London, ON, Canada
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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30
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Haluck-Kangas A, Peter ME. CD95/Fas ligand induced toxicity. Biochem Soc Trans 2023; 51:21-29. [PMID: 36629505 PMCID: PMC10149114 DOI: 10.1042/bst20211187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
The role of CD95/Fas ligand (CD95L/FasL) in the induction of CD95-mediated extrinsic apoptosis is well characterized. Trimerized, membrane-bound CD95L ligates the CD95 receptor activating downstream signaling resulting in the execution of cells by caspase proteins. However, the expression of CD95L has been reported to induce cell death in contexts in which this pathway is unlikely to be activated, such as in cell autonomous activation induced cell death (AICD) and in CD95-resistant cancer cell lines. Recent data suggests that the CD95L mRNA exerts toxicity through death induced by survival gene elimination (DISE). DISE results from the targeting of networks of survival genes by toxic short RNA (sRNA)s in the RNA-induced silencing complex (RISC). CD95L mRNA contributes to this death directly, through the processing of its mRNA into toxic sRNAs that are loaded into the RISC, and indirectly, by promoting the loading of other toxic sRNAs. Interestingly, CD95L is not the only mRNA that is processed and loaded into the RISC. Protein-coding mRNAs involved in protein translation are also selectively loaded. We propose a model in which networks of mRNA-derived sRNAs modulate DISE, with networks of genes providing non-toxic RISC substrate sRNAs that protect against DISE, and opposing networks of stress-activated genes that produce toxic RISC substrate sRNAs that promote DISE.
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Affiliation(s)
- Ashley Haluck-Kangas
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Marcus E. Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL
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31
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Stankov S, Vitali C, Park J, Nguyen D, Mayne L, Englander SW, Levin MG, Vujkovic M, Hand NJ, Phillips MC, Rader DJ. Comparison of the structure-function properties of wild-type human apoA-V and a C-terminal truncation associated with elevated plasma triglycerides. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.21.23286268. [PMID: 36865344 PMCID: PMC9980232 DOI: 10.1101/2023.02.21.23286268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Background Plasma triglycerides (TGs) are causally associated with coronary artery disease and acute pancreatitis. Apolipoprotein A-V (apoA-V, gene APOA5) is a liver-secreted protein that is carried on triglyceride-rich lipoproteins and promotes the enzymatic activity of lipoprotein lipase (LPL), thereby reducing TG levels. Little is known about apoA-V structure-function; naturally occurring human APOA5 variants can provide novel insights. Methods We used hydrogen-deuterium exchange mass spectrometry to determine the secondary structure of human apoA-V in lipid-free and lipid-associated conditions and identified a C-terminal hydrophobic face. Then, we used genomic data in the Penn Medicine Biobank to identify a rare variant, Q252X, predicted to specifically eliminate this region. We interrogated the function of apoA-V Q252X using recombinant protein in vitro and in vivo in apoa5 knockout mice. Results Human apoA-V Q252X carriers exhibited elevated plasma TG levels consistent with loss of function. Apoa5 knockout mice injected with AAV vectors expressing wildtype and variant APOA5-AAV recapitulated this phenotype. Part of the loss of function is due to reduced mRNA expression. Functionally, recombinant apoA-V Q252X was more readily soluble in aqueous solutions and more exchangeable with lipoproteins than WT apoA-V. Despite lacking the C-terminal hydrophobic region (a putative lipid binding domain) this protein also decreased plasma TG in vivo. Conclusions Deletion of apoA-V's C-terminus leads to reduced apoA-V bioavailability in vivo and higher TG levels. However, the C-terminus is not required for lipoprotein binding or enhancement of intravascular lipolytic activity. WT apoA-V is highly prone to aggregation, and this property is markedly reduced in recombinant apoA-V lacking the C-terminus.
