1
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Riggs CL, Kedersha N, Amarsanaa M, Zubair SN, Ivanov P, Anderson P. UBAP2L contributes to formation of P-bodies and modulates their association with stress granules. J Cell Biol 2024; 223:e202307146. [PMID: 39007803 PMCID: PMC11248227 DOI: 10.1083/jcb.202307146] [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: 07/28/2023] [Revised: 03/06/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Stress triggers the formation of two distinct cytoplasmic biomolecular condensates: stress granules (SGs) and processing bodies (PBs), both of which may contribute to stress-responsive translation regulation. Though PBs can be present constitutively, stress can increase their number and size and lead to their interaction with stress-induced SGs. The mechanism of such interaction, however, is largely unknown. Formation of canonical SGs requires the RNA binding protein Ubiquitin-Associated Protein 2-Like (UBAP2L), which is a central SG node protein in the RNA-protein interaction network of SGs and PBs. UBAP2L binds to the essential SG and PB proteins G3BP and DDX6, respectively. Research on UBAP2L has mostly focused on its role in SGs, but not its connection to PBs. We find that UBAP2L is not solely an SG protein but also localizes to PBs in certain conditions, contributes to PB biogenesis and SG-PB interactions, and can nucleate hybrid granules containing SG and PB components in cells. These findings inform a new model for SG and PB formation in the context of UBAP2L's role.
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Affiliation(s)
- Claire L Riggs
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nancy Kedersha
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Misheel Amarsanaa
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Safiyah Noor Zubair
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul Anderson
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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2
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Lu L, Zhang J, Zheng X, Xia N, Diao Z, Wang X, Chen Z, Tang D, Li S. OsMPK12 positively regulates rice blast resistance via OsEDC4-mediated transcriptional regulation of immune-related genes. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38770581 DOI: 10.1111/pce.14955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Mitogen-activated protein kinase (MAPK) signalling cascades are functionally important signalling modules in eukaryotes. Transcriptome reprogramming of immune-related genes is a key process in plant immunity. Emerging evidence shows that plant MAPK cascade is associated with processing (P)-body components and contributes to transcriptome reprogramming of immune-related genes. However, it remains largely unknown how this process is regulated. Here, we show that OsMPK12, which is induced by Magnaporthe oryzae infection, positively regulates rice blast resistance. Further analysis revealed that OsMPK12 directly interacts with enhancer of mRNA decapping protein 4 (OsEDC4), a P-body-located protein, and recruits OsEDC4 to where OsMPK12 is enriched. Importantly, OsEDC4 directly interacts with two decapping complex members OsDCP1 and OsDCP2, indicating that OsEDC4 is a subunit of the mRNA decapping complex. Additionally, we found that OsEDC4 positively regulates rice blast resistance by regulating expression of immune-related genes and maintaining proper mRNA levels of some negatively-regulated genes. And OsMPK12 and OsEDC4 are also involved in rice growth and development regulation. Taken together, our data demonstrate that OsMPK12 positively regulates rice blast resistance via OsEDC4-mediated mRNA decay of immune-related genes, providing new insight into not only the new role of the MAPK signalling cascade, but also posttranscriptional regulation of immune-related genes.
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Affiliation(s)
- Ling Lu
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Zhang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingxing Zheng
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Na Xia
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhijuan Diao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xun Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiwei Chen
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengping Li
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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3
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Bienvenu AL, Ballut L, Picot S. Specifically Targeting Metacaspases of Candida: A New Therapeutic Opportunity. J Fungi (Basel) 2024; 10:90. [PMID: 38392762 PMCID: PMC10889698 DOI: 10.3390/jof10020090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
The World Health Organization (WHO) recently published a list of fungal priority pathogens, including Candida albicans and C. auris. The increased level of resistance of Candida is raising concern, considering the availability of only four classes of medicine. The WHO is seeking novel agent classes with different targets and mechanisms of action. Targeting Candida metacaspases to control intrinsic cell death could provide new therapeutic opportunities for invasive candidiasis. In this review, we provide the available evidence for Candida cell death, describe Candida metacaspases, and discuss the potential of Candida metacaspases to offer a new specific target. Targeting Candida cell death has good scientific rationale given that the fungicidal activity of many marketed antifungals is mediated, among others, by cell death triggering. But none of the available antifungals are specifically activating Candida metacaspases, making this target a new therapeutic opportunity for non-susceptible isolates. It is expected that antifungals based on the activation of fungi metacaspases will have a broad spectrum of action, as metacaspases have been described in many fungi, including filamentous fungi. Considering this original mechanism of action, it could be of great interest to combine these new antifungal candidates with existing antifungals. This approach would help to avoid the development of antifungal resistance, which is especially increasing in Candida.
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Affiliation(s)
- Anne-Lise Bienvenu
- Service Pharmacie, Groupement Hospitalier Nord, Hospices Civils de Lyon, 69004 Lyon, France
- Malaria Research Unit, University Lyon, UMR 5246 CNRS-INSA-CPE-University Lyon1, 69100 Villeurbanne, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, 69367 Lyon, France
| | - Stephane Picot
- Malaria Research Unit, University Lyon, UMR 5246 CNRS-INSA-CPE-University Lyon1, 69100 Villeurbanne, France
- Institute of Parasitology and Medical Mycology, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, 69004 Lyon, France
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4
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He F, Jacobson A. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. FEBS J 2023; 290:5057-5085. [PMID: 36098474 PMCID: PMC10008757 DOI: 10.1111/febs.16626] [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: 06/30/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Decapping is the enzymatic removal of 5' cap structures from mRNAs in eukaryotic cells. Cap structures normally enhance mRNA translation and stability, and their excision commits an mRNA to complete 5'-3' exoribonucleolytic digestion and generally ends the physical and functional cellular presence of the mRNA. Decapping plays a pivotal role in eukaryotic cytoplasmic mRNA turnover and is a critical and highly regulated event in multiple 5'-3' mRNA decay pathways, including general 5'-3' decay, nonsense-mediated mRNA decay (NMD), AU-rich element-mediated mRNA decay, microRNA-mediated gene silencing, and targeted transcript-specific mRNA decay. In the yeast Saccharomyces cerevisiae, mRNA decapping is carried out by a single Dcp1-Dcp2 decapping enzyme in concert with the accessory activities of specific regulators commonly known as decapping activators or enhancers. These regulatory proteins include the general decapping activators Edc1, 2, and 3, Dhh1, Scd6, Pat1, and the Lsm1-7 complex, as well as the NMD-specific factors, Upf1, 2, and 3. Here, we focus on in vivo mRNA decapping regulation in yeast. We summarize recently uncovered molecular mechanisms that control selective targeting of the yeast decapping enzyme and discuss new roles for specific decapping activators in controlling decapping enzyme targeting, assembly of target-specific decapping complexes, and the monitoring of mRNA translation. Further, we discuss the kinetic contribution of mRNA decapping for overall decay of different substrate mRNAs and highlight experimental evidence pointing to the functional coordination and physical coupling between events in mRNA deadenylation, decapping, and 5'-3' exoribonucleolytic decay.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01655
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5
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Chukrallah LG, Potgieter S, Chueh L, Snyder EM. Two RNA binding proteins, ADAD2 and RNF17, interact to form a heterogeneous population of novel meiotic germ cell granules with developmentally dependent organelle association. PLoS Genet 2023; 19:e1010519. [PMID: 37428816 PMCID: PMC10359003 DOI: 10.1371/journal.pgen.1010519] [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: 11/10/2022] [Revised: 07/20/2023] [Accepted: 06/17/2023] [Indexed: 07/12/2023] Open
Abstract
Mammalian male germ cell differentiation relies on complex RNA biogenesis events, many of which occur in non-membrane bound organelles termed RNA germ cell granules that are rich in RNA binding proteins (RBPs). Though known to be required for male germ cell differentiation, we understand little of the relationships between the numerous granule subtypes. ADAD2, a testis specific RBP, is required for normal male fertility and forms a poorly characterized granule in meiotic germ cells. This work aimed to understand the role of ADAD2 granules in male germ cell differentiation by clearly defining their molecular composition and relationship to other granules. Biochemical analyses identified RNF17, a testis specific RBP that forms meiotic male germ cell granules, as an ADAD2-interacting protein. Phenotypic analysis of Adad2 and Rnf17 mutants identified a rare post-meiotic chromatin defect, suggesting shared biological roles. ADAD2 and RNF17 were found to be dependent on one another for granularization and together form a previously unstudied set of germ cell granules. Based on co-localization studies with well-characterized granule RBPs and organelle-specific markers, a subset of the ADAD2-RNF17 granules are found to be associated with the intermitochondrial cement and piRNA biogenesis. In contrast, a second, morphologically distinct population of ADAD2-RNF17 granules co-localized with the translation regulators NANOS1 and PUM1, along with the molecular chaperone PDI. These large granules form a unique funnel-shaped structure that displays distinct protein subdomains and is tightly associated with the endoplasmic reticulum. Developmental studies suggest the different granule populations represent different phases of a granule maturation process. Lastly, a double Adad2-Rnf17 mutant model suggests the interaction between ADAD2 and RNF17, as opposed to loss of either, is the likely driver of the Adad2 and Rnf17 mutant phenotypes. These findings shed light on the relationship between germ cell granule pools and define new genetic approaches to their study.
