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Barnsby-Greer L, Mabbitt PD, Dery MA, Squair DR, Wood NT, Lamoliatte F, Lange SM, Virdee S. UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4. Nat Struct Mol Biol 2024; 31:351-363. [PMID: 38182926 PMCID: PMC10873205 DOI: 10.1038/s41594-023-01192-4] [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: 02/15/2023] [Accepted: 11/27/2023] [Indexed: 01/07/2024]
Abstract
UBR4 is a 574 kDa E3 ligase (E3) of the N-degron pathway with roles in neurodevelopment, age-associated muscular atrophy and cancer. The catalytic module that carries out ubiquitin (Ub) transfer remains unknown. Here we identify and characterize a distinct E3 module within human UBR4 consisting of a 'hemiRING' zinc finger, a helical-rich UBR zinc-finger interacting (UZI) subdomain, and an N-terminal region that can serve as an affinity factor for the E2 conjugating enzyme (E2). The structure of an E2-E3 complex provides atomic-level insight into the specificity determinants of the hemiRING toward the cognate E2s UBE2A/UBE2B. Via an allosteric mechanism, the UZI subdomain modestly activates the Ub-loaded E2 (E2∼Ub). We propose attenuated activation is complemented by the intrinsically high lysine reactivity of UBE2A, and their cooperation imparts a reactivity profile important for substrate specificity and optimal degradation kinetics. These findings reveal the mechanistic underpinnings of a neuronal N-degron E3, its specific recruitment of UBE2A, and highlight the underappreciated architectural diversity of cross-brace domains with Ub E3 activity.
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Affiliation(s)
- Lucy Barnsby-Greer
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Peter D Mabbitt
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
- Scion, Rotorua, New Zealand
| | - Marc-Andre Dery
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Daniel R Squair
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Nicola T Wood
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Sven M Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK.
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2
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Jeong DE, Lee HS, Ku B, Kim CH, Kim SJ, Shin HC. Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates. Commun Biol 2023; 6:1214. [PMID: 38030679 PMCID: PMC10687169 DOI: 10.1038/s42003-023-05602-7] [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: 05/21/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.
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Affiliation(s)
- Da Eun Jeong
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, 34141, Republic of Korea
| | - Cheol-Hee Kim
- Department of Bioscience & Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seung Jun Kim
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Ho-Chul Shin
- Critical Disease Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea.
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3
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Gaudio A, Gotta F, Ponti C, Sanguineri F, Trevisan L, Geroldi A, Patrone S, Gemelli C, Cabona C, Astrea G, Fiorillo C, Gustincich S, Grandis M, Mandich P. Case report: Episodic ataxia without ataxia? Front Neurol 2023; 14:1224241. [PMID: 37965175 PMCID: PMC10640972 DOI: 10.3389/fneur.2023.1224241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/03/2023] [Indexed: 11/16/2023] Open
Abstract
Hereditary myopathies represent a clinically and genetically heterogeneous group of neuromuscular disorders, characterized by highly variable clinical presentations and frequently overlapping phenotypes with other neuromuscular disorders, likely influenced by genetic and environmental modifiers. Genetic testing is often challenging due to ambiguous clinical diagnosis. Here, we present the case of a family with clinical and Electromyography (EMG) features resembling a myotonia-like disorder in which Whole Exome Sequencing (WES) analysis revealed the co-segregation of two rare missense variants in UBR4 and HSPG2, genes previously associated with episodic ataxia 8 (EA8). A review of the literature highlighted a striking overlap between the clinical and the molecular features of our family and the previously described episodic ataxias (EAs), which raises concerns about the genotype-phenotype correlation, clinical variability, and the confounding overlap in these groups of disorders. This emphasizes the importance of thoroughly framing the patient's phenotype. The more clear-cut the diagnosis, the easier the identification of a genetic determinant, and the better the prognosis and the treatment of patients.