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Affiliation(s)
- Sylvia Stankov
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cecilia Vitali
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Park
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Nguyen
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leland Mayne
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S. Walter Englander
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Michael G. Levin
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
| | - Marijana Vujkovic
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
| | - Nicholas J. Hand
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C. Phillips
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J. Rader
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Jackson JJ, Mao Y, White TR, Foye C, Oliver KE. Features of CFTR mRNA and implications for therapeutics development. Front Genet 2023; 14:1166529. [PMID: 37168508 PMCID: PMC10165737 DOI: 10.3389/fgene.2023.1166529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease impacting ∼100,000 people worldwide. This lethal disorder is caused by mutation of the CF transmembrane conductance regulator (CFTR) gene, which encodes an ATP-binding cassette-class C protein. More than 2,100 variants have been identified throughout the length of CFTR. These defects confer differing levels of severity in mRNA and/or protein synthesis, folding, gating, and turnover. Drug discovery efforts have resulted in recent development of modulator therapies that improve clinical outcomes for people living with CF. However, a significant portion of the CF population has demonstrated either no response and/or adverse reactions to small molecules. Additional therapeutic options are needed to restore underlying genetic defects for all patients, particularly individuals carrying rare or refractory CFTR variants. Concerted focus has been placed on rescuing variants that encode truncated CFTR protein, which also harbor abnormalities in mRNA synthesis and stability. The current mini-review provides an overview of CFTR mRNA features known to elicit functional consequences on final protein conformation and function, including considerations for RNA-directed therapies under investigation. Alternative exon usage in the 5'-untranslated region, polypyrimidine tracts, and other sequence elements that influence splicing are discussed. Additionally, we describe mechanisms of CFTR mRNA decay and post-transcriptional regulation mediated through interactions with the 3'-untranslated region (e.g. poly-uracil sequences, microRNAs). Contributions of synonymous single nucleotide polymorphisms to CFTR transcript utilization are also examined. Comprehensive understanding of CFTR RNA biology will be imperative for optimizing future therapeutic endeavors intended to address presently untreatable forms of CF.
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Affiliation(s)
- JaNise J. Jackson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Yiyang Mao
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Tyshawn R. White
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Catherine Foye
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
- *Correspondence: Kathryn E. Oliver,
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Helton NS, Moon SL. Is bRaQCing bad? New roles for ribosome associated quality control factors in stress granule regulation. Biochem Soc Trans 2022; 50:1715-1724. [PMID: 36484689 PMCID: PMC11368206 DOI: 10.1042/bst20220549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 11/21/2022] [Indexed: 09/04/2024]
Abstract
Maintenance of proteostasis is of utmost importance to cellular viability and relies on the coordination of many post-transcriptional processes to respond to stressful stimuli. Stress granules (SGs) are RNA-protein condensates that form after translation initiation is inhibited, such as during the integrated stress response (ISR), and may facilitate cellular adaptation to stress. The ribosome-associated quality control (RQC) pathway is a critical translation monitoring system that recognizes aberrant mRNAs encoding potentially toxic nascent peptides to target them for degradation. Both SG regulation and the RQC pathway are directly associated with translation regulation, thus it is of no surprise recent developments have demonstrated a connection between them. VCP's function in the stress activated RQC pathway, ribosome collisions activating the ISR, and the regulation of the 40S ribosomal subunit by canonical SG proteins during the RQC all connect SGs to the RQC pathway. Because mutations in genes that are involved in both SG and RQC regulation are associated with degenerative and neurological diseases, understanding the coordination and interregulation of SGs and RQC may shed light on disease mechanisms. This minireview will highlight recent advances in understanding how SGs and the RQC pathway interact in health and disease contexts.
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Affiliation(s)
- Noah S Helton
- The Center for RNA Biomedicine and the Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, U.S.A
| | - Stephanie L Moon
- The Center for RNA Biomedicine and the Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, U.S.A
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Deubiquitinase OTUD1 Resolves Stalled Translation on polyA and Rare Codon Rich mRNAs. Mol Cell Biol 2022; 42:e0026522. [PMID: 36445135 PMCID: PMC9753717 DOI: 10.1128/mcb.00265-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
OTUD1 is a deubiquitinating enzyme involved in many cellular processes including cancer and innate, immune signaling pathways. Here, we perform a proximity labeling-based interactome study that identifies OTUD1 largely present in the translation and RNA metabolism protein complexes. Biochemical analysis validates OTUD1 association with ribosome subunits, elongation factors and the E3 ubiquitin ligase ZNF598 but not with the translation initiation machinery. OTUD1 catalytic activity suppresses polyA triggered ribosome stalling through inhibition of ZNF598-mediated RPS10 ubiquitination and stimulates formation of polysomes. Finally, analysis of gene expression suggests that OTUD1 regulates the stability of rare codon rich mRNAs by antagonizing ZNF598.