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Affiliation(s)
- Lauren G. Chukrallah
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Potgieter
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Lisa Chueh
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Elizabeth M. Snyder
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
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6
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He F, Wu C, Jacobson A. Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes. eLife 2022; 11:74410. [PMID: 35604319 PMCID: PMC9170289 DOI: 10.7554/elife.74410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 05/22/2022] [Indexed: 11/13/2022] Open
Abstract
A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs for decapping-dependent 5' to 3' decay, but the molecular mechanisms controlling mRNA selectivity by the enzyme remain elusive. Through extensive genetic analyses we reveal that Dcp2 C-terminal domain cis-regulatory elements control decapping enzyme target specificity by orchestrating formation of distinct decapping complexes. Two Upf1-binding motifs direct the decapping enzyme to NMD substrates, a single Edc3-binding motif targets both Edc3 and Dhh1 substrates, and Pat1-binding leucine-rich motifs target Edc3 and Dhh1 substrates under selective conditions. Although it functions as a unique targeting component of specific complexes, Edc3 is a common component of multiple complexes. Scd6 and Xrn1 also have specific binding sites on Dcp2, allowing them to be directly recruited to decapping complexes. Collectively, our results demonstrate that Upf1, Edc3, Scd6, and Pat1 function as regulatory subunits of the holo-decapping enzyme, controlling both its substrate specificity and enzymatic activation.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Chan Wu
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, United States
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7
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Tishinov K, Spang A. The mRNA decapping complex is buffered by nuclear localization. J Cell Sci 2021; 134:272313. [PMID: 34435633 DOI: 10.1242/jcs.259156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/17/2021] [Indexed: 01/08/2023] Open
Abstract
mRNA decay is a key step in regulating the cellular proteome. Processing bodies (P-bodies) are thought to be sites of mRNA decay and/or storage. P-body units assemble into P-body granules under stress conditions. How this assembly is regulated, however, remains poorly understood. Here, we show, in the yeast Saccharomyces cerevisiae, that the translational repressor Scd6 and the decapping stimulator Edc3 act partially redundantly in P-body assembly by sequestering the Dcp1-Dcp2 (denoted Dcp1/2) decapping complex in the cytoplasm and preventing it from becoming imported into the nucleus by the karyopherin β protein Kap95. One of two nuclear localization signals in Dcp2 overlaps with the RNA-binding site, suggesting an additional mechanism to regulate Dcp1/2 localization. Nuclear Dcp1/2 does not drive mRNA decay and might be stored there as a readily releasable pool, indicating a dynamic equilibrium between cytoplasmic and nuclear Dcp1/2. Cytoplasmic Dcp1/2 is linked to Dhh1 via Edc3. Functional P-bodies are present at the endoplasmic reticulum where Dcp2 potentially acts to increase the local concentration of Dhh1 through interaction with Edc3 to drive phase separation and hence P-body formation.
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Affiliation(s)
- Kiril Tishinov
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
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8
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Bearss JJ, Padi SKR, Singh N, Cardo‐Vila M, Song JH, Mouneimne G, Fernandes N, Li Y, Harter MR, Gard JMC, Cress AE, Peti W, Nelson ADL, Buchan JR, Kraft AS, Okumura K. EDC3 phosphorylation regulates growth and invasion through controlling P-body formation and dynamics. EMBO Rep 2021; 22:e50835. [PMID: 33586867 PMCID: PMC8025014 DOI: 10.15252/embr.202050835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/20/2020] [Accepted: 01/13/2021] [Indexed: 12/18/2022] Open
Abstract
Regulation of mRNA stability and translation plays a critical role in determining protein abundance within cells. Processing bodies (P-bodies) are critical regulators of these processes. Here, we report that the Pim1 and 3 protein kinases bind to the P-body protein enhancer of mRNA decapping 3 (EDC3) and phosphorylate EDC3 on serine (S)161, thereby modifying P-body assembly. EDC3 phosphorylation is highly elevated in many tumor types, is reduced upon treatment of cells with kinase inhibitors, and blocks the localization of EDC3 to P-bodies. Prostate cancer cells harboring an EDC3 S161A mutation show markedly decreased growth, migration, and invasion in tissue culture and in xenograft models. Consistent with these phenotypic changes, the expression of integrin β1 and α6 mRNA and protein is reduced in these mutated cells. These results demonstrate that EDC3 phosphorylation regulates multiple cancer-relevant functions and suggest that modulation of P-body activity may represent a new paradigm for cancer treatment.
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Affiliation(s)
| | - Sathish KR Padi
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Molecular Biology and BiophysicsUConn Health CenterFarmingtonCTUSA
| | - Neha Singh
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
| | - Marina Cardo‐Vila
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Otolaryngology‐Head and Neck SurgeryUniversity of ArizonaTucsonAZUSA
| | - Jin H Song
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZUSA
| | - Ghassan Mouneimne
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZUSA
| | - Nikita Fernandes
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonAZUSA
| | - Yang Li
- Department of Molecular Biology and BiophysicsUConn Health CenterFarmingtonCTUSA
- Department of Chemistry and BiochemistryUniversity of ArizonaTucsonAZUSA
| | - Matthew R Harter
- Department of Chemistry and BiochemistryUniversity of ArizonaTucsonAZUSA
| | - Jaime MC Gard
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
| | - Anne E Cress
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZUSA
| | - Wolfgang Peti
- Department of Molecular Biology and BiophysicsUConn Health CenterFarmingtonCTUSA
- Department of Chemistry and BiochemistryUniversity of ArizonaTucsonAZUSA
| | | | - J Ross Buchan
- Department of Molecular and Cellular BiologyUniversity of ArizonaTucsonAZUSA
| | - Andrew S Kraft
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of MedicineUniversity of ArizonaTucsonAZUSA
| | - Koichi Okumura
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZUSA
- Department of PhysiologyUniversity of ArizonaTucsonAZUSA
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9
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Mutations in genes encoding regulators of mRNA decapping and translation initiation: links to intellectual disability. Biochem Soc Trans 2021; 48:1199-1211. [PMID: 32412080 PMCID: PMC7329352 DOI: 10.1042/bst20200109] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) affects at least 1% of the population, and typically presents in the first few years of life. ID is characterized by impairments in cognition and adaptive behavior and is often accompanied by further delays in language and motor skills, as seen in many neurodevelopmental disorders (NDD). Recent widespread high-throughput approaches that utilize whole-exome sequencing or whole-genome sequencing have allowed for a considerable increase in the identification of these pathogenic variants in monogenic forms of ID. Notwithstanding this progress, the molecular and cellular consequences of the identified mutations remain mostly unknown. This is particularly important as the associated protein dysfunctions are the prerequisite to the identification of targets for novel drugs of these rare disorders. Recent Next-Generation sequencing-based studies have further established that mutations in genes encoding proteins involved in RNA metabolism are a major cause of NDD. Here, we review recent studies linking germline mutations in genes encoding factors mediating mRNA decay and regulators of translation, namely DCPS, EDC3, DDX6 helicase and ID. These RNA-binding proteins have well-established roles in mRNA decapping and/or translational repression, and the mutations abrogate their ability to remove 5′ caps from mRNA, diminish their interactions with cofactors and stabilize sub-sets of transcripts. Additional genes encoding RNA helicases with roles in translation including DDX3X and DHX30 have also been linked to NDD. Given the speed in the acquisition, analysis and sharing of sequencing data, and the importance of post-transcriptional regulation for brain development, we anticipate mutations in more such factors being identified and functionally characterized.
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10
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Kim M, van Hoof A. Suppressors of mRNA Decapping Defects Restore Growth Without Major Effects on mRNA Decay Rates or Abundance. Genetics 2020; 216:1051-1069. [PMID: 32998951 PMCID: PMC7768250 DOI: 10.1534/genetics.120.303641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/28/2020] [Indexed: 01/09/2023] Open
Abstract
Faithful degradation of mRNAs is a critical step in gene expression, and eukaryotes share a major conserved mRNA decay pathway. In this major pathway, the two rate-determining steps in mRNA degradation are the initial gradual removal of the poly(A) tail, followed by removal of the cap structure. Removal of the cap structure is carried out by the decapping enzyme, containing the Dcp2 catalytic subunit. Although the mechanism and regulation of mRNA decay is well understood, the consequences of defects in mRNA degradation are less clear. Dcp2 has been reported as either essential or nonessential. Here, we clarify that Dcp2 is not absolutely required for spore germination and extremely slow growth, but in practical terms it is impossible to continuously culture dcp2∆ under laboratory conditions without suppressors arising. We show that null mutations in at least three different genes are each sufficient to restore growth to a dcp2∆, of which kap123∆ and tl(gag)g∆ appear the most specific. We show that kap123∆ and tl(gag)g∆ suppress dcp2 by mechanisms that are different from each other and from previously isolated dcp2 suppressors. The suppression mechanism for tL(GAG)G is determined by the unique GAG anticodon of this tRNA, and thus likely by translation of some CUC or CUU codons. Unlike previously reported suppressors of decapping defects, these suppressors do not detectably restore decapping or mRNA decay to normal rates, but instead allow survival while only modestly affecting RNA homeostasis. These results provide important new insight into the importance of decapping, resolve previously conflicting publications about the essentiality of DCP2, provide the first phenotype for a tl(gag)g mutant, and show that multiple distinct mechanisms can bypass Dcp2 requirement.
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Affiliation(s)
- Minseon Kim
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Ambro van Hoof
- Microbiology and Molecular Genetics Department, University of Texas Health Science Center at Houston, Houston, Texas 77030
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11
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Charenton C, Gaudon-Plesse C, Back R, Ulryck N, Cosson L, Séraphin B, Graille M. Pby1 is a direct partner of the Dcp2 decapping enzyme. Nucleic Acids Res 2020; 48:6353-6366. [PMID: 32396195 PMCID: PMC7293026 DOI: 10.1093/nar/gkaa337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022] Open
Abstract
Most eukaryotic mRNAs harbor a characteristic 5′ m7GpppN cap that promotes pre-mRNA splicing, mRNA nucleocytoplasmic transport and translation while also protecting mRNAs from exonucleolytic attacks. mRNA caps are eliminated by Dcp2 during mRNA decay, allowing 5′-3′ exonucleases to degrade mRNA bodies. However, the Dcp2 decapping enzyme is poorly active on its own and requires binding to stable or transient protein partners to sever the cap of target mRNAs. Here, we analyse the role of one of these partners, the yeast Pby1 factor, which is known to co-localize into P-bodies together with decapping factors. We report that Pby1 uses its C-terminal domain to directly bind to the decapping enzyme. We solved the structure of this Pby1 domain alone and bound to the Dcp1–Dcp2–Edc3 decapping complex. Structure-based mutant analyses reveal that Pby1 binding to the decapping enzyme is required for its recruitment into P-bodies. Moreover, Pby1 binding to the decapping enzyme stimulates growth in conditions in which decapping activation is compromised. Our results point towards a direct connection of Pby1 with decapping and P-body formation, both stemming from its interaction with the Dcp1–Dcp2 holoenzyme.
