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Huang H, Ji F, Hu C, Huang J, Liu F, Han Z, Liu L, Cao M, Fu G. Identifying Novel Proteins for Chronic Pain: Integration of Human Brain Proteomes and Genome-wide Association Data. THE JOURNAL OF PAIN 2024:104610. [PMID: 38909833 DOI: 10.1016/j.jpain.2024.104610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/25/2024]
Abstract
Numerous genome-wide association studies have identified risk genes for chronic pain, yet the mechanisms by which genetic variants modify susceptibility have remained elusive. We sought to identify key genes modulating chronic pain risk by regulating brain protein expression. We integrated brain proteomic data with the largest genome-wide dataset for multisite chronic pain (N = 387,649) in a proteome-wide association study (PWAS) using discovery and confirmatory proteomic datasets (N = 376 and 152) from the dorsolateral prefrontal cortex. Leveraging summary data-based Mendelian randomization and Bayesian colocalization analysis, we pinpointed potential causal genes, while a transcriptome-wide association study integrating 452 human brain transcriptomes investigated whether cis-effects on protein abundance extended to the transcriptome. Single-cell RNA-sequencing data and single-nucleus transcriptomic data revealed cell-type-specific expression patterns for identified causal genes in the dorsolateral prefrontal cortex and dorsal root ganglia (DRG), complemented by RNA microarray analysis of expression profiles in other pain-related brain regions. Of the 22 genes cis-regulating protein abundance identified by the discovery PWAS, 18 (82%) were deemed causal by summary data-based Mendelian randomization or Bayesian colocalization analysis analyses, with 7 of these 18 genes (39%) replicating in the confirmatory PWAS, including guanosine diphosphate-mannose pyrophosphorylase B, which also associated at the transcriptome level. Several causal genes exhibited selective expression in excitatory and inhibitory neurons, oligodendrocytes, and astrocytes, while most identified genes were expressed across additional pain-related brain regions. This integrative proteogenomic approach identified 18 high-confidence causal genes for chronic pain, regulated by cis-effects on brain protein levels, suggesting promising avenues for treatment research and indicating a contributory role for the DRG. PERSPECTIVE: The current post genome-wide association study analyses identified 18 high-confidence causal genes regulating chronic pain risk via cis-modulation of brain protein abundance, suggesting promising avenues for future chronic pain therapies. Additionally, the significant expression of these genes in the DRG indicated a potential contributory role, warranting further investigation.
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Affiliation(s)
- Haoquan Huang
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Medical Research Center of Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Shanwei, China
| | - Fengtao Ji
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Chuwen Hu
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jingxuan Huang
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Fan Liu
- Medical Research Center of Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Shanwei, China
| | - Zhixiao Han
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ling Liu
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Minghui Cao
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Medical Research Center of Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Shanwei, China
| | - Ganglan Fu
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Medical Research Center of Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Shanwei, China.
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2
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Park J, Kim M, Yi H, Baeg K, Choi Y, Lee YS, Lim J, Kim VN. Short poly(A) tails are protected from deadenylation by the LARP1-PABP complex. Nat Struct Mol Biol 2023; 30:330-338. [PMID: 36849640 DOI: 10.1038/s41594-023-00930-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
Abstract
Deadenylation generally constitutes the first and pivotal step in eukaryotic messenger RNA decay. Despite its importance in posttranscriptional regulations, the kinetics of deadenylation and its regulation remain largely unexplored. Here we identify La ribonucleoprotein 1, translational regulator (LARP1) as a general decelerator of deadenylation, which acts mainly in the 30-60-nucleotide (nt) poly(A) length window. We measured the steady-state and pulse-chased distribution of poly(A)-tail length, and found that deadenylation slows down in the 30-60-nt range. LARP1 associates preferentially with short tails and its depletion results in accelerated deadenylation specifically in the 30-60-nt range. Consistently, LARP1 knockdown leads to a global reduction of messenger RNA abundance. LARP1 interferes with the CCR4-NOT-mediated deadenylation in vitro by forming a ternary complex with poly(A)-binding protein (PABP) and poly(A). Together, our work reveals a dynamic nature of deadenylation kinetics and a role of LARP1 as a poly(A) length-specific barricade that creates a threshold for deadenylation.
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Affiliation(s)
- Joha Park
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Myeonghwan Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hyerim Yi
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Stanford University School of Medicine, Stanford, CA, USA
| | - Kyungmin Baeg
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
| | - Yongkuk Choi
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
- Yale School of Medicine, New Haven, CT, USA
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.
- School of Biological Sciences, Seoul National University, Seoul, Korea.
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3
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Bouron A, Fauvarque MO. Genome-wide analysis of genes encoding core components of the ubiquitin system during cerebral cortex development. Mol Brain 2022; 15:72. [PMID: 35974412 PMCID: PMC9380329 DOI: 10.1186/s13041-022-00958-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Ubiquitination involves three types of enzymes (E1, E2, and E3) that sequentially attach ubiquitin (Ub) to target proteins. This posttranslational modification controls key cellular processes, such as the degradation, endocytosis, subcellular localization and activity of proteins. Ubiquitination, which can be reversed by deubiquitinating enzymes (DUBs), plays important roles during brain development. Furthermore, deregulation of the Ub system is linked to the pathogenesis of various diseases, including neurodegenerative disorders. We used a publicly available RNA-seq database to perform an extensive genome-wide gene expression analysis of the core components of the ubiquitination machinery, covering Ub genes as well as E1, E2, E3 and DUB genes. The ubiquitination network was governed by only Uba1 and Ube2m, the predominant E1 and E2 genes, respectively; their expression was positively regulated during cortical formation. The principal genes encoding HECT (homologous to the E6-AP carboxyl terminus), RBR (RING-in-between-RING), and RING (really interesting new gene) E3 Ub ligases were also highly regulated. Pja1, Dtx3 (RING ligases) and Stub1 (U-box RING) were the most highly expressed E3 Ub ligase genes and displayed distinct developmental expression patterns. Moreover, more than 80 DUB genes were expressed during corticogenesis, with two prominent genes, Uch-l1 and Usp22, showing highly upregulated expression. Several components of the Ub system overexpressed in cancers were also highly expressed in the cerebral cortex under conditions not related to tumour formation or progression. Altogether, this work provides an in-depth overview of transcriptomic changes during embryonic formation of the cerebral cortex. The data also offer new insight into the characterization of the Ub system and may contribute to a better understanding of its involvement in the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Alexandre Bouron
- Université Grenoble Alpes, Inserm, CEA, UMR 1292, 38000, Grenoble, France. .,Genetics and Chemogenomics Lab, Building C3, CEA, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France.