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Jürgens L, Wethmar K. The Emerging Role of uORF-Encoded uPeptides and HLA uLigands in Cellular and Tumor Biology. Cancers (Basel) 2022; 14:6031. [PMID: 36551517 PMCID: PMC9776223 DOI: 10.3390/cancers14246031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Recent technological advances have facilitated the detection of numerous non-canonical human peptides derived from regulatory regions of mRNAs, long non-coding RNAs, and other cryptic transcripts. In this review, we first give an overview of the classification of these novel peptides and summarize recent improvements in their annotation and detection by ribosome profiling, mass spectrometry, and individual experimental analysis. A large fraction of the novel peptides originates from translation at upstream open reading frames (uORFs) that are located within the transcript leader sequence of regular mRNA. In humans, uORF-encoded peptides (uPeptides) have been detected in both healthy and malignantly transformed cells and emerge as important regulators in cellular and immunological pathways. In the second part of the review, we focus on various functional implications of uPeptides. As uPeptides frequently act at the transition of translational regulation and individual peptide function, we describe the mechanistic modes of translational regulation through ribosome stalling, the involvement in cellular programs through protein interaction and complex formation, and their role within the human leukocyte antigen (HLA)-associated immunopeptidome as HLA uLigands. We delineate how malignant transformation may lead to the formation of novel uORFs, uPeptides, or HLA uLigands and explain their potential implication in tumor biology. Ultimately, we speculate on a potential use of uPeptides as peptide drugs and discuss how uPeptides and HLA uLigands may facilitate translational inhibition of oncogenic protein messages and immunotherapeutic approaches in cancer therapy.
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Affiliation(s)
| | - Klaus Wethmar
- University Hospital Münster, Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, 48149 Münster, Germany
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Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation. Nat Commun 2022; 13:4492. [PMID: 35918345 PMCID: PMC9345940 DOI: 10.1038/s41467-022-32220-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
The small intestine is a rapidly proliferating organ that is maintained by a small population of Lgr5-expressing intestinal stem cells (ISCs). However, several Lgr5-negative ISC populations have been identified, and this remarkable plasticity allows the intestine to rapidly respond to both the local environment and to damage. However, the mediators of such plasticity are still largely unknown. Using intestinal organoids and mouse models, we show that upon ribosome impairment (driven by Rptor deletion, amino acid starvation, or low dose cyclohexamide treatment) ISCs gain an Lgr5-negative, fetal-like identity. This is accompanied by a rewiring of metabolism. Our findings suggest that the ribosome can act as a sensor of nutrient availability, allowing ISCs to respond to the local nutrient environment. Mechanistically, we show that this phenotype requires the activation of ZAKɑ, which in turn activates YAP, via SRC. Together, our data reveals a central role for ribosome dynamics in intestinal stem cells, and identify the activation of ZAKɑ as a critical mediator of stem cell identity. Intestinal stem cells are responsible for replenishing cells within the high-turnover intestinal epithelium. Here they show that ribosome dynamics affect intestinal stem cell identity through a mechanism that is triggered by changes in nutrient availability.
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Ko W, Porter JJ, Sipple MT, Edwards KM, Lueck JD. Efficient suppression of endogenous CFTR nonsense mutations using anticodon-engineered transfer RNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:685-701. [PMID: 35664697 PMCID: PMC9126842 DOI: 10.1016/j.omtn.2022.04.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
Nonsense mutations or premature termination codons (PTCs) comprise ∼11% of all genetic lesions, which result in over 7,000 distinct genetic diseases. Due to their outsized impact on human health, considerable effort has been made to find therapies for nonsense-associated diseases. Suppressor tRNAs have long been identified as a possible therapeutic for nonsense-associated diseases; however, their ability to inhibit nonsense-mediated mRNA decay (NMD) and support significant protein translation from endogenous transcripts has not been determined in mammalian cells. Here, we investigated the ability of anticodon edited (ACE)-tRNAs to suppress cystic fibrosis (CF) causing PTCs in the cystic fibrosis transmembrane regulator (CFTR) gene in gene-edited immortalized human bronchial epithelial (16HBEge) cells. Delivery of ACE-tRNAs to 16HBEge cells harboring three common CF mutations G542XUGA-, R1162XUGA-, and W1282XUGA-CFTR PTCs significantly inhibited NMD and rescued endogenous mRNA expression. Furthermore, delivery of our highly active leucine-encoding ACE-tRNA resulted in rescue of W1282X-CFTR channel function to levels that significantly exceed the necessary CFTR channel function for therapeutic relevance. This study establishes the ACE-tRNA approach as a potential standalone therapeutic for nonsense-associated diseases due to its ability to rescue both mRNA and full-length protein expression from PTC-containing endogenous genes.