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Affiliation(s)
- Clément Charenton
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Claudine Gaudon-Plesse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Régis Back
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Loreline Cosson
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
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12
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Kumar-Singh A, Shrinet J, Parniewska MM, Fuxe J, Dobra K, Hjerpe A. Mapping the Interactome of the Nuclear Heparan Sulfate Proteoglycan Syndecan-1 in Mesothelioma Cells. Biomolecules 2020; 10:biom10071034. [PMID: 32664515 PMCID: PMC7408266 DOI: 10.3390/biom10071034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 01/27/2023] Open
Abstract
Syndecan-1 (SDC1) is a cell surface heparan sulfate proteoglycan (HSPG), which regulates various signaling pathways controlling the proliferation and migration of malignant mesothelioma and other types of cancer. We have previously shown that SDC1 can translocate to the nucleus in mesothelioma cells through a tubulin-dependent transport mechanism. However, the role of nuclear SDC1 is largely unknown. Here, we performed co-immunoprecipitation (Co-IP) of SDC1 in a mesothelioma cell line to identify SDC1 interacting proteins. The precipitates contained a large number of proteins, indicating the recovery of protein networks. Proteomic analysis with a focus on nuclear proteins revealed an association with pathways related to cell proliferation and RNA synthesis, splicing and transport. In support of this, the top RNA splicing candidates were verified to interact with SDC1 by Co-IP and subsequent Western blot analysis. Further loss- and gain-of-function experiments showed that SDC1 influences RNA levels in mesothelioma cells. The results identify a proteomic map of SDC1 nuclear interactors in a mesothelioma cell line and suggest a previously unknown role for SDC1 in RNA biogenesis. The results should serve as a fundament for further studies to discover the role of nuclear SDC1 in normal and cancer cells of different origin.
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Affiliation(s)
- Ashish Kumar-Singh
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, SE-14186 Stockholm, Sweden; (A.K.-S.); (J.F.); (M.M.P.); (A.H.)
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA;
| | - Malgorzata Maria Parniewska
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, SE-14186 Stockholm, Sweden; (A.K.-S.); (J.F.); (M.M.P.); (A.H.)
| | - Jonas Fuxe
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, SE-14186 Stockholm, Sweden; (A.K.-S.); (J.F.); (M.M.P.); (A.H.)
| | - Katalin Dobra
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, SE-14186 Stockholm, Sweden; (A.K.-S.); (J.F.); (M.M.P.); (A.H.)
- Division of Clinical Pathology/Cytology, Karolinska University Laboratory, Karolinska University Hospital, SE-14186 Stockholm, Sweden
- Correspondence: ; Tel.:+46-8-484-1093
| | - Anders Hjerpe
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, SE-14186 Stockholm, Sweden; (A.K.-S.); (J.F.); (M.M.P.); (A.H.)
- Division of Clinical Pathology/Cytology, Karolinska University Laboratory, Karolinska University Hospital, SE-14186 Stockholm, Sweden
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13
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Rieckher M, Markaki M, Princz A, Schumacher B, Tavernarakis N. Maintenance of Proteostasis by P Body-Mediated Regulation of eIF4E Availability during Aging in Caenorhabditis elegans. Cell Rep 2020; 25:199-211.e6. [PMID: 30282029 PMCID: PMC6180348 DOI: 10.1016/j.celrep.2018.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/01/2018] [Accepted: 09/05/2018] [Indexed: 11/16/2022] Open
Abstract
Aging is accompanied by a pervasive collapse of proteostasis, while reducing general protein synthesis promotes longevity across taxa. Here, we show that the eIF4E isoform IFE-2 is increasingly sequestered in mRNA processing (P) bodies during aging and upon stress in Caenorhabditis elegans. Loss of the enhancer of mRNA decapping EDC-3 causes further entrapment of IFE-2 in P bodies and lowers protein synthesis rates in somatic tissues. Animals lacking EDC-3 are long lived and stress resistant, congruent with IFE-2-deficient mutants. Notably, neuron-specific expression of EDC-3 is sufficient to reverse lifespan extension, while sequestration of IFE-2 in neuronal P bodies counteracts age-related neuronal decline. The effects of mRNA decapping deficiency on stress resistance and longevity are orchestrated by a multimodal stress response involving the transcription factor SKN-1, which mediates lifespan extension upon reduced protein synthesis. Our findings elucidate a mechanism of proteostasis control during aging through P body-mediated regulation of protein synthesis in the soma.
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Affiliation(s)
- Matthias Rieckher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece; Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, 50931 Cologne, Germany
| | - Maria Markaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece
| | - Andrea Princz
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, 50931 Cologne, Germany
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece; Department of Basic Sciences, School of Medicine, University of Crete, Heraklion 71110, Greece.
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14
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Wurm JP, Sprangers R. Dcp2: an mRNA decapping enzyme that adopts many different shapes and forms. Curr Opin Struct Biol 2019; 59:115-123. [PMID: 31473440 PMCID: PMC6900585 DOI: 10.1016/j.sbi.2019.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/22/2019] [Accepted: 07/30/2019] [Indexed: 02/01/2023]
Abstract
Structure of the active state of the Dcp2 decapping enzyme. Insights into the structural states that are sampled in solution. Details regarding the intermolecular network that Dcp2 is embedded in.
Eukaryotic mRNAs contain a 5’ cap structure that protects the transcript against rapid exonucleolytic degradation. The regulation of cellular mRNA levels therefore depends on a precise control of the mRNA decapping pathways. The major mRNA decapping enzyme in eukaryotic cells is Dcp2. It is regulated by interactions with several activators, including Dcp1, Edc1, and Edc3, as well as by an autoinhibition mechanism. The structural and mechanistical characterization of Dcp2 complexes has long been impeded by the high flexibility and dynamic nature of the enzyme. Here we review recent insights into the catalytically active conformation of the mRNA decapping complex, the mode of action of decapping activators and the large interactions network that Dcp2 is embedded in.
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Affiliation(s)
- Jan Philip Wurm
- Department of Biophysics I, University of Regensburg, 93053, Regensburg, Germany.
| | - Remco Sprangers
- Department of Biophysics I, University of Regensburg, 93053, Regensburg, Germany.
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15
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Janapala Y, Preiss T, Shirokikh NE. Control of Translation at the Initiation Phase During Glucose Starvation in Yeast. Int J Mol Sci 2019; 20:E4043. [PMID: 31430885 PMCID: PMC6720308 DOI: 10.3390/ijms20164043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/10/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Glucose is one of the most important sources of carbon across all life. Glucose starvation is a key stress relevant to all eukaryotic cells. Glucose starvation responses have important implications in diseases, such as diabetes and cancer. In yeast, glucose starvation causes rapid and dramatic effects on the synthesis of proteins (mRNA translation). Response to glucose deficiency targets the initiation phase of translation by different mechanisms and with diverse dynamics. Concomitantly, translationally repressed mRNAs and components of the protein synthesis machinery may enter a variety of cytoplasmic foci, which also form with variable kinetics and may store or degrade mRNA. Much progress has been made in understanding these processes in the last decade, including with the use of high-throughput/omics methods of RNA and RNA:protein detection. This review dissects the current knowledge of yeast reactions to glucose starvation systematized by the stage of translation initiation, with the focus on rapid responses. We provide parallels to mechanisms found in higher eukaryotes, such as metazoans, for the most critical responses, and point out major remaining gaps in knowledge and possible future directions of research on translational responses to glucose starvation.
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Affiliation(s)
- Yoshika Janapala
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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16
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Ford AE, Denicourt C, Morano KA. Thiol stress-dependent aggregation of the glycolytic enzyme triose phosphate isomerase in yeast and human cells. Mol Biol Cell 2019; 30:554-565. [PMID: 30601716 PMCID: PMC6589699 DOI: 10.1091/mbc.e18-10-0616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The eukaryotic cytosolic proteome is vulnerable to changes in proteostatic and redox balance caused by temperature, pH, oxidants, and xenobiotics. Cysteine-containing proteins are especially at risk, as the thiol side chain is subject to oxidation, adduction, and chelation by thiol-reactive compounds. The thiol-chelating heavy metal cadmium is a highly toxic environmental pollutant demonstrated to induce the heat shock response and recruit protein chaperones to sites of presumed protein aggregation in the budding yeast Saccharomyces cerevisiae. However, endogenous targets of cadmium toxicity responsible for these outcomes are largely unknown. Using fluorescent protein fusion to cytosolic proteins with known redox-active cysteines, we identified the yeast glycolytic enzyme triose phosphate isomerase as being aggregation-prone in response to cadmium and to glucose depletion in chronologically aging cultures. Cadmium-induced aggregation was limited to newly synthesized Tpi1 that was recruited to foci containing the disaggregase Hsp104 and the peroxiredoxin chaperone Tsa1. Misfolding of nascent Tpi1 in response to both cadmium and glucose-depletion stress required both cysteines, implying that thiol status in this protein directly influences folding. We also demonstrate that cadmium proteotoxicity is conserved between yeast and human cells, as HEK293 and HCT116 cell lines exhibit recruitment of the protein chaperone Hsp70 to visible foci. Moreover, human TPI, mutations in which cause a glycolytic deficiency syndrome, also forms aggregates in response to cadmium treatment, suggesting that this conserved enzyme is folding-labile and may be a useful endogenous model for investigating thiol-specific proteotoxicity.