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Affiliation(s)
- Andrea Gaudio
- IRCCS Ospedale Policlinico San Martino—UOC Genetica Medica, Genova, Italy
| | - Fabio Gotta
- IRCCS Ospedale Policlinico San Martino—UOC Genetica Medica, Genova, Italy
| | - Clarissa Ponti
- IRCCS Ospedale Policlinico San Martino—UOC Genetica Medica, Genova, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
| | - Francesca Sanguineri
- IRCCS Ospedale Policlinico San Martino—UOC Genetica Medica, Genova, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
| | - Lucia Trevisan
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
- IRCCS Ospedale Policlinico San Martino—SS Centro Tumori Ereditari, Genova, Italy
| | - Alessandro Geroldi
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
| | - Serena Patrone
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
| | - Chiara Gemelli
- IRCCS-Ospedale Policlinico San Martino—UOC Clinica Neurologica, Genova, Italy
| | - Corrado Cabona
- IRCCS-Ospedale Policlinico San Martino—UOC Neurofisiopatologia, Genova, Italy
| | | | - Chiara Fiorillo
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
- IRCCS Istituto Giannina Gaslini—UOC Neuropsichiatria Infantile, Genova, Italy
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Marina Grandis
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
- IRCCS-Ospedale Policlinico San Martino—UOC Clinica Neurologica, Genova, Italy
| | - Paola Mandich
- IRCCS Ospedale Policlinico San Martino—UOC Genetica Medica, Genova, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Genova, Italy
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4
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Chen M, Zhao J, Ding X, Qin Y, Wu X, Li X, Wang L, Jiang G. Ketogenic diet and calorie-restricted diet attenuate ischemic brain injury via UBR4 and downstream CamkⅡ/TAK1/JNK signaling. J Funct Foods 2023. [DOI: 10.1016/j.jff.2022.105368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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5
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Haddadi M, Ataei R. wde, calpA, if, dap160, and poe genes knock down Drosophila models exhibit neurofunctional deficit. Gene 2022; 829:146499. [PMID: 35447243 DOI: 10.1016/j.gene.2022.146499] [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: 01/07/2022] [Revised: 03/14/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022]
Abstract
Intellectual disability (ID) is a heterogeneous disorder with high prevalence and remarkable social and cost burdens. Novel genetic variants of ATF7IP, CAPN9, ITGAV, ITSN1, and UBR4 genes are reported to be associated with the ID among Iranian families. However, in vivo validation is required to confirm the functional role of these variants in ID development. Drosophila melanogaster is a convenient model for such functional investigations as its genome bears ortholog of more than 75% of the disease-causing genes in human and represents numerous approaches to study defects in neuronal function. In this connection, RNAi gene silencing was applied to wde, calpA, if, dap160, and poe genes, the Drosophila ortholog of the selected human genes, and then consequent structural and functional changes in neurons were studied by means of immunohistochemistry and confocal microscopy of mushroom bodies (MBs) and validated behavioural assays including larvae and adult conditioning learning and memories, and ethanol sensitivity. Down-regulation of these genes led to neuronal loss which was evident by decline in total fluorescent signal intensity in micrographs of MBs structure. The gene silencing caused neuronal dysfunction and induction of ID-like symptoms manifested by deficits in larval preference learning, and short-term olfactory memory and courtship suppression learning in adults. Moreover, the RNAi flies showed higher sensitivity to ethanol vapour. Interestingly, the poe knock-down flies exhibited the most severe phenotypes among other genes. Altogether, we believe this study is first-of-its-kind and findings are highly applicable to confirm pathogenecity of the selected ID gene variants in Iranian population.
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Affiliation(s)
- Mohammad Haddadi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran.
| | - Reza Ataei
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
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6
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Niu F, Han P, Zhang J, She Y, Yang L, Yu J, Zhuang M, Tang K, Shi Y, Yang B, Liu C, Peng B, Ji SJ. The m 6A reader YTHDF2 is a negative regulator for dendrite development and maintenance of retinal ganglion cells. eLife 2022; 11:75827. [PMID: 35179492 PMCID: PMC8906807 DOI: 10.7554/elife.75827] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/16/2022] [Indexed: 11/29/2022] Open
Abstract
The precise control of growth and maintenance of the retinal ganglion cell (RGC) dendrite arborization is critical for normal visual functions in mammals. However, the underlying mechanisms remain elusive. Here, we find that the N6-methyladenosine (m6A) reader YTHDF2 is highly expressed in the mouse RGCs. Conditional knockout (cKO) of Ythdf2 in the retina leads to increased RGC dendrite branching, resulting in more synapses in the inner plexiform layer. Interestingly, the Ythdf2 cKO mice show improved visual acuity compared with control mice. We further demonstrate that Ythdf2 cKO in the retina protects RGCs from dendrite degeneration caused by the experimental acute glaucoma model. We identify the m6A-modified YTHDF2 target transcripts which mediate these effects. This study reveals mechanisms by which YTHDF2 restricts RGC dendrite development and maintenance. YTHDF2 and its target mRNAs might be valuable in developing new treatment approaches for glaucomatous eyes.