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Wang T, Liu W, Wang C, Ma X, Akhtar MF, Li Y, Li L. MRKNs: Gene, Functions, and Role in Disease and Infection. Front Oncol 2022; 12:862206. [PMID: 35463379 PMCID: PMC9024132 DOI: 10.3389/fonc.2022.862206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
The makorin RING finger protein (MKRN) gene family encodes proteins (makorins) with a characteristic array of zinc-finger motifs present in a wide array from invertebrates to vertebrates. MKRNs (MKRN1, MKRN2, MKRN3, MKRN4) as RING finger E3 ligases that mediate substrate degradation are related with conserved RING finger domains that control multiple cellular components via the ubiquitin-proteasome system (UPS), including p53, p21, FADD, PTEN, p65, Nptx1, GLK, and some viral or bacterial proteins. MKRNs also served as diverse roles in disease, like MKRN1 in transcription regulation, metabolic disorders, and tumors; MKRN2 in testis physiology, neurogenesis, apoptosis, and mutation of MKRN2 regulation signals transduction, inflammatory responses, melanoma, and neuroblastoma; MKRN3 in central precocious puberty (CPP) therapy; and MKRN4 firstly reported as a novel E3 ligase instead of a pseudogene to contribute to systemic lupus erythematosus (SLE). Here, we systematically review advances in the gene’s expression, function, and role of MKRNs orthologs in disease and pathogens infection. Further, MKRNs can be considered targets for the host’s innate intracellular antiviral defenses and disease therapy.
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Affiliation(s)
- Tongtong Wang
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Wenqiang Liu
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Xuelian Ma
- Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | | | - Yubao Li
- College of Agronomy, Liaocheng University, Liaocheng, China
- *Correspondence: Yubao Li, ; Liangliang Li,
| | - Liangliang Li
- College of Agronomy, Liaocheng University, Liaocheng, China
- *Correspondence: Yubao Li, ; Liangliang Li,
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5
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Schob C, Hempel M, Safka Brozkova D, Jiang H, Kim SY, Batzir NA, Orenstein N, Bierhals T, Johannsen J, Uhrova Meszarosova A, Chae JH, Seeman P, Woidy M, Fang F, Kubisch C, Kindler S, Denecke J. Dominant KPNA3 Mutations Cause Infantile-Onset Hereditary Spastic Paraplegia. Ann Neurol 2021; 90:738-750. [PMID: 34564892 DOI: 10.1002/ana.26228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Hereditary spastic paraplegia (HSP) is a highly heterogeneous neurologic disorder characterized by lower-extremity spasticity. Here, we set out to determine the genetic basis of an autosomal dominant, pure, and infantile-onset form of HSP in a cohort of 8 patients with a uniform clinical presentation. METHODS Trio whole-exome sequencing was used in 5 index patients with infantile-onset pure HSP to determine the genetic cause of disease. The functional impact of identified genetic variants was verified using bioinformatics and complementary cellular and biochemical assays. RESULTS Distinct heterozygous KPNA3 missense variants were found to segregate with the clinical phenotype in 8 patients; in 4 of them KPNA3 variants had occurred de novo. Mutant karyopherin-α3 proteins exhibited a variable pattern of altered expression level, subcellular distribution, and protein interaction. INTERPRETATION Our genetic findings implicate heterozygous variants in KPNA3 as a novel cause for autosomal dominant, early-onset, and pure HSP. Mutant karyopherin-α3 proteins display varying deficits in molecular and cellular functions, thus, for the first time, implicating dysfunctional nucleocytoplasmic shuttling as a novel pathomechanism causing HSP. ANN NEUROL 2021;90:738-750.