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Affiliation(s)
- Amy E Ford
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX 77030.,MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX 77030
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, University of Texas McGovern Medical School at Houston, Houston, TX 77030
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX 77030
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17
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Zeidan Q, He F, Zhang F, Zhang H, Jacobson A, Hinnebusch AG. Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo. PLoS Genet 2018; 14:e1007806. [PMID: 30532217 PMCID: PMC6307823 DOI: 10.1371/journal.pgen.1007806] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/27/2018] [Accepted: 11/02/2018] [Indexed: 12/21/2022] Open
Abstract
Scd6 protein family members are evolutionarily conserved components of translationally silent mRNA granules. Yeast Scd6 interacts with Dcp2 and Dhh1, respectively a subunit and a regulator of the mRNA decapping enzyme, and also associates with translation initiation factor eIF4G to inhibit translation in cell extracts. However, the role of Scd6 in mRNA turnover and translational repression in vivo is unclear. We demonstrate that tethering Scd6 to a GFP reporter mRNA reduces mRNA abundance via Dcp2 and suppresses reporter mRNA translation via Dhh1. Thus, in a dcp2Δ mutant, tethered Scd6 reduces GFP protein expression with little effect on mRNA abundance, whereas tethered Scd6 has no impact on GFP protein or mRNA expression in a dcp2Δ dhh1Δ double mutant. The conserved LSm domain of Scd6 is required for translational repression and mRNA turnover by tethered Scd6. Both functions are enhanced in a ccr4Δ mutant, suggesting that the deadenylase function of Ccr4-Not complex interferes with a more efficient repression pathway enlisted by Scd6. Ribosome profiling and RNA-Seq analysis of scd6Δ and dhh1Δ mutants suggests that Scd6 cooperates with Dhh1 in translational repression and turnover of particular native mRNAs, with both processes dependent on Dcp2. Our results suggest that Scd6 can (i) recruit Dhh1 to confer translational repression and (ii) activate mRNA decapping by Dcp2 with attendant degradation of specific mRNAs in vivo, in a manner dependent on the Scd6 LSm domain and modulated by Ccr4.
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Affiliation(s)
- Quira Zeidan
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Fan Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Hongen Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Alan G. Hinnebusch
- Eunice Kennedy Shriver National Institute of Child Health and Development, National Institutes of Health, Bethesda, MD, United States of America
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18
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Zhang Q, Xie H, Chen D, Yu B, Huang Z, Zheng P, Mao X, Yu J, Luo Y, Luo J, He J. Dietary Daidzein Supplementation During Pregnancy Facilitates Fetal Growth in Rats. Mol Nutr Food Res 2018; 62:e1800921. [PMID: 30365232 DOI: 10.1002/mnfr.201800921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/18/2018] [Indexed: 11/06/2022]
Abstract
SCOPE Daidzein, a natural isoflavone with estrogen-like activity, has been implicated in the regulation of reproductive performance in mammals. However, little is known about the molecular mechanisms involved. Here, the effects and potential mechanisms of daidzein supplementation on fetal growth in rats have been explored. METHODS AND RESULTS Thirty-six pregnant Sprague-Dawley rats are assigned to receive either an AIN-93M diet or an AIN-93M diet supplemented with 50 mg kg-1 daidzein. Blood, placental, and fetus samples were collected on day 15 of gestation. It is shown that daidzein significantly improves the rat reproductive performance, which is associated with a higher fetus number, and the weight of the fetus and placenta (p < 0.05). Daidzein also increases the maternal serum estrogen and leptin concentrations, and the activity of superoxide dismutase (SOD) (p < 0.05). Notably, the isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics analysis identifies 43 differentially expressed (DE) proteins in the placenta upon daidzein supplementation (p < 0.05). Interestingly, critical proteins involved in amino acid transport and metabolism, embryonic development, ubiquitination processes, and immune responses are upregulated in the daidzein group (p < 0.05). CONCLUSION These results not only indicate a beneficial effect of daidzein supplementation on reproductive performance but also offer potential mechanisms behind daidzein-facilitated fetal growth in rats.
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Affiliation(s)
- Qiqi Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Hongmei Xie
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China.,Shandong Vocational Animal Science and Veterinary College, Weifang, Shandon, 261061, P. R. China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Bing Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Ping Zheng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Xiangbing Mao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Jie Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Yuheng Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Junqiu Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
| | - Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, 611130, P. R. China
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19
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Nemoto S, Ohnuki S, Abe F, Ohya Y. Simulated microgravity triggers characteristic morphology and stress response in Saccharomyces cerevisiae. Yeast 2018; 36:85-97. [PMID: 30350382 DOI: 10.1002/yea.3361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/20/2023] Open
Abstract
Reduction of gravity results in changes in gene expression and morphology in the budding yeast Saccharomyces cerevisiae. We studied the genes responsible for the morphological changes induced by simulated microgravity (SMG) using the yeast morphology data. We comprehensively captured the features of the morphological changes in yeast cells cultured in SMG with CalMorph, a high-throughput image-processing system. Statistical analysis revealed that 95 of 501 morphological traits were significantly affected, which included changes in bud direction, the ratio of daughter to mother cell size, the random daughter cell shape, the large mother cell size, bright nuclei in the M phase, and the decrease in angle between two nuclei. We identified downregulated genes that impacted the morphological changes in conditions of SMG by focusing on each of the morphological features individually. Gene Ontology (GO)-enrichment analysis indicated that morphological changes under conditions of SMG were caused by cooperative downregulation of 103 genes annotated to six GO terms, which included cytoplasmic ribonucleoprotein granule, RNA elongation, mitotic cell cycle phase transition, nucleocytoplasmic transport, protein-DNA complex subunit organization, and RNA localization. P-body formation was also promoted under conditions of SMG. These results suggest that cooperative downregulation of multiple genes occurs in conditions of SMG.
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Affiliation(s)
- Shota Nemoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Japan
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20
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Mugridge JS, Tibble RW, Ziemniak M, Jemielity J, Gross JD. Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Nat Commun 2018; 9:1152. [PMID: 29559651 PMCID: PMC5861098 DOI: 10.1038/s41467-018-03536-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/22/2018] [Indexed: 11/17/2022] Open
Abstract
The conserved decapping enzyme Dcp2 recognizes and removes the 5′ eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1–Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1–Dcp1–Dcp2–Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis. The decapping enzyme Dcp2 removes the 5′ eukaryotic cap from mRNA transcripts and acts in concert with its essential activator Dcp1 and various coactivators. Here the authors present the structure of the fully-activated mRNA decapping complex, which reveals how Dcp2 recognizes the cap substrate and coactivators Edc1 and Edc3 activate catalysis.
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Affiliation(s)
- Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ryan W Tibble
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland.,Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA.
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21
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Hammond TG, Allen PL, Gunter MA, Chiang J, Giaever G, Nislow C, Birdsall HH. Physical Forces Modulate Oxidative Status and Stress Defense Meditated Metabolic Adaptation of Yeast Colonies: Spaceflight and Microgravity Simulations. MICROGRAVITY SCIENCE AND TECHNOLOGY 2017; 30:195-208. [PMID: 31258252 PMCID: PMC6560652 DOI: 10.1007/s12217-017-9588-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/19/2017] [Indexed: 06/09/2023]
Abstract
Baker's yeast (Saccharomyces cerevisiae) has broad genetic homology to human cells. Although typically grown as 1-2mm diameter colonies under certain conditions yeast can form very large (10 + mm in diameter) or 'giant' colonies on agar. Giant yeast colonies have been used to study diverse biomedical processes such as cell survival, aging, and the response to cancer pharmacogenomics. Such colonies evolve dynamically into complex stratified structures that respond differentially to environmental cues. Ammonia production, gravity driven ammonia convection, and shear defense responses are key differentiation signals for cell death and reactive oxygen system pathways in these colonies. The response to these signals can be modulated by experimental interventions such as agar composition, gene deletion and application of pharmaceuticals. In this study we used physical factors including colony rotation and microgravity to modify ammonia convection and shear stress as environmental cues and observed differences in the responses of both ammonia dependent and stress response dependent pathways We found that the effects of random positioning are distinct from rotation. Furthermore, both true and simulated microgravity exacerbated both cellular redox responses and apoptosis. These changes were largely shear-response dependent but each model had a unique response signature as measured by shear stress genes and the promoter set which regulates them These physical techniques permitted a graded manipulation of both convection and ammonia signaling and are primed to substantially contribute to our understanding of the mechanisms of drug action, cell aging, and colony differentiation.
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Affiliation(s)
- Timothy G. Hammond
- Durham VA Medical Center, Medicine Service Line, 508 Fulton Street, Durham, NC 27705 USA
- Nephrology Division, Department of Medicine, Duke University School of Medicine, Durham, NC 27710 USA
- Space Policy Institute, Elliott School of International Affairs, George Washington University, Washington, DC 20052 USA
| | - Patricia L. Allen
- Durham VA Medical Center, Medicine Service Line, 508 Fulton Street, Durham, NC 27705 USA
| | | | - Jennifer Chiang
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Holly H. Birdsall
- Space Policy Institute, Elliott School of International Affairs, George Washington University, Washington, DC 20052 USA
- Department of Veterans Affairs, Veterans Healthcare Administration, Office of Research, Washington, DC 20420 USA
- Departments of Otorhinolaryngology, Immunology, and Psychiatry, Baylor College of Medicine, Houston, TX 77030 USA
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22
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An improved MS2 system for accurate reporting of the mRNA life cycle. Nat Methods 2017; 15:81-89. [PMID: 29131164 PMCID: PMC5843578 DOI: 10.1038/nmeth.4502] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/04/2017] [Indexed: 12/19/2022]
Abstract
The MS2-MCP system enables researchers to image multiple steps of the mRNA life cycle with high temporal and spatial resolution. However, for short-lived mRNAs, the tight binding of the MS2 coat protein (MCP) to the MS2 binding sites (MBS) protects the RNA from being efficiently degraded, and this confounds the study of mRNA regulation. Here, we describe a reporter system (MBSV6) with reduced affinity for the MCP, which allows mRNA degradation while preserving single-molecule detection determined by single-molecule FISH (smFISH) or live imaging. Constitutive mRNAs (MDN1 and DOA1) and highly-regulated mRNAs (GAL1 and ASH1) endogenously tagged with MBSV6 in Saccharomyces cerevisiae degrade normally. As a result, short-lived mRNAs were imaged throughout their complete life cycle. The MBSV6 reporter revealed that, in contrast to previous findings, coordinated recruitment of mRNAs at specialized structures such as P-bodies during stress did not occur, and mRNA degradation was heterogeneously distributed in the cytoplasm.