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Affiliation(s)
- Wooree Ko
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joseph J. Porter
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Matthew T. Sipple
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Katherine M. Edwards
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John D. Lueck
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
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Zhang W, Ye F, Chen S, Peng J, Pang N, Yin F. Splicing Interruption by Intron Variants in CSNK2B Causes Poirier–Bienvenu Neurodevelopmental Syndrome: A Focus on Genotype–Phenotype Correlations. Front Neurosci 2022; 16:892768. [PMID: 35774559 PMCID: PMC9237577 DOI: 10.3389/fnins.2022.892768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
CSNK2B has recently been identified as the causative gene for Poirier–Bienvenu neurodevelopmental syndrome (POBINDS). POBINDS is a rare neurodevelopmental disorder characterized by early-onset epilepsy, developmental delay, hypotonia, and dysmorphism. Limited by the scarcity of patients, the genotype–phenotype correlations in POBINDS are still unclear. In the present study, we describe the clinical and genetic characteristics of eight individuals with POBINDS, most of whom suffered developmental delay, generalized epilepsy, and hypotonia. Minigene experiments confirmed that two intron variants (c.367+5G>A and c.367+6T>C) resulted in the skipping of exon 5, leading to a premature termination of mRNA transcription. Combining our data with the available literature, the types of POBINDS-causing variants included missense, nonsense, frameshift, and splicing, but the variant types do not reflect the clinical severity. Reduced casein kinase 2 holoenzyme activity may represent a unifying pathogenesis. We also found that individuals with missense variants in the zinc finger domain had manageable seizures (p = 0.009) and milder intellectual disability (p = 0.003) than those with missense variants in other domains of CSNK2B. This is the first study of genotype–phenotype correlations in POBINDS, drawing attention to the pathogenicity of intron variants and expanding the understanding of neurodevelopmental disorders.
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Affiliation(s)
- Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
- Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Fanghua Ye
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Shimeng Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
- Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
- Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
- Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Nan Pang,
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
- Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
- Fei Yin,
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Chhipi-Shrestha JK, Schneider-Poetsch T, Suzuki T, Mito M, Khan K, Dohmae N, Iwasaki S, Yoshida M. Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns. Cell Chem Biol 2022; 29:259-275.e10. [PMID: 34520743 PMCID: PMC8857039 DOI: 10.1016/j.chembiol.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/10/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022]
Abstract
Chemical splicing modulators that bind to the spliceosome have provided an attractive avenue for cancer treatment. Splicing modulators induce accumulation and subsequent translation of a subset of intron-retained mRNAs. However, the biological effect of proteins containing translated intron sequences remains unclear. Here, we identify a number of truncated proteins generated upon treatment with the splicing modulator spliceostatin A (SSA) via genome-wide ribosome profiling and bio-orthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry. A subset of these truncated proteins has intrinsically disordered regions, forms insoluble cellular condensates, and triggers the proteotoxic stress response through c-Jun N-terminal kinase (JNK) phosphorylation, thereby inhibiting the mTORC1 pathway. In turn, this reduces global translation. These findings indicate that creating an overburden of condensate-prone proteins derived from introns represses translation and prevents further production of harmful truncated proteins. This mechanism appears to contribute to the antiproliferative and proapoptotic activity of splicing modulators.
