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Ma Z, Sharma R, Rogers AN. Physiological Consequences of Nonsense-Mediated Decay and Its Role in Adaptive Responses. Biomedicines 2024; 12:1110. [PMID: 38791071 PMCID: PMC11117581 DOI: 10.3390/biomedicines12051110] [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: 04/07/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway is a quality control mechanism that degrades aberrant mRNA containing one or more premature termination codons (PTCs). Recent discoveries indicate that NMD also differentially regulates mRNA from wild-type protein-coding genes despite lacking PTCs. Together with studies showing that NMD is involved in development and adaptive responses that influence health and longevity, these findings point to an expanded role of NMD that adds a new layer of complexity in the post-transcriptional regulation of gene expression. However, the extent of its control, whether different types of NMD play different roles, and the resulting physiological outcomes remain unclear and need further elucidation. Here, we review different branches of NMD and what is known of the physiological outcomes associated with this type of regulation. We identify significant gaps in the understanding of this process and the utility of genetic tools in accelerating progress in this area.
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Affiliation(s)
- Zhengxin Ma
- MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ratna Sharma
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA;
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Zhang X, Kebaara BW. Nonsense-mediated mRNA decay of metal-binding activator MAC1 is dependent on copper levels and 3'-UTR length in Saccharomyces cerevisiae. Curr Genet 2024; 70:5. [PMID: 38709348 DOI: 10.1007/s00294-024-01291-9] [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: 12/09/2023] [Revised: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway was initially identified as a surveillance pathway that degrades mRNAs containing premature termination codons (PTCs). NMD is now also recognized as a post-transcriptional regulatory pathway that regulates the expression of natural mRNAs. Earlier studies demonstrated that regulation of functionally related natural mRNAs by NMD can be differential and condition-specific in Saccharomyces cerevisiae. Here, we investigated the regulation of MAC1 mRNAs by NMD in response to copper as well as the role the MAC1 3'-UTR plays in this regulation. MAC1 is a copper-sensing transcription factor that regulates the high-affinity copper uptake system. MAC1 expression is activated upon copper deprivation. We found that MAC1 mRNAs are regulated by NMD under complete minimal (CM) but escaped NMD under low and high copper conditions. Mac1 protein regulated gene, CTR1 is not regulated by NMD in conditions where MAC1 mRNAs are NMD sensitive. We also found that the MAC1 3'-UTR is the NMD targeting feature on the mRNAs, and that MAC1 mRNAs lacking 3'-UTRs were stabilized during copper deprivation. Our results demonstrate a mechanism of regulation for a metal-sensing transcription factor, at both the post-transcriptional and post-translational levels, where MAC1 mRNA levels are regulated by NMD and copper, while the activity of Mac1p is controlled by copper levels.
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Affiliation(s)
- Xinyi Zhang
- Department of Biology, Baylor University, One Bear Place #97388, Waco, TX, 76798, USA
| | - Bessie W Kebaara
- Department of Biology, Baylor University, One Bear Place #97388, Waco, TX, 76798, USA.
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Zhang X, Kebaara BW. Nonsense-mediated mRNA decay and metal ion homeostasis and detoxification in Saccharomyces cerevisiae. Biometals 2022; 35:1145-1156. [PMID: 36255607 PMCID: PMC9674712 DOI: 10.1007/s10534-022-00450-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022]
Abstract
The highly conserved Nonsense-mediated mRNA decay (NMD) pathway is a translation dependent mRNA degradation pathway. Although NMD is best known for its role in degrading mRNAs with premature termination codons (PTCs) generated during transcription, splicing, or damage to the mRNAs, NMD is now also recognized as a pathway with additional important functions. Notably, NMD precisely regulates protein coding natural mRNAs, hence controlling gene expression within several physiologically significant pathways. Such pathways affected by NMD include nutritional bio-metal homeostasis and metal ion detoxification, as well as crosstalk between these pathways. Here, we focus on the relationships between NMD and various metal homeostasis and detoxification pathways. We review the described role that the NMD pathway plays in magnesium, zinc, iron, and copper homeostasis, as well as cadmium detoxification.
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Affiliation(s)
- Xinyi Zhang
- grid.252890.40000 0001 2111 2894Department of Biology, Baylor University, One Bear Place #97388, Waco, TX 76798 USA
| | - Bessie W. Kebaara
- grid.252890.40000 0001 2111 2894Department of Biology, Baylor University, One Bear Place #97388, Waco, TX 76798 USA
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Wong A, Lam EM, Pai C, Gunderson A, Carter TE, Kebaara BW. Variation of the response to metal ions and nonsense-mediated mRNA decay across different Saccharomyces cerevisiae genetic backgrounds. Yeast 2021; 38:507-520. [PMID: 33955055 DOI: 10.1002/yea.3565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/20/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of mRNA steady-state levels is important in controlling gene expression particularly in response to environmental stimuli. This allows cells to rapidly respond to environment changes. The highly conserved nonsense-mediated mRNA decay (NMD) pathway was initially identified as a pathway that degrades aberrant mRNAs. NMD is now recognized as a pathway with additional functions including precisely regulating the expression of select natural mRNAs. Majority of these natural mRNAs encode fully functional proteins. Regulation of natural mRNAs by NMD is activated by NMD targeting features and environmental cues. Here, we show that Saccharomyces cerevisiae strains from three genetic backgrounds respond differentially to NMD depending on the environmental stimuli. We found that wild type and NMD mutant W303a, BY4741, and RM11-1a yeast strains respond similarly to copper in the environment but respond differentially to toxic cadmium. Furthermore, the PCA1 alleles encoding different mRNAs from W303a and RM11-1a strains are regulated similarly by NMD in response to the bio-metal copper but differentially in response to toxic cadmium.