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Affiliation(s)
- Claudia Schob
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dana Safka Brozkova
- Neurogenetic Laboratory, Department of Pediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Huafang Jiang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Soo Yeon Kim
- Department of Genomics Medicine, Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Nurit Assia Batzir
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel
| | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Uhrova Meszarosova
- Neurogenetic Laboratory, Department of Pediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jong-Hee Chae
- Department of Genomics Medicine, Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pavel Seeman
- Neurogenetic Laboratory, Department of Pediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Mathias Woidy
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Kindler
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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6
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Fang YC, Fu SJ, Hsu PH, Chang PT, Huang JJ, Chiu YC, Liao YF, Jow GM, Tang CY, Jeng CJ. Identification of MKRN1 as a second E3 ligase for Eag1 potassium channels reveals regulation via differential degradation. J Biol Chem 2021; 296:100484. [PMID: 33647316 PMCID: PMC8039722 DOI: 10.1016/j.jbc.2021.100484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/17/2021] [Accepted: 02/25/2021] [Indexed: 11/02/2022] Open
Abstract
Mutations in the human gene encoding the neuron-specific Eag1 voltage-gated K+ channel are associated with neurodevelopmental diseases, indicating an important role of Eag1 during brain development. A disease-causing Eag1 mutation is linked to decreased protein stability that involves enhanced protein degradation by the E3 ubiquitin ligase cullin 7 (CUL7). The general mechanisms governing protein homeostasis of plasma membrane- and endoplasmic reticulum (ER)-localized Eag1 K+ channels, however, remain unclear. By using yeast two-hybrid screening, we identified another E3 ubiquitin ligase, makorin ring finger protein 1 (MKRN1), as a novel binding partner primarily interacting with the carboxyl-terminal region of Eag1. MKRN1 mainly interacts with ER-localized immature core-glycosylated, as well as nascent nonglycosylated, Eag1 proteins. MKRN1 promotes polyubiquitination and ER-associated proteasomal degradation of immature Eag1 proteins. Although both CUL7 and MKRN1 contribute to ER quality control of immature core-glycosylated Eag1 proteins, MKRN1, but not CUL7, associates with and promotes degradation of nascent, nonglycosylated Eag1 proteins at the ER. In direct contrast to the role of CUL7 in regulating both ER and peripheral quality controls of Eag1, MKRN1 is exclusively responsible for the early stage of Eag1 maturation at the ER. We further demonstrated that both CUL7 and MKRN1 contribute to protein quality control of additional disease-causing Eag1 mutants associated with defective protein homeostasis. Our data suggest that the presence of this dual ubiquitination system differentially maintains Eag1 protein homeostasis and may ensure efficient removal of disease-associated misfolded Eag1 mutant channels.
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Affiliation(s)
- Ya-Ching Fang
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ssu-Ju Fu
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Hao Hsu
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Tzu Chang
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jing-Jia Huang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Chih Chiu
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Fan Liao
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Guey-Mei Jow
- School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Chih-Yung Tang
- Department of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Chung-Jiuan Jeng
- Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Brain Research Center, National Yang-Ming University, Taipei, Taiwan.
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MKRN2 Physically Interacts with GLE1 to Regulate mRNA Export and Zebrafish Retinal Development. Cell Rep 2020; 31:107693. [DOI: 10.1016/j.celrep.2020.107693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/25/2020] [Accepted: 05/05/2020] [Indexed: 12/31/2022] Open
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Dold A, Han H, Liu N, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY, Lasko P. Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLoS Genet 2020; 16:e1008581. [PMID: 31978041 PMCID: PMC7001992 DOI: 10.1371/journal.pgen.1008581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 02/05/2020] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila, maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar (osk). We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3’ UTR in a region adjacent to A-rich sequences. Using Drosophila S2R+ cultured cells we show that this binding site overlaps with a Bruno1 (Bru1) responsive element (BREs) that regulates osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3’ UTR. To ensure accurate development of the Drosophila embryo, proteins and mRNAs are positioned at specific sites within the embryo. Many of these factors are produced and localized during the development of the egg in the mother. One protein essential for this process that has been heavily studied is Oskar (Osk), which is positioned at the posterior pole. During the localization of osk mRNA, its translation is repressed by the RNA-binding protein Bruno1 (Bru1), ensuring that Osk protein is not present outside of the posterior where it is harmful. At the posterior pole, osk mRNA is activated through mechanisms that are not yet understood. In this work, we show that the conserved protein Makorin 1 (Mkrn1) is a novel factor involved in the translational activation of osk. Mkrn1 binds specifically to osk mRNA, overlapping with a binding site of Bru1, thus alleviating the association of Bru1 with osk. Moreover, Mkrn1 is stabilized by poly(A) binding protein (pAbp), a translational activator that binds osk mRNA in close proximity to one Mkrn1 binding site. Our work thus helps to answer a long-standing question in the field, providing insight about the function of Mkrn1 and more generally into embryonic patterning in animals.
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Affiliation(s)
- Annabelle Dold
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Hong Han
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Niankun Liu
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andrea Hildebrandt
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany.,Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Cornelia Rücklé
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Heike Hänel
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Anke Busch
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Petra Beli
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julian König
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Jean-Yves Roignant
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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Thapa P, Shanmugam N, Pokrzywa W. Ubiquitin Signaling Regulates RNA Biogenesis, Processing, and Metabolism. Bioessays 2019; 42:e1900171. [PMID: 31778250 DOI: 10.1002/bies.201900171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/29/2019] [Indexed: 12/17/2022]
Abstract
The fate of eukaryotic proteins, from their synthesis to destruction, is supervised by the ubiquitin-proteasome system (UPS). The UPS is the primary pathway responsible for selective proteolysis of intracellular proteins, which is guided by covalent attachment of ubiquitin to target proteins by E1 (activating), E2 (conjugating), and E3 (ligating) enzymes in a process known as ubiquitylation. The UPS can also regulate protein synthesis by influencing multiple steps of RNA (ribonucleic acid) metabolism. Here, recent publications concerning the interplay between the UPS and different types of RNA are reviewed. This interplay mainly involves specific RNA-binding E3 ligases that link RNA-dependent processes with protein ubiquitylation. The emerging understanding of their modes of RNA binding, their RNA targets, and their molecular and cellular functions are primarily focused on. It is discussed how the UPS adapted to interact with different types of RNA and how RNA molecules influence the ubiquitin signaling components.
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Affiliation(s)
- Pankaj Thapa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
| | - Nilesh Shanmugam
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
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10
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Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P. The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol 2019; 20:216. [PMID: 31640799 PMCID: PMC6805484 DOI: 10.1186/s13059-019-1814-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide via ribosome-associated quality control. RESULTS Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at poly(A) sequences during ribosome-associated quality control. We show that MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) and associates with polysomes. MKRN1 is positioned upstream of poly(A) tails in mRNAs in a PABPC1-dependent manner. Ubiquitin remnant profiling and in vitro ubiquitylation assays uncover PABPC1 and ribosomal protein RPS10 as direct ubiquitylation substrates of MKRN1. CONCLUSIONS We propose that MKRN1 mediates the recognition of poly(A) tails to prevent the production of erroneous proteins from prematurely polyadenylated transcripts, thereby maintaining proteome integrity.