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23
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Numerous interactions act redundantly to assemble a tunable size of P bodies in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2017; 114:E9569-E9578. [PMID: 29078371 DOI: 10.1073/pnas.1712396114] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic cells contain multiple RNA-protein assemblies referred to as RNP granules, which are thought to form through multiple protein-protein interactions analogous to a liquid-liquid phase separation. One class of RNP granules consists of P bodies, which consist of nontranslating mRNAs and the general translation repression and mRNA degradation machinery. P bodies have been suggested to form predominantly through interactions of Edc3 and a prion-like domain on Lsm4. In this work, we provide evidence that P-body assembly can be driven by multiple different protein-protein and/or protein-RNA interactions, including interactions involving Dhh1, Psp2, and Pby1. Moreover, the relative importance of specific interactions can vary with different growth conditions. Based on these observations, we develop a summative model wherein the P-body assembly phenotype of a given mutant can be predicted from the number of currently known protein-protein interactions between P-body components.
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24
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Wang M, Ly M, Lugowski A, Laver JD, Lipshitz HD, Smibert CA, Rissland OS. ME31B globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-to-zygotic transition. eLife 2017; 6:27891. [PMID: 28875934 PMCID: PMC5779226 DOI: 10.7554/elife.27891] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/04/2017] [Indexed: 12/27/2022] Open
Abstract
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). We show that the RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay. In a process dependent on the PNG kinase, levels of ME31B and its partners, Cup and Trailer Hitch (TRAL), decrease by over 10-fold during the MZT, leading to a change in the composition of mRNA-protein complexes. We propose that ME31B is a global repressor whose regulatory impact changes based on its biological context.
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Affiliation(s)
- Miranda Wang
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael Ly
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Andrew Lugowski
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Olivia S Rissland
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States.,RNA Bioscience Initiative, University of Colorado Denver School of Medicine, Aurora, United States
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25
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Jin M, Fuller GG, Han T, Yao Y, Alessi AF, Freeberg MA, Roach N, Moresco JJ, Karnovsky A, Baba M, Yates JR, Gitler AD, Inoki K, Klionsky DJ, Kim JK. Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress. Cell Rep 2017; 20:895-908. [PMID: 28746874 PMCID: PMC5586494 DOI: 10.1016/j.celrep.2017.06.082] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/12/2017] [Accepted: 06/27/2017] [Indexed: 12/15/2022] Open
Abstract
Glycolysis is upregulated under conditions such as hypoxia and high energy demand to promote cell proliferation, although the mechanism remains poorly understood. We find that hypoxia in Saccharomyces cerevisiae induces concentration of glycolytic enzymes, including the Pfk2p subunit of the rate-limiting phosphofructokinase, into a single, non-membrane-bound granule termed the "glycolytic body" or "G body." A yeast kinome screen identifies the yeast ortholog of AMP-activated protein kinase, Snf1p, as necessary for G-body formation. Many G-body components identified by proteomics are required for G-body integrity. Cells incapable of forming G bodies in hypoxia display abnormal cell division and produce inviable daughter cells. Conversely, cells with G bodies show increased glucose consumption and decreased levels of glycolytic intermediates. Importantly, G bodies form in human hepatocarcinoma cells in hypoxia. Together, our results suggest that G body formation is a conserved, adaptive response to increase glycolytic output during hypoxia or tumorigenesis.
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Affiliation(s)
- Meiyan Jin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Ting Han
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Yao Yao
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Amelia F Alessi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Mallory A Freeberg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Misuzu Baba
- Research Institute for Science and Technology, Kogakuin University, Hachioji, Tokyo 192-0015 Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Ken Inoki
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Molecular and Integrative Physiology and the Division of Nephrology in the Department of Internal Medicine
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA,corresponding authors: John K Kim, Ph.D., Department of Biology, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD, 21218-2683, . Daniel J Klionsky, Ph.D., Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216,
| | - John K Kim
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109,corresponding authors: John K Kim, Ph.D., Department of Biology, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD, 21218-2683, . Daniel J Klionsky, Ph.D., Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216,
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26
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Valkov E, Jonas S, Weichenrieder O. Mille viae in eukaryotic mRNA decapping. Curr Opin Struct Biol 2017; 47:40-51. [PMID: 28591671 DOI: 10.1016/j.sbi.2017.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Abstract
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2. Together with structure-based insight into decapping network assembly, we propose that DCP2-mediated decapping follows more than one path.
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Affiliation(s)
- Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Stefanie Jonas
- Institute of Biochemistry, ETH Zürich, Otto-Stern Weg 3, 8093 Zürich, Switzerland.
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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27
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Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 2017; 18:285-298. [PMID: 28225081 PMCID: PMC7434221 DOI: 10.1038/nrm.2017.7] [Citation(s) in RCA: 3161] [Impact Index Per Article: 451.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated.
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Affiliation(s)
- Salman F. Banani
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyun O. Lee
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Michael K. Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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28
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An mRNA decapping mutant deficient in P body assembly limits mRNA stabilization in response to osmotic stress. Sci Rep 2017; 7:44395. [PMID: 28290514 PMCID: PMC5349606 DOI: 10.1038/srep44395] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/07/2017] [Indexed: 01/19/2023] Open
Abstract
Yeast is exposed to changing environmental conditions and must adapt its genetic program to provide a homeostatic intracellular environment. An important stress for yeast in the wild is high osmolarity. A key response to this stress is increased mRNA stability primarily by the inhibition of deadenylation. We previously demonstrated that mutations in decapping activators (edc3∆ lsm4∆C), which result in defects in P body assembly, can destabilize mRNA under unstressed conditions. We wished to examine whether mRNA would be destabilized in the edc3∆ lsm4∆C mutant as compared to the wild-type in response to osmotic stress, when P bodies are intense and numerous. Our results show that the edc3∆ lsm4∆C mutant limits the mRNA stability in response to osmotic stress, while the magnitude of stabilization was similar as compared to the wild-type. The reduced mRNA stability in the edc3∆ lsm4∆C mutant was correlated with a shorter PGK1 poly(A) tail. Similarly, the MFA2 mRNA was more rapidly deadenylated as well as significantly stabilized in the ccr4∆ deadenylation mutant in the edc3∆ lsm4∆C background. These results suggest a role for these decapping factors in stabilizing mRNA and may implicate P bodies as sites of reduced mRNA degradation.
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29
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Sekhar AR, Sariki SK, Reddy RVR, Bisai A, Sahu PK, Tomar RS, Sankar J. Zwitterionic BODIPYs with large stokes shift: small molecular biomarkers for live cells. Chem Commun (Camb) 2017; 53:1096-1099. [PMID: 28054075 DOI: 10.1039/c6cc09325f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The two first examples of zwitterionic BODIPYs have been synthesized via a simple SN-Ar methodology. The molecules exhibit excellent optical behavior, such as a large Stokes shift in solution and therefore a very intense emission, and can thus avoid self-quenching. The zwitterionic nature of the molecules was unambiguously elucidated using single crystal XRD studies. The electronic conjugation was investigated by NMR, DFT (NICS (0)) and XRD analysis. Due to their inherent ionic nature, their enhanced solubility in aqueous conditions was exploited for their utility in bio-imaging and cell viability studies. These molecules demonstrate promising localization inside live yeast cells.
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Affiliation(s)
- Adiki Raja Sekhar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, India.
| | - Santhosh Kumar Sariki
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, India
| | - R V Ramana Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, India.
| | - Alakesh Bisai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, India.
| | - Pushpendra Kumar Sahu
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, India
| | - Raghuvir S Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, India
| | - Jeyaraman Sankar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, India.
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30
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Jeong JH, Lee SE, Kim J. Mutational analysis of metacaspase CaMca1 and decapping activator Edc3 in the pathogenicity of Candida albicans. Fungal Genet Biol 2016; 97:18-23. [DOI: 10.1016/j.fgb.2016.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/26/2016] [Accepted: 10/31/2016] [Indexed: 11/29/2022]
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31
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Huch S, Müller M, Muppavarapu M, Gommlich J, Balagopal V, Nissan T. The decapping activator Edc3 and the Q/N-rich domain of Lsm4 function together to enhance mRNA stability and alter mRNA decay pathway dependence in Saccharomyces cerevisiae. Biol Open 2016; 5:1388-1399. [PMID: 27543059 PMCID: PMC5087693 DOI: 10.1242/bio.020487] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The rate and regulation of mRNA decay are major elements in the proper control of gene expression. Edc3 and Lsm4 are two decapping activator proteins that have previously been shown to function in the assembly of RNA granules termed P bodies. Here, we show that deletion of edc3, when combined with a removal of the glutamine/asparagine rich region of Lsm4 (edc3Δ lsm4ΔC) reduces mRNA stability and alters pathways of mRNA degradation. Multiple tested mRNAs exhibited reduced stability in the edc3Δ lsm4ΔC mutant. The destabilization was linked to an increased dependence on Ccr4-mediated deadenylation and mRNA decapping. Unlike characterized mutations in decapping factors that either are neutral or are able to stabilize mRNA, the combined edc3Δ lsm4ΔC mutant reduced mRNA stability. We characterized the growth and activity of the major mRNA decay systems and translation in double mutant and wild-type yeast. In the edc3Δ lsm4ΔC mutant, we observed alterations in the levels of specific mRNA decay factors as well as nuclear accumulation of the catalytic subunit of the decapping enzyme Dcp2. Hence, we suggest that the effects on mRNA stability in the edc3Δ lsm4ΔC mutant may originate from mRNA decay protein abundance or changes in mRNPs, or alternatively may imply a role for P bodies in mRNA stabilization. Summary: A strain mutated in two decapping activators, previously implicated in P body assembly, has reduced mRNA stability and increased dependence on decapping and Ccr4-dependent deadenylation for mRNA degradation.