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Affiliation(s)
- Jagat K. Chhipi-Shrestha
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Khalid Khan
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Wako, Saitama 351-0198, Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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Yordanova MM, Loughran G, Atkins JF, Baranov PV. Stop codon readthrough contexts influence reporter expression differentially depending on the presence of an IRES. Wellcome Open Res 2022; 5:221. [PMID: 35187266 PMCID: PMC8831848 DOI: 10.12688/wellcomeopenres.16231.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Previously we reported the discovery of stop codon readthrough in AMD1 mRNA followed by ribosome stalling at the end of a conserved Open Reading Frame (ORF) that we termed AMD1. To explain the severe suppression of reporters fused to AMD1 tail we proposed a mechanism invoking ribosome queueing. In the original study, we tested this hypothesis, by placing the reporter stop codon in the context of readthrough permissive sequences in a dual reporter vector with downstream reporter expression driven by the EMCV IRES. In accordance with our hypothesis, we observed a striking disproportional reduction of upstream reporter activity in response to increased readthrough levels. Methods: Here we employ dual luciferase assays, western blotting and RT-qPCR to explore the effects of test sequences downstream to the reporter stop codon on its expression in dual and monocistronic reporter vectors. Results: With the dual reporter system, the disproportionate reduction of upstream reporter activity is not specific to AMD1 tail and occurs as long as the readthrough stop codon context is present at the end of the reporter's ORF. In a monocistronic vector without an IRES, the test sequences had distinct effects which were reflective of their properties e.g., AMD1 tail inhibitory effect. We further show by employing RT-qPCR that in the IRES vectors, the Fluc activity levels measured by the luciferase assay are an accurate proxy of RNA levels. Conclusions: While our findings provide little new information regarding the functional role of AMD1 tail, they raise caution for the use of viral IRES elements in expression vectors for studying mechanisms of mRNA translation. These findings may also be pertinent to the natural properties of readthrough permissive sequences and of IRES elements, though these require a separate investigation.
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Affiliation(s)
- Martina M. Yordanova
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russian Federation
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Vigh ML, Bressendorff S, Thieffry A, Arribas-Hernández L, Brodersen P. Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis. Nucleic Acids Res 2022; 50:1396-1415. [PMID: 35037064 PMCID: PMC8860578 DOI: 10.1093/nar/gkab1289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that inactivation of the exosome subunit RRP45B and SKI2 results in similar patterns of miRNA-induced siRNA production. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that in exosome mutants, miRNA targets can be sorted into producers and non-producers of illicit secondary siRNAs based on trigger miRNA levels and miRNA:target affinity rather than on presence of 5′-cleavage fragments. We propose that stalled RNA-Induced Silencing Complex (RISC) and ribosomes, but not mRNA cleavage fragments released from RISC, trigger siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.
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Affiliation(s)
- Maria L Vigh
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simon Bressendorff
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Axel Thieffry
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Laura Arribas-Hernández
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Brodersen
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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De S, Mühlemann O. A comprehensive coverage insurance for cells: revealing links between ribosome collisions, stress responses and mRNA surveillance. RNA Biol 2021; 19:609-621. [PMID: 35491909 PMCID: PMC9067528 DOI: 10.1080/15476286.2022.2065116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/02/2022] [Indexed: 11/02/2022] Open
Abstract
Cells of metazoans respond to internal and external stressors by activating stress response pathways that aim for re-establishing cellular homoeostasis or, if this cannot be achieved, triggering programmed cell death. Problems during translation, arising from defective mRNAs, tRNAs, ribosomes or protein misfolding, can activate stress response pathways as well as mRNA surveillance and ribosome quality control programs. Recently, ribosome collisions have emerged as a central signal for translational stress and shown to elicit different stress responses. Here, we review our current knowledge about the intricate mutual connections between ribosome collisions, stress response pathways and mRNA surveillance. A central factor connecting the sensing of collided ribosomes with degradation of the nascent polypeptides, dissociation of the stalled ribosomes and degradation of the mRNA by no-go or non-stop decay is the E3-ligase ZNF598. We tested whether ZNF598 also plays a role in nonsense-mediated mRNA decay (NMD) but found that it is dispensable for this translation termination-associated mRNA surveillance pathway, which in combination with other recent data argues against stable ribosome stalling at termination codons being the NMD-triggering signal.