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Affiliation(s)
- Andrea Hildebrandt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Cornelia Rücklé
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Martin M Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | | | - Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Annabelle Dold
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Génopode Building, CH-1015, Lausanne, Switzerland
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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11
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Naulé L, Kaiser UB. Evolutionary Conservation of MKRN3 and Other Makorins and Their Roles in Puberty Initiation and Endocrine Functions. Semin Reprod Med 2019; 37:166-173. [PMID: 31972861 PMCID: PMC8603287 DOI: 10.1055/s-0039-3400965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Puberty is a critical period of development regulated by genetic, nutritional, and environmental factors. The role of makorin ring finger protein 3 (MKRN3) in the regulation of pubertal timing was revealed when loss-of-function mutations were identified in patients with central precocious puberty (CPP). To date, MKRN3 mutations are the most common known genetic cause of CPP. MKRN3 is a member of the makorin family of ubiquitin ligases, together with MKRN1 and MKRN2. The Mkrn genes have been identified in both vertebrates and invertebrates and show high evolutionary conservation of their gene and protein structures. While the existence of Mkrn orthologues in a wide spectrum of species suggests a vital cellular role of the makorins, their role in puberty initiation and endocrine functions is just beginning to be investigated. In this review, we discuss recent studies that have shown the involvement of Mkrn3 and other makorins in the regulation of pubertal development and other endocrine functions, including metabolism and fertility, as well as their underlying mechanisms of action.
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Affiliation(s)
- Lydie Naulé
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ursula B. Kaiser
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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12
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Jeong EB, Jeong SS, Cho E, Kim EY. Makorin 1 is required for Drosophila oogenesis by regulating insulin/Tor signaling. PLoS One 2019; 14:e0215688. [PMID: 31009498 PMCID: PMC6476528 DOI: 10.1371/journal.pone.0215688] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/05/2019] [Indexed: 01/02/2023] Open
Abstract
Reproduction is a process that is extremely sensitive to changes in nutritional status. The nutritional control of oogenesis via insulin signaling has been reported; however, the mechanism underlying its sensitivity and tissue specificity has not been elucidated. Here, we determined that Drosophila Makorin RING finger protein 1 gene (Mkrn1) functions in the metabolic regulation of oogenesis. Mkrn1 was endogenously expressed at high levels in ovaries and Mkrn1 knockout resulted in female sterility. Mkrn1-null egg chambers were previtellogenic without egg production. FLP-FRT mosaic analysis revealed that Mkrn1 is essential in germline cells, but not follicle cells, for ovarian function. As well, AKT phosphorylation via insulin signaling was greatly reduced in the germline cells, but not the follicle cells, of the mutant clones in the ovaries. Furthermore, protein-rich diet elevated Mkrn1 protein levels, without increased mRNA levels. The p-AKT and p-S6K levels, downstream targets of insulin/Tor signaling, were significantly increased by a nutrient-rich diet in wild-type ovaries whereas those were low in Mkrn1exS compared to wild-type ovaries. Taken together, our results suggest that nutrient availability upregulates the Mkrn1 protein, which acts as a positive regulator of insulin signaling to confer sensitivity and tissue specificity in the ovaries for proper oogenesis based on nutritional status.
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Affiliation(s)
- Eui Beom Jeong
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
| | - Seong Su Jeong
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
| | - Eunjoo Cho
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- * E-mail: (EYK); (EC)
| | - Eun Young Kim
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, Kyunggi-do, Republic of Korea
- * E-mail: (EYK); (EC)
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13
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Zuo H, Yang L, Zheng J, Su Z, Weng S, He J, Xu X. A single C4 Zinc finger-containing protein from Litopenaeus vannamei involved in antibacterial responses. FISH & SHELLFISH IMMUNOLOGY 2018; 81:493-501. [PMID: 30064017 DOI: 10.1016/j.fsi.2018.07.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/18/2018] [Accepted: 07/27/2018] [Indexed: 06/08/2023]
Abstract
The Zinc finger domains (ZnFs), which contain finger-like protrusions stabilized by zinc ions and function to bind DNA, RNA, protein and lipid substrates, are ubiquitously present in a large number of proteins. In this study, a novel protein containing a single C4 type Znf domain (SZnf) was identified from Pacific white shrimp, Litopenaeus vannamei and its role in immunity was further investigated. The ZnF domain of SZnF but not other regions shared high homology with those of fushi tarazu-factor 1 (FTZ-F1) proteins. The SZnF protein was mainly localized in the cytoplasm and was also present in the nucleus at a small level. SZnF was high expressed in the scape and muscle tissues of healthy shrimp and its expression in gill and heptopancreas was strongly up-regulated during bacterial infection. Silencing of SZnf in vivo could strongly increase the susceptibility of shrimp to infection with Vibrio parahaemolyticus but not white spot syndrome virus (WSSV), suggesting that SZnf could be mainly involved in antibacterial responses. Both dual luciferase reporter assays and real-time PCR analysis demonstrated that SZnf could positively regulate the expression of various antimicrobial peptides in vitro and in vivo, which could be part of the mechanism underlying its antibacterial effects. In summary, the current study could help learn more about the function of ZnF-containing proteins and the regulatory mechanisms of immune responses against pathogen infection in crustaceans.