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Affiliation(s)
- Angelo Wong
- Department of Biology, Baylor University, Waco, Texas, 76798, USA
| | - Ernest Moses Lam
- Department of Biology, Baylor University, Waco, Texas, 76798, USA
| | - Cheryl Pai
- Department of Biology, Baylor University, Waco, Texas, 76798, USA
| | - Annika Gunderson
- Department of Biology, Baylor University, Waco, Texas, 76798, USA
| | - Tamar E Carter
- Department of Biology, Baylor University, Waco, Texas, 76798, USA
| | - Bessie W Kebaara
- Department of Biology, Baylor University, Waco, Texas, 76798, USA
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Celis-Arias V, Loera-Serna S, Beltrán HI, Álvarez-Zeferino JC, Garrido E, Ruiz-Ramos R. The fungicide effect of HKUST-1 on Aspergillus niger, Fusarium solani and Penicillium chrysogenum. NEW J CHEM 2018. [DOI: 10.1039/c8nj00120k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We evaluated the fungicide effect of HKUST-1 and related materials on Aspergillus niger, Fusarium solani and Penicillium chrysogenum strains.
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Affiliation(s)
- Vanessa Celis-Arias
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana Azcapotzalco
- Ciudad de México
- Mexico
| | - Sandra Loera-Serna
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana Azcapotzalco
- Ciudad de México
- Mexico
| | - Hiram I. Beltrán
- Departamento de Ciencias Naturales
- DCNI
- Universidad Autónoma Metropolitana Cuajimalpa
- Ciudad de México
- Mexico
| | - J. Carlos Álvarez-Zeferino
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana Azcapotzalco
- Ciudad de México
- Mexico
- Instituto de Ingeniería
| | - Efrain Garrido
- Departamento de Genética y Bilogía Molecular
- CINVESTAV-IPN
- Ciudad de México
- Mexico
| | - Rubén Ruiz-Ramos
- Instituto de Medicina Forense
- Universidad Veracruzana
- Boca del Río
- Mexico
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Peccarelli M, Scott TD, Steele M, Kebaara BW. mRNAs involved in copper homeostasis are regulated by the nonsense-mediated mRNA decay pathway depending on environmental conditions. Fungal Genet Biol 2016; 86:81-90. [DOI: 10.1016/j.fgb.2015.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 12/20/2022]
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Regulation of natural mRNAs by the nonsense-mediated mRNA decay pathway. EUKARYOTIC CELL 2014; 13:1126-35. [PMID: 25038084 DOI: 10.1128/ec.00090-14] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway is a specialized mRNA degradation pathway that degrades select mRNAs. This pathway is conserved in all eukaryotes examined so far, and it triggers the degradation of mRNAs that prematurely terminate translation. Originally identified as a pathway that degrades mRNAs with premature termination codons as a result of errors during transcription, splicing, or damage to the mRNA, NMD is now also recognized as a pathway that degrades some natural mRNAs. The degradation of natural mRNAs by NMD has been identified in multiple eukaryotes, including Saccharomyces cerevisiae, Drosophila melanogaster, Arabidopsis thaliana, and humans. S. cerevisiae is used extensively as a model to study natural mRNA regulation by NMD. Inactivation of the NMD pathway in S. cerevisiae affects approximately 10% of the transcriptome. Similar percentages of natural mRNAs in the D. melanogaster and human transcriptomes are also sensitive to the pathway, indicating that NMD is important for the regulation of gene expression in multiple organisms. NMD can either directly or indirectly regulate the decay rate of natural mRNAs. Direct NMD targets possess NMD-inducing features. This minireview focuses on the regulation of natural mRNAs by the NMD pathway, as well as the features demonstrated to target these mRNAs for decay by the pathway in S. cerevisiae. We also compare NMD-targeting features identified in S. cerevisiae with known NMD-targeting features in other eukaryotic organisms.
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Lou CH, Shao A, Shum EY, Espinoza JL, Huang L, Karam R, Wilkinson MF. Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway. Cell Rep 2014; 6:748-64. [PMID: 24529710 DOI: 10.1016/j.celrep.2014.01.028] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 12/11/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
The mechanisms dictating whether a cell proliferates or differentiates have undergone intense scrutiny, but they remain poorly understood. Here, we report that UPF1, a central component in the nonsense-mediated RNA decay (NMD) pathway, plays a key role in this decision by promoting the proliferative, undifferentiated cell state. UPF1 acts, in part, by destabilizing the NMD substrate encoding the TGF-β inhibitor SMAD7 and stimulating TGF-β signaling. UPF1 also promotes the decay of mRNAs encoding many other proteins that oppose the proliferative, undifferentiated cell state. Neural differentiation is triggered when NMD is downregulated by neurally expressed microRNAs (miRNAs). This UPF1-miRNA circuitry is highly conserved and harbors negative feedback loops that act as a molecular switch. Our results suggest that the NMD pathway collaborates with the TGF-β signaling pathway to lock in the stem-like state, a cellular state that is stably reversed when neural differentiation signals that induce NMD-repressive miRNAs are received.
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Affiliation(s)
- Chih H Lou
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Ada Shao
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Eleen Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Josh L Espinoza
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Lulu Huang
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Rachid Karam
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA.
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