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Affiliation(s)
- Soumasree De
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Oliver Mühlemann
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
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Molecular Determinants and Specificity of mRNA with Alternatively-Spliced UPF1 Isoforms, Influenced by an Insertion in the 'Regulatory Loop'. Int J Mol Sci 2021; 22:ijms222312744. [PMID: 34884553 PMCID: PMC8657986 DOI: 10.3390/ijms222312744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 01/25/2023] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway rapidly detects and degrades mRNA containing premature termination codons (PTCs). UP-frameshift 1 (UPF1), the master regulator of the NMD process, has two alternatively-spliced isoforms; one carries 353-GNEDLVIIWLR-363 insertion in the ‘regulatory loop (involved in mRNA binding)’. Such insertion can induce catalytic and/or ATPase activity, as determined experimentally; however, the kinetics and molecular level information are not fully understood. Herein, applying all-atom molecular dynamics, we probe the binding specificity of UPF1 with different GC- and AU-rich mRNA motifs and the influence of insertion to the viable control over UPF1 catalytic activity. Our results indicate two distinct conformations between 1B and RecA2 domains of UPF1: ‘open (isoform_2; without insertion)’ and ‘closed (isoform_1; with insertion)’. These structural movements correspond to an important stacking pattern in mRNA motifs, i.e., absence of stack formation in mRNA, with UPF1 isoform_2 results in the ‘open conformation’. Particularly, for UPF1 isoform_1, the increased distance between 1B and RecA2 domains has resulted in reducing the mRNA–UPF1 interactions. Lower fluctuating GC-rich mRNA motifs have better binding with UPF1, compared with AU-rich sequences. Except CCUGGGG, all other GC-rich motifs formed a 4-stack pattern with UPF1. High occupancy R363, D364, T627, and G862 residues were common binding GC-rich motifs, as were R363, N535, and T627 for the AU-rich motifs. The GC-rich motifs behave distinctly when bound to either of the isoforms; lower stability was observed with UPF1 isoform_2. The cancer-associated UPF1 variants (P533L/T and A839T) resulted in decreased protein–mRNA binding efficiency. Lack of mRNA stacking poses in the UPF1P533T system significantly decreased UPF1-mRNA binding efficiency and increased distance between 1B-RecA2. These novel findings can serve to further inform NMD-associated mechanistic and kinetic studies.
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Park J, Lee J, Kim JH, Lee J, Park H, Lim C. ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD. Nucleic Acids Res 2021; 49:11294-11311. [PMID: 34551427 PMCID: PMC8565315 DOI: 10.1093/nar/gkab834] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
C9ORF72-derived dipeptide repeat proteins have emerged as the pathogenic cause of neurodegeneration in amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). However, the mechanisms underlying their expression are not fully understood. Here, we demonstrate that ZNF598, the rate-limiting factor for ribosome-associated quality control (RQC), co-translationally titrates the expression of C9ORF72-derived poly(GR) protein. A Drosophila genetic screen identified key RQC factors as potent modifiers of poly(GR)-induced neurodegeneration. ZNF598 overexpression in human neuroblastoma cells inhibited the nuclear accumulation of poly(GR) protein and decreased its cytotoxicity, whereas ZNF598 deletion had opposing effects. Poly(GR)-encoding sequences in the reporter RNAs caused translational stalling and generated ribosome-associated translation products, sharing molecular signatures with canonical RQC substrates. Furthermore, ZNF598 and listerin 1, the RQC E3 ubiquitin-protein ligase, promoted poly(GR) degradation via the ubiquitin-proteasome pathway. An ALS-relevant ZNF598R69C mutant displayed loss-of-function effects on poly(GR) expression, as well as on general RQC. Moreover, RQC function was impaired in C9-ALS patient-derived neurons, whereas lentiviral overexpression of ZNF598 lowered their poly(GR) expression and suppressed proapoptotic caspase-3 activation. Taken together, we propose that an adaptive nature of the RQC-relevant ZNF598 activity allows the co-translational surveillance to cope with the atypical expression of pathogenic poly(GR) protein, thereby acquiring a neuroprotective function in C9-ALS/FTD.