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Affiliation(s)
- Hongliang Zuo
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Linwei Yang
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Jiefu Zheng
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Ziqi Su
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Shaoping Weng
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
| | - Xiaopeng Xu
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
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14
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Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII. J Virol 2018; 92:JVI.01154-17. [PMID: 29142133 DOI: 10.1128/jvi.01154-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/12/2017] [Indexed: 11/20/2022] Open
Abstract
Human adenoviruses (HAdVs) are common human pathogens encoding a highly abundant histone-like core protein, VII, which is involved in nuclear delivery and protection of viral DNA as well as in sequestering immune danger signals in infected cells. The molecular details of how protein VII acts as a multifunctional protein have remained to a large extent enigmatic. Here we report the identification of several cellular proteins interacting with the precursor pVII protein. We show that the cellular E3 ubiquitin ligase MKRN1 is a novel precursor pVII-interacting protein in HAdV-C5-infected cells. Surprisingly, the endogenous MKRN1 protein underwent proteasomal degradation during the late phase of HAdV-C5 infection in various human cell lines. MKRN1 protein degradation occurred independently of the HAdV E1B55K and E4orf6 proteins. We provide experimental evidence that the precursor pVII protein binding enhances MKRN1 self-ubiquitination, whereas the processed mature VII protein is deficient in this function. Based on these data, we propose that the pVII protein binding promotes MKRN1 self-ubiquitination, followed by proteasomal degradation of the MKRN1 protein, in HAdV-C5-infected cells. In addition, we show that measles virus and vesicular stomatitis virus infections reduce the MKRN1 protein accumulation in the recipient cells. Taken together, our results expand the functional repertoire of the HAdV-C5 precursor pVII protein in lytic virus infection and highlight MKRN1 as a potential common target during different virus infections.IMPORTANCE Human adenoviruses (HAdVs) are common pathogens causing a wide range of diseases. To achieve pathogenicity, HAdVs have to counteract a variety of host cell antiviral defense systems, which would otherwise hamper virus replication. In this study, we show that the HAdV-C5 histone-like core protein pVII binds to and promotes self-ubiquitination of a cellular E3 ubiquitin ligase named MKRN1. This mutual interaction between the pVII and MKRN1 proteins may prime MKRN1 for proteasomal degradation, because the MKRN1 protein is efficiently degraded during the late phase of HAdV-C5 infection. Since MKRN1 protein accumulation is also reduced in measles virus- and vesicular stomatitis virus-infected cells, our results signify the general strategy of viruses to target MKRN1.
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15
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Barragán-Iglesias P, Lou TF, Bhat VD, Megat S, Burton MD, Price TJ, Campbell ZT. Inhibition of Poly(A)-binding protein with a synthetic RNA mimic reduces pain sensitization in mice. Nat Commun 2018; 9:10. [PMID: 29295980 PMCID: PMC5750225 DOI: 10.1038/s41467-017-02449-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/30/2017] [Indexed: 12/26/2022] Open
Abstract
Nociceptors rely on cap-dependent translation to rapidly induce protein synthesis in response to pro-inflammatory signals. Comparatively little is known regarding the role of the regulatory factors bound to the 3' end of mRNA in nociceptor sensitization. Poly(A)-binding protein (PABP) stimulates translation initiation by bridging the Poly(A) tail to the eukaryotic initiation factor 4F complex associated with the mRNA cap. Here, we use unbiased assessment of PABP binding specificity to generate a chemically modified RNA-based competitive inhibitor of PABP. The resulting RNA mimic, which we designated as the Poly(A) SPOT-ON, is more stable than unmodified RNA and binds PABP with high affinity and selectivity in vitro. We show that injection of the Poly(A) SPOT-ON at the site of an injury can attenuate behavioral response to pain. Collectively, these results suggest that PABP is integral for nociceptive plasticity. The general strategy described here provides a broad new source of mechanism-based inhibitors for RNA-binding proteins and is applicable for in vivo studies.
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Affiliation(s)
| | - Tzu-Fang Lou
- Department of Biological Sciences, University of Texas Dallas, Richardson, TX, 75080, USA
| | - Vandita D Bhat
- Department of Biological Sciences, University of Texas Dallas, Richardson, TX, 75080, USA
| | - Salim Megat
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Michael D Burton
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Theodore J Price
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX, 75080, USA.
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas Dallas, Richardson, TX, 75080, USA.
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16
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De Novo Missense Mutations in DHX30 Impair Global Translation and Cause a Neurodevelopmental Disorder. Am J Hum Genet 2017; 101:716-724. [PMID: 29100085 DOI: 10.1016/j.ajhg.2017.09.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/19/2017] [Indexed: 11/21/2022] Open
Abstract
DHX30 is a member of the family of DExH-box helicases, which use ATP hydrolysis to unwind RNA secondary structures. Here we identified six different de novo missense mutations in DHX30 in twelve unrelated individuals affected by global developmental delay (GDD), intellectual disability (ID), severe speech impairment and gait abnormalities. While four mutations are recurrent, two are unique with one affecting the codon of one recurrent mutation. All amino acid changes are located within highly conserved helicase motifs and were found to either impair ATPase activity or RNA recognition in different in vitro assays. Moreover, protein variants exhibit an increased propensity to trigger stress granule (SG) formation resulting in global translation inhibition. Thus, our findings highlight the prominent role of translation control in development and function of the central nervous system and also provide molecular insight into how DHX30 dysfunction might cause a neurodevelopmental disorder.