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Affiliation(s)
- Susanne Huch
- Department of Molecular Biology, Umeå University, Umeå SE-901 87, Sweden
| | - Maren Müller
- Department of Molecular Biology, Umeå University, Umeå SE-901 87, Sweden
| | | | - Jessie Gommlich
- Department of Molecular Biology, Umeå University, Umeå SE-901 87, Sweden
| | - Vidya Balagopal
- Department of Molecular Biology, Umeå University, Umeå SE-901 87, Sweden
| | - Tracy Nissan
- Department of Molecular Biology, Umeå University, Umeå SE-901 87, Sweden
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32
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Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to m 7GDP and its Edc3 activator. Nat Struct Mol Biol 2016; 23:982-986. [PMID: 27694841 DOI: 10.1038/nsmb.3300] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/01/2016] [Indexed: 01/19/2023]
Abstract
Elimination of the 5' cap of eukaryotic mRNAs, known as decapping, is considered to be a crucial, irreversible and highly regulated step required for the rapid degradation of mRNA by Xrn1, the major cytoplasmic 5'-3' exonuclease. Decapping is accomplished by the recruitment of a protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor. However, this complex has a low intrinsic enzymatic activity and requires several accessory proteins such as the Lsm1-7 complex, Pat1, Edc1-Edc2 and/or Edc3 to be fully active. Here we present the crystal structure of the active form of the yeast Kluyveromyces lactis Dcp1-Dcp2 enzyme bound to its product (m7GDP) and its potent activator Edc3. This structure of the Dcp1-Dcp2 complex bound to a cap analog further explains previously published data on substrate binding and provides hints as to the mechanism of Edc3-mediated Dcp2 activation.
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33
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Wurm JP, Overbeck J, Sprangers R. The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface. RNA (NEW YORK, N.Y.) 2016; 22:1360-72. [PMID: 27354705 PMCID: PMC4986892 DOI: 10.1261/rna.057315.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/22/2016] [Indexed: 05/19/2023]
Abstract
The removal of the 5' 7-methylguanosine mRNA cap structure (decapping) is a central step in the 5'-3' mRNA degradation pathway and is performed by the Dcp1:Dcp2 decapping complex. The activity of this complex is tightly regulated to prevent premature degradation of the transcript. Here, we establish that the aromatic groove of the EVH1 domain of Schizosaccharomyces pombe Dcp1 can interact with proline-rich sequences in the exonuclease Xrn1, the scaffolding protein Pat1, the helicase Dhh1, and the C-terminal disordered region of Dcp2. We show that this region of Dcp1 can also recruit a previously unidentified enhancer of decapping protein (Edc1) and solved the crystal structure of the complex. NMR relaxation dispersion experiments reveal that the Dcp1 binding site can adopt multiple conformations, thus providing the plasticity that is required to accommodate different ligands. We show that the activator Edc1 makes additional contacts with the regulatory domain of Dcp2 and that an activation motif in Edc1 increases the RNA affinity of Dcp1:Dcp2. Our data support a model where Edc1 stabilizes the RNA in the active site, which results in enhanced decapping rates. In summary, we show that multiple decapping factors, including the Dcp2 C-terminal region, compete with Edc1 for Dcp1 binding. Our data thus reveal a network of interactions that can fine-tune the catalytic activity of the decapping complex.
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Affiliation(s)
- Jan Philip Wurm
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jan Overbeck
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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34
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Poblete-Durán N, Prades-Pérez Y, Vera-Otarola J, Soto-Rifo R, Valiente-Echeverría F. Who Regulates Whom? An Overview of RNA Granules and Viral Infections. Viruses 2016; 8:v8070180. [PMID: 27367717 PMCID: PMC4974515 DOI: 10.3390/v8070180] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/10/2016] [Accepted: 06/21/2016] [Indexed: 12/22/2022] Open
Abstract
After viral infection, host cells respond by mounting an anti-viral stress response in order to create a hostile atmosphere for viral replication, leading to the shut-off of mRNA translation (protein synthesis) and the assembly of RNA granules. Two of these RNA granules have been well characterized in yeast and mammalian cells, stress granules (SGs), which are translationally silent sites of RNA triage and processing bodies (PBs), which are involved in mRNA degradation. This review discusses the role of these RNA granules in the evasion of anti-viral stress responses through virus-induced remodeling of cellular ribonucleoproteins (RNPs).
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Affiliation(s)
- Natalia Poblete-Durán
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Yara Prades-Pérez
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago 8330024, Chile.
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
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35
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Chuang TW, Lee KM, Lou YC, Lu CC, Tarn WY. A Point Mutation in the Exon Junction Complex Factor Y14 Disrupts Its Function in mRNA Cap Binding and Translation Enhancement. J Biol Chem 2016; 291:8565-74. [PMID: 26887951 DOI: 10.1074/jbc.m115.704544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic mRNA biogenesis involves a series of interconnected steps mediated by RNA-binding proteins. The exon junction complex core protein Y14 is required for nonsense-mediated mRNA decay (NMD) and promotes translation. Moreover, Y14 binds the cap structure of mRNAs and inhibits the activity of the decapping enzyme Dcp2. In this report, we show that an evolutionarily conserved tryptophan residue (Trp-73) of Y14 is critical for its binding to the mRNA cap structure. A Trp-73 mutant (W73V) bound weakly to mRNAs and failed to protect them from degradation. However, this mutant could still interact with the NMD and mRNA degradation factors and retained partial NMD activity. In addition, we found that the W73V mutant could not interact with translation initiation factors. Overexpression of W73V suppressed reporter mRNA translation in vitro and in vivo and reduced the level of a set of nascent proteins. These results reveal a residue of Y14 that confers cap-binding activity and is essential for Y14-mediated enhancement of translation. Finally, we demonstrated that Y14 may selectively and differentially modulate protein biosynthesis.
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Affiliation(s)
- Tzu-Wei Chuang
- From the Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kuo-Ming Lee
- From the Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yuan-Chao Lou
- From the Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Chen Lu
- From the Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Woan-Yuh Tarn
- From the Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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36
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Bilanchone V, Clemens K, Kaake R, Dawson AR, Matheos D, Nagashima K, Sitlani P, Patterson K, Chang I, Huang L, Sandmeyer S. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes. PLoS Genet 2015; 11:e1005528. [PMID: 26421679 PMCID: PMC4589538 DOI: 10.1371/journal.pgen.1005528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/24/2015] [Indexed: 01/15/2023] Open
Abstract
Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5' to 3' exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs.
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Affiliation(s)
- Virginia Bilanchone
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kristina Clemens
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Robyn Kaake
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Anthony R. Dawson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Dina Matheos
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kunio Nagashima
- Electron Microscope Laboratory, NCI-Frederick, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Parth Sitlani
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kurt Patterson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Ivan Chang
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Suzanne Sandmeyer
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
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Cary GA, Vinh DBN, May P, Kuestner R, Dudley AM. Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly. G3 (BETHESDA, MD.) 2015; 5:2497-511. [PMID: 26392412 PMCID: PMC4632068 DOI: 10.1534/g3.115.021444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/16/2015] [Indexed: 12/18/2022]
Abstract
P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci when cells are exposed to stress. Although the conserved mRNA decay and translational repression machineries are known components of PB, how and why cells assemble RNP complexes into large foci remain unclear. Using mass spectrometry to analyze proteins immunoisolated with the core PB protein Dhh1, we show that a considerable number of proteins contain low-complexity sequences, similar to proteins highly represented in mammalian RNP granules. We also show that the Hsp40 chaperone Ydj1, which contains an low-complexity domain and controls prion protein aggregation, is required for the formation of Dhh1-GFP foci on glucose depletion. New classes of proteins that reproducibly coenrich with Dhh1-GFP during PB induction include proteins involved in nucleotide or amino acid metabolism, glycolysis, transfer RNA aminoacylation, and protein folding. Many of these proteins have been shown to form foci in response to other stresses. Finally, analysis of RNA associated with Dhh1-GFP shows enrichment of mRNA encoding the PB protein Pat1 and catalytic RNAs along with their associated mitochondrial RNA-binding proteins. Thus, global characterization of PB composition has uncovered proteins important for PB assembly and evidence suggesting an active role for RNA in PB function.
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Affiliation(s)
- Gregory A Cary
- Institute for Systems Biology, Seattle, Washington 98109 Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Dani B N Vinh
- Institute for Systems Biology, Seattle, Washington 98109
| | - Patrick May
- Institute for Systems Biology, Seattle, Washington 98109 Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Esch-sur-Alzette, Luxembourg L-4362
| | - Rolf Kuestner
- Institute for Systems Biology, Seattle, Washington 98109
| | - Aimée M Dudley
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195 Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
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38
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Jungfleisch J, Chowdhury A, Alves-Rodrigues I, Tharun S, Díez J. The Lsm1-7-Pat1 complex promotes viral RNA translation and replication by differential mechanisms. RNA (NEW YORK, N.Y.) 2015; 21:1469-79. [PMID: 26092942 PMCID: PMC4509936 DOI: 10.1261/rna.052209.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/11/2015] [Indexed: 05/20/2023]
Abstract
The Lsm1-7-Pat1 complex binds to the 3' end of cellular mRNAs and promotes 3' end protection and 5'-3' decay. Interestingly, this complex also specifically binds to cis-acting regulatory sequences of viral positive-strand RNA genomes promoting their translation and subsequent recruitment from translation to replication. Yet, how the Lsm1-7-Pat1 complex regulates these two processes remains elusive. Here, we show that Lsm1-7-Pat1 complex acts differentially in these processes. By using a collection of well-characterized lsm1 mutant alleles and a system that allows the replication of Brome mosaic virus (BMV) in yeast we show that the Lsm1-7-Pat1 complex integrity is essential for both, translation and recruitment. However, the intrinsic RNA-binding ability of the complex is only required for translation. Consistent with an RNA-binding-independent function of the Lsm1-7-Pat1 complex on BMV RNA recruitment, we show that the BMV 1a protein, the sole viral protein required for recruitment, interacts with this complex in an RNA-independent manner. Together, these results support a model wherein Lsm1-7-Pat1 complex binds consecutively to BMV RNA regulatory sequences and the 1a protein to promote viral RNA translation and later recruitment out of the host translation machinery to the viral replication complexes.