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Affiliation(s)
- Jumin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jongbo Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ji-Hyung Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Heeju Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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Morris C, Cluet D, Ricci EP. Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1658. [PMID: 33949788 PMCID: PMC8519046 DOI: 10.1002/wrna.1658] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/01/2022]
Abstract
Eukaryotic gene expression is closely regulated by translation and turnover of mRNAs. Recent advances highlight the importance of translation in the control of mRNA degradation, both for aberrant and apparently normal mRNAs. During translation, the information contained in mRNAs is decoded by ribosomes, one codon at a time, and tRNAs, by specifically recognizing codons, translate the nucleotide code into amino acids. Such a decoding step does not process regularly, with various obstacles that can hinder ribosome progression, then leading to ribosome stalling or collisions. The progression of ribosomes is constantly monitored by the cell which has evolved several translation-dependent mRNA surveillance pathways, including nonsense-mediated decay (NMD), no-go decay (NGD), and non-stop decay (NSD), to degrade certain problematic mRNAs and the incomplete protein products. Recent progress in sequencing and ribosome profiling has made it possible to discover new mechanisms controlling ribosome dynamics, with numerous crosstalks between translation and mRNA decay. We discuss here various translation features critical for mRNA decay, with particular focus on current insights from the complexity of the genetic code and also the emerging role for the ribosome as a regulatory hub orchestrating mRNA decay, quality control, and stress signaling. Even if the interplay between mRNA translation and degradation is no longer to be demonstrated, a better understanding of their precise coordination is worthy of further investigation. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Christelle Morris
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
| | - David Cluet
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
| | - Emiliano P. Ricci
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
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The birth of piRNAs: how mammalian piRNAs are produced, originated, and evolved. Mamm Genome 2021; 33:293-311. [PMID: 34724117 PMCID: PMC9114089 DOI: 10.1007/s00335-021-09927-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
PIWI-interacting RNAs (piRNAs), small noncoding RNAs 24–35 nucleotides long, are essential for animal fertility. They play critical roles in a range of functions, including transposable element suppression, gene expression regulation, imprinting, and viral defense. In mammals, piRNAs are the most abundant small RNAs in adult testes and the only small RNAs that direct epigenetic modification of chromatin in the nucleus. The production of piRNAs is a complex process from transcription to post-transcription, requiring unique machinery often distinct from the biogenesis of other RNAs. In mice, piRNA biogenesis occurs in specialized subcellular locations, involves dynamic developmental regulation, and displays sexual dimorphism. Furthermore, the genomic loci and sequences of piRNAs evolve much more rapidly than most of the genomic regions. Understanding piRNA biogenesis should reveal novel RNA regulations recognizing and processing piRNA precursors and the forces driving the gain and loss of piRNAs during animal evolution. Such findings may provide the basis for the development of engineered piRNAs capable of modulating epigenetic regulation, thereby offering possible single-dose RNA therapy without changing the genomic DNA. In this review, we focus on the biogenesis of piRNAs in mammalian adult testes that are derived from long non-coding RNAs. Although piRNA biogenesis is believed to be evolutionarily conserved from fruit flies to humans, recent studies argue for the existence of diverse, mammalian-specific RNA-processing pathways that convert precursor RNAs into piRNAs, perhaps associated with the unique features of mammalian piRNAs or germ cell development. We end with the discussion of major questions in the field, including substrate recognition and the birth of new piRNAs.
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Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs. Nat Commun 2021; 12:5970. [PMID: 34645830 PMCID: PMC8514520 DOI: 10.1038/s41467-021-26233-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting small RNAs (piRNAs) protect the germline genome and are essential for fertility. piRNAs originate from transposable element (TE) RNAs, long non-coding RNAs, or 3´ untranslated regions (3´UTRs) of protein-coding messenger genes, with the last being the least characterized of the three piRNA classes. Here, we demonstrate that the precursors of 3´UTR piRNAs are full-length mRNAs and that post-termination 80S ribosomes guide piRNA production on 3´UTRs in mice and chickens. At the pachytene stage, when other co-translational RNA surveillance pathways are sequestered, piRNA biogenesis degrades mRNAs right after pioneer rounds of translation and fine-tunes protein production from mRNAs. Although 3´UTR piRNA precursor mRNAs code for distinct proteins in mice and chickens, they all harbor embedded TEs and produce piRNAs that cleave TEs. Altogether, we discover a function of the piRNA pathway in fine-tuning protein production and reveal a conserved piRNA biogenesis mechanism that recognizes translating RNAs in amniotes.