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17
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Deans PM, Raval P, Sellers KJ, Gatford NJ, Halai S, Duarte RR, Shum C, Warre-Cornish K, Kaplun VE, Cocks G, Hill M, Bray NJ, Price J, Srivastava DP. Psychosis Risk Candidate ZNF804A Localizes to Synapses and Regulates Neurite Formation and Dendritic Spine Structure. Biol Psychiatry 2017; 82:49-61. [PMID: 27837918 PMCID: PMC5482321 DOI: 10.1016/j.biopsych.2016.08.038] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Variation in the gene encoding zinc finger binding protein 804A (ZNF804A) is associated with schizophrenia and bipolar disorder. Evidence suggests that ZNF804A is a regulator of gene transcription and is present in nuclear and extranuclear compartments. However, a detailed examination of ZNF804A distribution and its neuronal functions has yet to be performed. METHODS The localization of ZNF804A protein was examined in neurons derived from human neural progenitor cells, human induced pluripotent stem cells, or in primary rat cortical neurons. In addition, small interfering RNA-mediated knockdown of ZNF804A was conducted to determine its role in neurite formation, maintenance of dendritic spine morphology, and responses to activity-dependent stimulations. RESULTS Endogenous ZNF804A protein localized to somatodendritic compartments and colocalized with the putative synaptic markers in young neurons derived from human neural progenitor cells and human induced pluripotent stem cells. In mature rat neurons, Zfp804A, the homolog of ZNF804A, was present in a subset of dendritic spines and colocalized with synaptic proteins in specific nanodomains, as determined by super-resolution microscopy. Interestingly, knockdown of ZNF804A attenuated neurite outgrowth in young neurons, an effect potentially mediated by reduced neuroligin-4 expression. Furthermore, knockdown of ZNF804A in mature neurons resulted in the loss of dendritic spine density and impaired responses to activity-dependent stimulation. CONCLUSIONS These data reveal a novel subcellular distribution for ZNF804A within somatodendritic compartments and a nanoscopic organization at excitatory synapses. Moreover, our results suggest that ZNF804A plays an active role in neurite formation, maintenance of dendritic spines, and activity-dependent structural plasticity.
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Affiliation(s)
- P.J. Michael Deans
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Pooja Raval
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Katherine J. Sellers
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Nicholas J.F. Gatford
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Sanjay Halai
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Rodrigo R.R. Duarte
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Carole Shum
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Katherine Warre-Cornish
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Victoria E. Kaplun
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Graham Cocks
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London
| | - Matthew Hill
- MRC Centre for Neuropsychiatric Genetics & Genomics, Cardiff, United Kingdom,Neuroscience and Mental Health Research Institute, College of Biomedical and Life Sciences, Cardiff University School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Nicholas J. Bray
- MRC Centre for Neuropsychiatric Genetics & Genomics, Cardiff, United Kingdom
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London,MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London; United Kingdom
| | - Deepak P. Srivastava
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London,MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London; United Kingdom,Address correspondence to: Deepak P. Srivastava, Ph.D., Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, SE5 9RT, United KingdomDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College LondonLondonSE5 9RTUnited Kingdom
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18
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Deficiency of Mkrn2 causes abnormal spermiogenesis and spermiation, and impairs male fertility. Sci Rep 2016; 6:39318. [PMID: 28008940 PMCID: PMC5180214 DOI: 10.1038/srep39318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022] Open
Abstract
Although recent studies have shed insights on some of the potential causes of male infertility, new underlining molecular mechanisms still remain to be elucidated. Makorin-2 (Mkrn2) is an evolutionarily conserved gene whose biological functions are not fully known. We developed an Mrkn2 knockout mouse model to study the role of this gene, and found that deletion of Mkrn2 in mice led to male infertility. Mkrn2 knockout mice produced abnormal sperms characterized by low number, poor motility, and aberrant morphology. Disruption of Mkrn2 also caused failure of sperm release (spermiation failure) and misarrangement of ectoplasmic specialization (ES) in testes, thus impairing spermiogenesis and spermiation. To understand the molecular mechanism, we found that expression of Odf2, a vital protein in spermatogenesis, was significantly decreased. In addition, we found that expression levels of Odf2 were decreased in Mkrn2 knockout mice. We also found that MKRN2 was prominently expressed in the sperm of normal men, but was significantly reduced in infertile men. This result indicates that our finding is clinically relevant. The results of our study provided insights into a new mechanism of male infertility caused by the MKRN2 downregulation.
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19
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Abstract
RNA-binding proteins are often multifunctional, interact with a variety of protein partners and display complex localizations within cells. Mammalian cytoplasmic poly(A)-binding proteins (PABPs) are multifunctional RNA-binding proteins that regulate multiple aspects of mRNA translation and stability. Although predominantly diffusely cytoplasmic at steady state, they shuttle through the nucleus and can be localized to a variety of cytoplasmic foci, including those associated with mRNA storage and localized translation. Intriguingly, PABP sub-cellular distribution can alter dramatically in response to cellular stress or viral infection, becoming predominantly nuclear and/or being enriched in induced cytoplasmic foci. However, relatively little is known about the mechanisms that govern this distribution/relocalization and in many cases PABP functions within specific sites remain unclear. Here we discuss the emerging evidence with respect to these questions in mammals.
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20
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Herrera RA, Kiontke K, Fitch DHA. Makorin ortholog LEP-2 regulates LIN-28 stability to promote the juvenile-to-adult transition in Caenorhabditis elegans. Development 2016; 143:799-809. [PMID: 26811380 DOI: 10.1242/dev.132738] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/16/2016] [Indexed: 12/27/2022]
Abstract
The heterochronic genes lin-28, let-7 and lin-41 regulate fundamental developmental transitions in animals, such as stemness versus differentiation and juvenile versus adult states. We identify a new heterochronic gene, lep-2, in Caenorhabditis elegans. Mutations in lep-2 cause a delay in the juvenile-to-adult transition, with adult males retaining pointed, juvenile tail tips, and displaying defective sexual behaviors. In both sexes, lep-2 mutants fail to cease molting or produce an adult cuticle. We find that LEP-2 post-translationally regulates LIN-28 by promoting LIN-28 protein degradation. lep-2 encodes the sole C. elegans ortholog of the Makorin (Mkrn) family of proteins. Like lin-28 and other heterochronic pathway members, vertebrate Mkrns are involved in developmental switches, including the timing of pubertal onset in humans. Based on shared roles, conservation and the interaction between lep-2 and lin-28 shown here, we propose that Mkrns, together with other heterochronic genes, constitute an evolutionarily ancient conserved module regulating switches in development.