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Affiliation(s)
- Jennifer Jungfleisch
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Ashis Chowdhury
- Department of Biochemistry, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland 20814-4799, USA
| | - Isabel Alves-Rodrigues
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Sundaresan Tharun
- Department of Biochemistry, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland 20814-4799, USA
| | - Juana Díez
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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39
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Steffens A, Bräutigam A, Jakoby M, Hülskamp M. The BEACH Domain Protein SPIRRIG Is Essential for Arabidopsis Salt Stress Tolerance and Functions as a Regulator of Transcript Stabilization and Localization. PLoS Biol 2015; 13:e1002188. [PMID: 26133670 PMCID: PMC4489804 DOI: 10.1371/journal.pbio.1002188] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
Abstract
Members of the highly conserved class of BEACH domain containing proteins (BDCPs) have been established as broad facilitators of protein-protein interactions and membrane dynamics in the context of human diseases like albinism, bleeding diathesis, impaired cellular immunity, cancer predisposition, and neurological dysfunctions. Also, the Arabidopsis thaliana BDCP SPIRRIG (SPI) is important for membrane integrity, as spi mutants exhibit split vacuoles. In this work, we report a novel molecular function of the BDCP SPI in ribonucleoprotein particle formation. We show that SPI interacts with the P-body core component DECAPPING PROTEIN 1 (DCP1), associates to mRNA processing bodies (P-bodies), and regulates their assembly upon salt stress. The finding that spi mutants exhibit salt hypersensitivity suggests that the local function of SPI at P-bodies is of biological relevance. Transcriptome-wide analysis revealed qualitative differences in the salt stress-regulated transcriptional response of Col-0 and spi. We show that SPI regulates the salt stress-dependent post-transcriptional stabilization, cytoplasmic agglomeration, and localization to P-bodies of a subset of salt stress-regulated mRNAs. Finally, we show that the PH-BEACH domains of SPI and its human homolog FAN (Factor Associated with Neutral sphingomyelinase activation) interact with DCP1 isoforms from plants, mammals, and yeast, suggesting the evolutionary conservation of an association of BDCPs and P-bodies.
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Affiliation(s)
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
- Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- * E-mail:
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40
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Kim EC, Kim J. Deletion analysis of LSm, FDF, and YjeF domains of Candida albicans Edc3 in hyphal growth and oxidative-stress response. J Microbiol 2015; 53:111-5. [PMID: 25626365 DOI: 10.1007/s12275-015-4727-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
Abstract
Candida albicans is an opportunistic fungal pathogen whose responses to environmental changes are associated with the virulence attributes. Edc3 is known to be an enhancer of the mRNA decapping reactions and a scaffold protein of cytoplasmic processing bodies (P-bodies). Recent studies of C. albicans Edc3 suggested its critical roles in filamentous growth and stress-induced apoptotic cell death. The edc3/edc3 deletion mutant strain showed increased cell survival and less ROS accumulation upon treatment with hydrogen peroxide. To investigate the diverse involvement of Edc3 in the cellular processes, deletion mutations of LSm, FDF, or YjeF domain of Edc3 were constructed. The edc3-LSmΔ or edc3-YjeFΔ mutation showed the filamentation defect, resistance to oxidative stress, and decreased ROS accumulation. In contrast, the edc3-FDFΔ mutation exhibited a wild-type level of filamentous growth and a mild defect in ROS accumulation. These results suggest that Lsm and YjeF domains of Edc3 are critical in hyphal growth and oxidative stress response.
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Affiliation(s)
- Eung-Chul Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 305-764, Republic of Korea
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41
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Mota S, Vieira N, Barbosa S, Delaveau T, Torchet C, Le Saux A, Garcia M, Pereira A, Lemoine S, Coulpier F, Darzacq X, Benard L, Casal M, Devaux F, Paiva S. Role of the DHH1 gene in the regulation of monocarboxylic acids transporters expression in Saccharomyces cerevisiae. PLoS One 2014; 9:e111589. [PMID: 25365506 PMCID: PMC4218774 DOI: 10.1371/journal.pone.0111589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/26/2014] [Indexed: 01/05/2023] Open
Abstract
Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2 (Paiva S, Althoff S, Casal M, Leao C. FEMS Microbiol Lett, 1999, 170:301-306). In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. In these conditions, the stabilized JEN1 mRNA was associated to polysomes but no Jen1 protein could be detected, either by measurable lactate carrier activity, Jen1-GFP fluorescence detection or western blots. These results revealed the complexity of the expression regulation of JEN1 in S. cerevisiae and evidenced the importance of DHH1 in this process. Additionally, microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.
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Affiliation(s)
- Sandra Mota
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Centre of Health and Environmental Research (CISA), School of Allied Health Sciences, Polytechnic Institute of Porto, Vila Nova de Gaia, Portugal
| | - Neide Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Sónia Barbosa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Thierry Delaveau
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
- CNRS, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
| | - Claire Torchet
- CNRS, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie UPMC, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
| | - Agnès Le Saux
- CNRS, FRE3630, Laboratoire de l’Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris, France
| | - Mathilde Garcia
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
- CNRS, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
| | - Ana Pereira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Sophie Lemoine
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
- Inserm, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
| | - Fanny Coulpier
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
- Inserm, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
| | - Xavier Darzacq
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
- Inserm, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
| | - Lionel Benard
- CNRS, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie UPMC, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
| | - Margarida Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Frédéric Devaux
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
- CNRS, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
| | - Sandra Paiva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
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Jung JH, Kim J. Roles of Edc3 in the oxidative stress response and CaMCA1-encoded metacaspase expression in Candida albicans. FEBS J 2014; 281:4841-51. [PMID: 25158786 DOI: 10.1111/febs.13022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/21/2014] [Accepted: 08/22/2014] [Indexed: 12/14/2022]
Abstract
The Edc3 protein is an enhancer of mRNA decapping, and acts as a scaffold protein for the mRNA granules that are known as processing bodies in yeast. In the pathogenic yeast Candida albicans, various stresses, such as glucose depletion, oxidative stress, and filamentation defects, induce the accumulation of processing bodies. Here, we report that the edc3/edc3 deletion strain showed increased resistance to various stresses, including hydrogen peroxide, acetic acid, and high temperature. Oxidative stress is known to induce the intracellular accumulation of reactive oxygen species (ROS) and apoptotic cell death in C. albicans. We found that the ROS level was lower in edc3/edc3 cells than in wild-type cells following oxidative stress. We also observed that expression of the metacaspase gene CaMCA1 was decreased in edc3/edc3 cells. Overexpression of CaMCA1 suppressed the decreased accumulation of ROS and the increased resistance to hydrogen peroxide in edc3/edc3 cells. The catalase Cat1 and the superoxide dismutase Sod1 were upregulated in edc3/edc3 cells as compared with wild-type cells. On the basis of these findings, we suggest that EDC3 plays a critical role in the expression of CaMCA1 and the oxidative stress response in C. albicans.
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Affiliation(s)
- Jong-Hwan Jung
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Korea
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43
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GOV ESRA, ARGA KAZIMYALCIN. GENETIC MUTATIONS ARE CHARACTERIZED BY INCREASE IN ENTROPY AT THE TRANSCRIPTIONAL LEVEL. J BIOL SYST 2014. [DOI: 10.1142/s0218339014500132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Predicting the genomic and phenotypic re-programming in organisms undergoing genetic perturbations is a challenging task in modern biology. It is hypothesized that genomic alterations perturb the dynamics of biological information flow. In the present study, a statistical data analysis framework was designed and the network entropy concept was employed to quantify the level of disorder at the transcriptional level as a result of the genomic re-programming of S. cerevisiae cells under genetic perturbations. The customized re-programming in transcription levels to different genetic modifications was observed and genetic mutations were characterized by enhanced network entropies, which revealed higher degree of randomness in mRNA expression levels. To our knowledge, this study constitutes the first numerical demonstration on the conservative energetic state of the microorganisms against genetic perturbations.
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Affiliation(s)
- ESRA GOV
- Department of Bioengineering, Faculty of Engineering, Marmara University, 34722 Göztepe, Istanbul, Turkey
| | - KAZIM YALCIN ARGA
- Department of Bioengineering, Faculty of Engineering, Marmara University, 34722 Göztepe, Istanbul, Turkey
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44
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Edc3 function in yeast and mammals is modulated by interaction with NAD-related compounds. G3-GENES GENOMES GENETICS 2014; 4:613-22. [PMID: 24504254 PMCID: PMC4059234 DOI: 10.1534/g3.114.010470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The control of mRNA translation and degradation is mediated in part by a set of proteins that can inhibit translation and promote decapping, as well as function in the assembly of cytoplasmic mRNP granules referred to as processing bodies (P-bodies). The conserved enhancer of mRNA decapping 3 (Edc3) protein functions to promote both decapping and P-body assembly. Crystal structures of the YjeF_N domain in hEdc3 identified a putative binding site for a small molecule. Structure modeling of the human Edc3 Yjef_N along with other Yjef_N-containing proteins suggests that this molecule is related to NAD(H). We now show human Edc3 directly binds NADH. We also show that human and yeast Edc3 chemically modify NAD in vitro. Mutations that are predicted to disrupt the binding and/or hydrolysis of an NAD-related molecule by yeast and human Edc3 affect the control of mRNA degradation and/or P-body composition in vivo. This suggests that the interaction of Edc3 with an NAD-related molecule affects its function in the regulation of mRNA translation and degradation and provides a possible mechanism to couple the energetics of the cell to posttranscriptional control. Moreover, this provides a unique example of and lends strength to the postulated connection of metabolites, enzymes, and RNA.