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Yordanova MM, Loughran G, Atkins JF, Baranov PV. Stop codon readthrough contexts influence reporter expression differentially depending on the presence of an IRES. Wellcome Open Res 2021; 5:221. [PMID: 35187266 PMCID: PMC8831848 DOI: 10.12688/wellcomeopenres.16231.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 08/23/2024] Open
Abstract
Background: Previously we reported the discovery of stop codon readthrough in AMD1 mRNA followed by ribosome stalling at the end of a conserved Open Reading Frame (ORF) that we termed AMD1. To explain the severe suppression of reporters fused to AMD1 tail we proposed a mechanism invoking ribosome queueing. To test this hypothesis, we placed the reporter stop codon in the context of readthrough permissive sequences in a dual reporter vector with downstream reporter expression driven by the EMCV IRES. In accordance with our hypothesis, we observed a striking disproportional reduction of upstream reporter activity in response to increased readthrough levels. Methods: We employ dual luciferase assays, western blotting and RT-qPCR to explore the effects of test sequences downstream to the reporter stop codon on its expression in dual and monocistronic reporter vectors. Results: With the dual reporter system, the disproportionate reduction of upstream reporter activity is not specific to AMD1 tail and occurs as long as the readthrough stop codon context is present at the end of the reporter's ORF. In a monocistronic vector without an IRES, the test sequences had distinct effects which were reflective of their properties e.g. AMD1 tail inhibitory effect. We further show with RT-qPCR that the EMCV IRES driven expression of a reporter is an accurate proxy of reporter RNA levels. Conclusions: While our findings provide little new information regarding the functional role of AMD1 tail, they raise caution for the use of viral IRES elements in expression vectors for studying mechanisms of mRNA translation. These findings may also be pertinent to the natural properties of read through permissive sequences and of IRES elements, though these require a separate investigation.
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Affiliation(s)
- Martina M. Yordanova
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russian Federation
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Park J, Park J, Lee J, Lim C. The trinity of ribosome-associated quality control and stress signaling for proteostasis and neuronal physiology. BMB Rep 2021. [PMID: 34488933 PMCID: PMC8505234 DOI: 10.5483/bmbrep.2021.54.9.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Translating ribosomes accompany co-translational regulation of nascent polypeptide chains, including subcellular targeting, protein folding, and covalent modifications. Ribosome-associated quality control (RQC) is a co-translational surveillance mechanism triggered by ribosomal collisions, an indication of atypical translation. The ribosome-associated E3 ligase ZNF598 ubiquitinates small subunit proteins at the stalled ribosomes. A series of RQC factors are then recruited to dissociate and triage aberrant translation intermediates. Regulatory ribosomal stalling may occur on endogenous transcripts for quality gene expression, whereas ribosomal collisions are more globally induced by ribotoxic stressors such as translation inhibitors, ribotoxins, and UV radiation. The latter are sensed by ribosome-associated kinases GCN2 and ZAKα, activating integrated stress response (ISR) and ribotoxic stress response (RSR), respectively. Hierarchical crosstalks among RQC, ISR, and RSR pathways are readily detectable since the collided ribosome is their common substrate for activation. Given the strong implications of RQC factors in neuronal physiology and neurological disorders, the interplay between RQC and ribosome-associated stress signaling may sustain proteostasis, adaptively determine cell fate, and contribute to neural pathogenesis. The elucidation of underlying molecular principles in relevant human diseases should thus provide unexplored therapeutic opportunities.
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Affiliation(s)
- Jumin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongmin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
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Abstract
Translation of the genetic information into proteins, performed by the ribosome, is a key cellular process in all organisms. Translation usually proceeds smoothly, but, unfortunately, undesirable events can lead to stalling of translating ribosomes. To rescue these faulty arrested ribosomes, bacterial cells possess three well-characterized quality control systems, tmRNA, ArfA, and ArfB. Recently, an additional ribosome rescue mechanism has been discovered in Bacillus subtilis. In contrast to the "canonical" systems targeting the 70S bacterial ribosome, this latter mechanism operates by first splitting the ribosome into the small (30S) and large (50S) subunits to then clearing the resultant jammed large subunit from the incomplete nascent polypeptide. Here, I will discuss the recent microbiological, biochemical, and structural data regarding functioning of this novel rescue system.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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