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Affiliation(s)
| | - Karin Kiontke
- Department of Biology, New York University, New York, NY 10003, USA
| | - David H A Fitch
- Department of Biology, New York University, New York, NY 10003, USA Faculty of Arts and Sciences, New York University-Shanghai, Shanghai 200122, China
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21
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Cassar PA, Carpenedo RL, Samavarchi-Tehrani P, Olsen JB, Park CJ, Chang WY, Chen Z, Choey C, Delaney S, Guo H, Guo H, Tanner RM, Perkins TJ, Tenenbaum SA, Emili A, Wrana JL, Gibbings D, Stanford WL. Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network. EMBO Rep 2015; 16:1334-57. [PMID: 26265008 PMCID: PMC4670460 DOI: 10.15252/embr.201540974] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 02/04/2023] Open
Abstract
In embryonic stem cells (ESCs), gene regulatory networks (GRNs) coordinate gene expression to maintain ESC identity; however, the complete repertoire of factors regulating the ESC state is not fully understood. Our previous temporal microarray analysis of ESC commitment identified the E3 ubiquitin ligase protein Makorin‐1 (MKRN1) as a potential novel component of the ESC GRN. Here, using multilayered systems‐level analyses, we compiled a MKRN1‐centered interactome in undifferentiated ESCs at the proteomic and ribonomic level. Proteomic analyses in undifferentiated ESCs revealed that MKRN1 associates with RNA‐binding proteins, and ensuing RIP‐chip analysis determined that MKRN1 associates with mRNAs encoding functionally related proteins including proteins that function during cellular stress. Subsequent biological validation identified MKRN1 as a novel stress granule‐resident protein, although MKRN1 is not required for stress granule formation, or survival of unstressed ESCs. Thus, our unbiased systems‐level analyses support a role for the E3 ligase MKRN1 as a ribonucleoprotein within the ESC GRN.
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Affiliation(s)
- Paul A Cassar
- Institute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada
| | - Richard L Carpenedo
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | | | - Jonathan B Olsen
- Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chang Jun Park
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Wing Y Chang
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Zhaoyi Chen
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Chandarong Choey
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Sean Delaney
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Huishan Guo
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Hongbo Guo
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - R Matthew Tanner
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Theodore J Perkins
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Scott A Tenenbaum
- Colleges of Nanoscale Science & Engineering SUNY Polytechnic Institute, Albany, NY, USA
| | - Andrew Emili
- Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jeffrey L Wrana
- Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Derrick Gibbings
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | - William L Stanford
- Institute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada Ottawa Institute of Systems Biology, Ottawa, ON, Canada
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22
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Eliseeva IA, Lyabin DN, Ovchinnikov LP. Poly(A)-binding proteins: structure, domain organization, and activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1377-91. [PMID: 24490729 DOI: 10.1134/s0006297913130014] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA-binding proteins are of vital importance for mRNA functioning. Among these, poly(A)-binding proteins (PABPs) are of special interest due to their participation in virtually all mRNA-dependent events that is caused by their high affinity for A-rich mRNA sequences. Apart from mRNAs, PABPs interact with many proteins, thus promoting their involvement in cellular events. In the nucleus, PABPs play a role in polyadenylation, determine the length of the poly(A) tail, and may be involved in mRNA export. In the cytoplasm, they participate in regulation of translation initiation and either protect mRNAs from decay through binding to their poly(A) tails or stimulate this decay by promoting mRNA interactions with deadenylase complex proteins. This review presents modern notions of the role of PABPs in mRNA-dependent events; peculiarities of regulation of PABP amount in the cell and activities are also discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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23
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Ambivero CT, Cilenti L, Main S, Zervos AS. Mulan E3 ubiquitin ligase interacts with multiple E2 conjugating enzymes and participates in mitophagy by recruiting GABARAP. Cell Signal 2014; 26:2921-9. [PMID: 25224329 DOI: 10.1016/j.cellsig.2014.09.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/05/2014] [Indexed: 12/21/2022]
Abstract
Mulan is an E3 ubiquitin ligase embedded in the outer mitochondrial membrane (OMM) with its RING finger facing the cytoplasm and a large domain located in the intermembrane space (IMS). Mulan is known to have an important role in cell growth, cell death, and more recently in mitophagy. The mechanism of its function is poorly understood; but as an E3 ligase it is expected to interact with specific E2 ubiquitin conjugating enzymes and these complexes will bind and ubiquitinate specific substrates. The unique topology of Mulan can provide a direct link of communicating mitochondrial signals to the cytoplasm. Our studies identified four different E2 conjugating enzymes (Ube2E2, Ube2E3, Ube2G2 and Ube2L3) as specific interactors of Mulan. Each of these E2 conjugating enzymes was fused to the RING finger domain of Mulan and used in a modified yeast two-hybrid screen. Several unique interactors for each Mulan-E2 complex were isolated. One such specific interactor of Mulan-Ube2E3 was the GABARAP (GABAA receptor-associated protein). GABARAP is a member of the Atg8 family of proteins that plays a major role in autophagy/mitophagy. The interaction of GABARAP with Mulan-Ube2E3 required an LC3-interacting region (LIR) located in the RING finger domain of Mulan as well as the presence of Ube2E3. The isolation of four different E2 conjugating enzymes, as specific partners of Mulan E3 ligase, suggests that Mulan is involved in multiple biological pathways. In addition, the interaction of GABARAP with Mulan-Ube2E3 supports the role of Mulan as an important regulator of mitophagy and provides a plausible mechanism for its function in this process.
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Affiliation(s)
- Camilla T Ambivero
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA
| | - Lucia Cilenti
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA
| | - Stacey Main
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA
| | - Antonis S Zervos
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA.