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45
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He F, Li C, Roy B, Jacobson A. Yeast Edc3 targets RPS28B mRNA for decapping by binding to a 3' untranslated region decay-inducing regulatory element. Mol Cell Biol 2014; 34:1438-51. [PMID: 24492965 PMCID: PMC3993580 DOI: 10.1128/mcb.01584-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 12/31/2013] [Accepted: 01/30/2014] [Indexed: 11/20/2022] Open
Abstract
mRNA decapping commits a transcript to complete turnover in eukaryotic cells. In yeast, general mRNA decapping requires the Dcp1/Dcp2 decapping enzyme and a set of decapping activators, including Pat1, Dhh1, Edc3, and the Lsm1-7 complex. The exact function and mode of action of each of these decapping activators in mRNA decapping largely remain elusive. Here, we analyzed the role of Edc3 in the decay of yeast RPS28B mRNA, a pathway triggered by a negative-feedback autoregulatory mechanism. We show that Edc3-mediated RPS28B mRNA decay requires either of two orthologous proteins, Rps28a and Rps28b, expressed from the RPS28A and RPS28B genes, respectively. Contrary to a generally accepted model, we found that Rps28b does not bind to the 3'-untranslated region (UTR) regulatory element in RPS28B mRNA. Instead, Edc3 is directly involved in binding the element, and Rps28b binds Edc3 and regulates its activity. Decay of RPS28B mRNA requires the Lsm and YjeF-N domains of Edc3, but surprisingly, decay of YRA1 pre-mRNA, the only other known substrate of Edc3, requires only the Lsm domain. Collectively, our experiments reveal a new role for Edc3 in mRNA substrate recognition and suggest that this activity is subject to intricate regulation by additional factors, including the Rps28 ribosomal protein.
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Affiliation(s)
- Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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46
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Jonas S, Izaurralde E. The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Genes Dev 2014; 27:2628-41. [PMID: 24352420 PMCID: PMC3877753 DOI: 10.1101/gad.227843.113] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Removal of the 5′ cap structure is a critical step in mRNA turnover, yet key questions regarding the assembly and regulation of decapping complexes remain unanswered. This review provides comprehensive insight into the structural and biochemical properties of decapping factors. Jonas and Izaurralde highlight the plasticity of the decapping network and cover recent advances that reveal how short linear motifs (SliMs) in disordered regions help maintain interactions between decapping network members. The removal of the 5′ cap structure by the decapping enzyme DCP2 inhibits translation and generally commits the mRNA to irreversible 5′-to-3′ exonucleolytic degradation by XRN1. DCP2 catalytic activity is stimulated by DCP1, and these proteins form the conserved core of the decapping complex. Additional decapping factors orchestrate the recruitment and activity of this complex in vivo. These factors include enhancer of decapping 3 (EDC3), EDC4, like Sm14A (LSm14A), Pat, the LSm1–7 complex, and the RNA helicase DDX6. Decapping factors are often modular and feature folded domains flanked or connected by low-complexity disordered regions. Recent studies have made important advances in understanding how these disordered regions contribute to the assembly of decapping complexes and promote phase transitions that drive RNP granule formation. These studies have also revealed that the decapping network is governed by interactions mediated by short linear motifs (SLiMs) in these disordered regions. Consequently, the network has rapidly evolved, and although decapping factors are conserved, individual interactions between orthologs have been rewired during evolution. The plasticity of the network facilitates the acquisition of additional subunits or domains in pre-existing subunits, enhances opportunities for regulating mRNA degradation, and eventually leads to the emergence of novel functions.
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Affiliation(s)
- Stefanie Jonas
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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47
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Cai Y, Futcher B. Effects of the yeast RNA-binding protein Whi3 on the half-life and abundance of CLN3 mRNA and other targets. PLoS One 2013; 8:e84630. [PMID: 24386402 PMCID: PMC3875557 DOI: 10.1371/journal.pone.0084630] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/15/2013] [Indexed: 11/20/2022] Open
Abstract
Whi3 is an RNA binding protein known to bind the mRNA of the yeast G1 cyclin gene CLN3. It inhibits CLN3 function, but the mechanism of this inhibition is unclear; in previous studies, Whi3 made no observable difference to CLN3 mRNA levels, translation, or protein abundance. Here, we re-approach this issue using microarrays, RNA-Seq, ribosome profiling, and other methods. By multiple methods, we find that the whi3 mutation causes a small but consistent increase in the abundance of hundreds of mRNAs, including the CLN3 mRNA. The effect on various mRNAs is roughly in proportion to the density of GCAU or UGCAU motifs carried by these mRNAs, which may be a binding site for Whi3. mRNA instability of Whi3 targets may in part depend on a 3′ AU rich element (ARE), AUUUUA. In addition, the whi3 mutation causes a small increase in the translational efficiency of CLN3 mRNA. The increase in CLN3 mRNA half-life and abundance together with the increase in translational efficiency is fully sufficient to explain the small-cell phenotype of whi3 mutants. Under stress conditions, Whi3 becomes a component of P-bodies or stress granules, but Whi3 also acts under non-stress condition, when no P-bodies are visible. We suggest that Whi3 may be a very broadly-acting, but mild, modulator of mRNA stability. In CLN3, Whi3 may bind to the 3′ GCAU motifs to attract the Ccr4-Not complex to promote RNA deadenylation and turnover, and Whi3 may bind to the 5′ GCAU motifs to inhibit translation.
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Affiliation(s)
- Ying Cai
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Bruce Futcher
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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48
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Sun M, Schwalb B, Pirkl N, Maier KC, Schenk A, Failmezger H, Tresch A, Cramer P. Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels. Mol Cell 2013; 52:52-62. [PMID: 24119399 DOI: 10.1016/j.molcel.2013.09.010] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 06/30/2013] [Accepted: 09/06/2013] [Indexed: 02/08/2023]
Abstract
The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative dynamic transcriptome analysis (cDTA) that uses nonperturbing metabolic RNA labeling. Here we present cDTA data for 46 yeast strains lacking genes involved in mRNA degradation and metabolism. In these strains, changes in mRNA degradation rates are generally compensated by changes in mRNA synthesis rates, resulting in a buffering of mRNA levels. We show that buffering of mRNA levels requires the RNA exonuclease Xrn1. The buffering is rapidly established when mRNA synthesis is impaired, but is delayed when mRNA degradation is impaired, apparently due to Xrn1-dependent transcription repressor induction. Cluster analysis of the data defines the general mRNA degradation machinery, reveals different substrate preferences for the two mRNA deadenylase complexes Ccr4-Not and Pan2-Pan3, and unveils an interwoven cellular mRNA surveillance network.
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Affiliation(s)
- Mai Sun
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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49
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Kolesnikova O, Back R, Graille M, Séraphin B. Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay. Nucleic Acids Res 2013; 41:9514-23. [PMID: 23956223 PMCID: PMC3814365 DOI: 10.1093/nar/gkt607] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA). We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein. This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum. Functional analyses indicate that the ability of Edc3 to interact with Rps28 is not required for its general function and for its role in the regulation of the YRA1 pre-mRNA decay. In contrast, this interaction appears to be exclusively required for the auto-regulatory mechanism controlling the RPS28B mRNA decay. These observations suggest a plausible model for the evolutionary appearance of a Rps28 binding motif in Edc3.
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Affiliation(s)
- Olga Kolesnikova
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France, Ecole Polytechnique, Laboratoire de Biochimie, CNRS UMR7654, 91128 Palaiseau Cedex, France and Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC), CNRS, UMR8619, Bat 430, Université Paris Sud, 91405 Orsay Cedex, France
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Ma J, Flemr M, Strnad H, Svoboda P, Schultz RM. Maternally recruited DCP1A and DCP2 contribute to messenger RNA degradation during oocyte maturation and genome activation in mouse. Biol Reprod 2013; 88:11. [PMID: 23136299 DOI: 10.1095/biolreprod.112.105312] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The oocyte-to-zygote transition entails transforming a highly differentiated oocyte into totipotent blastomeres and represents one of the earliest obstacles that must be successfully hurdled for continued development. Degradation of maternal mRNAs, which likely lies at the heart of this transition, is characterized by a transition from mRNA stability to instability during oocyte maturation. Although phosphorylation of the oocyte-specific RNA-binding protein MSY2 during maturation is implicated in making maternal mRNAs more susceptible to degradation, mechanisms underlying mRNA degradation during oocyte maturation remain poorly understood. We report that DCP1A and DCP2, proteins responsible for decapping mRNA, are encoded by maternal mRNAs recruited for translation during maturation via cytoplasmic polyadenylation elements located in their 3' untranslated regions. Both DCP1A and DCP2 are phosphorylated during maturation, with CDC2A being the kinase likely responsible for both, although MAPK may be involved in DCP1A phosphorylation. Inhibiting accumulation of DCP1A and DCP2 by RNA interference or morpholinos decreases not only degradation of mRNAs during meiotic maturation but also transcription of the zygotic genome. The results indicate that maternally recruited DCP1A and DCP2 are critical players in the transition from mRNA stability to instability during meiotic maturation and that proper maternal mRNA degradation must be successful to execute the oocyte-to-zygote transition.
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Affiliation(s)
- Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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