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24
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Di Liegro CM, Schiera G, Di Liegro I. Regulation of mRNA transport, localization and translation in the nervous system of mammals (Review). Int J Mol Med 2014; 33:747-62. [PMID: 24452120 PMCID: PMC3976132 DOI: 10.3892/ijmm.2014.1629] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/09/2013] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional control of mRNA trafficking and metabolism plays a critical role in the actualization and fine tuning of the genetic program of cells, both in development and in differentiated tissues. Cis-acting signals, responsible for post-transcriptional regulation, reside in the RNA message itself, usually in untranslated regions, 5′ or 3′ to the coding sequence, and are recognized by trans-acting factors: RNA-binding proteins (RBPs) and/or non-coding RNAs (ncRNAs). ncRNAs bind short mRNA sequences usually present in the 3′-untranslated (3′-UTR) region of their target messages. RBPs recognize specific nucleotide sequences and/or secondary/tertiary structures. Most RBPs assemble on mRNA at the moment of transcription and shepherd it to its destination, somehow determining its final fate. Regulation of mRNA localization and metabolism has a particularly important role in the nervous system where local translation of pre-localized mRNAs has been implicated in developing axon and dendrite pathfinding, and in synapse formation. Moreover, activity-dependent mRNA trafficking and local translation may underlie long-lasting changes in synaptic efficacy, responsible for learning and memory. This review focuses on the role of RBPs in neuronal development and plasticity, as well as possible connections between ncRNAs and RBPs.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Italia Di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo, I-90127 Palermo, Italy
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25
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Wadekar HB, Sahi VP, Morita EH, Abe S. MKRN expression pattern during embryonic and post-embryonic organogenesis in rice (Oryza sativa L. var. Nipponbare). PLANTA 2013; 237:1083-1095. [PMID: 23262670 DOI: 10.1007/s00425-012-1828-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 12/05/2012] [Indexed: 06/01/2023]
Abstract
Rice MKRN is a member of the makorin RING finger protein gene (MKRN) family, which encodes a protein with a characteristic array of zinc-finger motifs conserved in various eukaryotes. Using non-radioactive in situ hybridization, we investigated the spatio-temporal gene expression pattern of rice MKRN during embryogenesis, imbibition, seminal and lateral root development of Oryza sativa L. var. Nipponbare. MKRN expression was ubiquitous during early organogenesis in the embryo along the apical-basal and radial axes. The expression of MKRN decreased during embryonic organ elongation and maturation compared to early embryogenesis, but increased again during imbibition. Tissue-specific and position-dependent MKRN expression was found during embryonic and post-embryonic root and shoot development. Meristematic cells ubiquitously expressed MKRN transcripts, while differentiating cells showed a gradual reduction and termination of MKRN expression. Interestingly, during post-germination MKRN expression was prominent and continued in the metabolically active, differentiated companion cells of the phloem. The differential expression pattern was observed both in the differentiating and differentiated cells. Also, MKRN was expressed in the various developmental stages of the lateral root primordia and the cells surrounding them. Expression of MKRN was also observed after periclinal division of the presumptive pericycle founder cells. The MKRN expression pattern during development of various growth stages suggests an important role of makorin RING finger protein gene (MKRN) in embryonic and post-embryonic organogenesis in both apical-basal and radial developmental axes of rice.
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Affiliation(s)
- Hanumant Baburao Wadekar
- Laboratory of Molecular Cell Physiology, Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, 790-8566, Japan.
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Millan MJ. An epigenetic framework for neurodevelopmental disorders: from pathogenesis to potential therapy. Neuropharmacology 2012; 68:2-82. [PMID: 23246909 DOI: 10.1016/j.neuropharm.2012.11.015] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/11/2012] [Accepted: 11/22/2012] [Indexed: 12/12/2022]
Abstract
Neurodevelopmental disorders (NDDs) are characterized by aberrant and delayed early-life development of the brain, leading to deficits in language, cognition, motor behaviour and other functional domains, often accompanied by somatic symptoms. Environmental factors like perinatal infection, malnutrition and trauma can increase the risk of the heterogeneous, multifactorial and polygenic disorders, autism and schizophrenia. Conversely, discrete genetic anomalies are involved in Down, Rett and Fragile X syndromes, tuberous sclerosis and neurofibromatosis, the less familiar Phelan-McDermid, Sotos, Kleefstra, Coffin-Lowry and "ATRX" syndromes, and the disorders of imprinting, Angelman and Prader-Willi syndromes. NDDs have been termed "synaptopathies" in reference to structural and functional disturbance of synaptic plasticity, several involve abnormal Ras-Kinase signalling ("rasopathies"), and many are characterized by disrupted cerebral connectivity and an imbalance between excitatory and inhibitory transmission. However, at a different level of integration, NDDs are accompanied by aberrant "epigenetic" regulation of processes critical for normal and orderly development of the brain. Epigenetics refers to potentially-heritable (by mitosis and/or meiosis) mechanisms controlling gene expression without changes in DNA sequence. In certain NDDs, prototypical epigenetic processes of DNA methylation and covalent histone marking are impacted. Conversely, others involve anomalies in chromatin-modelling, mRNA splicing/editing, mRNA translation, ribosome biogenesis and/or the regulatory actions of small nucleolar RNAs and micro-RNAs. Since epigenetic mechanisms are modifiable, this raises the hope of novel therapy, though questions remain concerning efficacy and safety. The above issues are critically surveyed in this review, which advocates a broad-based epigenetic framework for understanding and ultimately treating a diverse assemblage of NDDs ("epigenopathies") lying at the interface of genetic, developmental and environmental processes. This article is part of the Special Issue entitled 'Neurodevelopmental Disorders'.
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Affiliation(s)
- Mark J Millan
- Unit for Research and Discovery in Neuroscience, IDR Servier, 125 chemin de ronde, 78290 Croissy sur Seine, Paris, France.
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