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Affiliation(s)
- Fugui Niu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Peng Han
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jian Zhang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Yuanchu She
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Lixin Yang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jun Yu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Mengru Zhuang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Kezhen Tang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuwei Shi
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Baisheng Yang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chunqiao Liu
- Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bo Peng
- Department of Neurosurgery, Fudan University, Shanghai, China
| | - Sheng-Jian Ji
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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7
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It's not just a phase; ubiquitination in cytosolic protein quality control. Biochem Soc Trans 2021; 49:365-377. [PMID: 33634825 PMCID: PMC7924994 DOI: 10.1042/bst20200694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/04/2023]
Abstract
The accumulation of misfolded proteins is associated with numerous degenerative conditions, cancers and genetic diseases. These pathological imbalances in protein homeostasis (termed proteostasis), result from the improper triage and disposal of damaged and defective proteins from the cell. The ubiquitin-proteasome system is a key pathway for the molecular control of misfolded cytosolic proteins, co-opting a cascade of ubiquitin ligases to direct terminally damaged proteins to the proteasome via modification with chains of the small protein, ubiquitin. Despite the evidence for ubiquitination in this critical pathway, the precise complement of ubiquitin ligases and deubiquitinases that modulate this process remains under investigation. Whilst chaperones act as the first line of defence against protein misfolding, the ubiquitination machinery has a pivotal role in targeting terminally defunct cytosolic proteins for destruction. Recent work points to a complex assemblage of chaperones, ubiquitination machinery and subcellular quarantine as components of the cellular arsenal against proteinopathies. In this review, we examine the contribution of these pathways and cellular compartments to the maintenance of the cytosolic proteome. Here we will particularly focus on the ubiquitin code and the critical enzymes which regulate misfolded proteins in the cytosol, the molecular point of origin for many neurodegenerative and genetic diseases.
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8
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He J, Zhang RX, Kim DS, Sun P, Liu H, Liu Z, Hetherington AM, Liang YK. ROS of Distinct Sources and Salicylic Acid Separate Elevated CO 2-Mediated Stomatal Movements in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:542. [PMID: 32457781 PMCID: PMC7225777 DOI: 10.3389/fpls.2020.00542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/09/2020] [Indexed: 05/12/2023]
Abstract
Elevated CO2 (eCO2) often reduces leaf stomatal aperture and density thus impacts plant physiology and productivity. We have previously demonstrated that the Arabidopsis BIG protein distinguishes between the processes of eCO2-induced stomatal closure and eCO2-inhibited stomatal opening. However, the mechanistic basis of this action is not fully understood. Here we show that eCO2-elicited reactive oxygen species (ROS) production in big mutants was compromised in stomatal closure induction but not in stomatal opening inhibition. Pharmacological and genetic studies show that ROS generated by both NADPH oxidases and cell wall peroxidases contribute to eCO2-induced stomatal closure, whereas inhibition of light-induced stomatal opening by eCO2 may rely on the ROS derived from NADPH oxidases but not from cell wall peroxidases. As with JA and ABA, SA is required for eCO2-induced ROS generation and stomatal closure. In contrast, none of these three signals has a significant role in eCO2-inhibited stomatal opening, unveiling the distinct roles of plant hormonal signaling pathways in the induction of stomatal closure and the inhibition of stomatal opening by eCO2. In conclusion, this study adds SA to a list of plant hormones that together with ROS from distinct sources distinguish two branches of eCO2-mediated stomatal movements.
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Affiliation(s)
- Jingjing He
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ruo-Xi Zhang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dae Sung Kim
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Peng Sun
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Honggang Liu
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhongming Liu
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
| | - Alistair M. Hetherington
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Yun-Kuan Liang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, China
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9
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Aagaard Nolting L, Brasch-Andersen C, Cox H, Kanani F, Parker M, Fry AE, Loddo S, Novelli A, Dentici ML, Joss S, Jørgensen JP, Fagerberg CR. A new 1p36.13-1p36.12 microdeletion syndrome characterized by learning disability, behavioral abnormalities, and ptosis. Clin Genet 2020; 97:927-932. [PMID: 32170730 DOI: 10.1111/cge.13739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 11/30/2022]
Abstract
Two 1p36 contiguous gene deletion syndromes are known so far: the terminal 1p36 deletion syndrome and a 1p36 deletion syndrome with a critical region located more proximal at 1p36.23-1p36.22. We present even more proximally located overlapping deletions from seven individuals, with the smallest region of overlap comprising 1 Mb at 1p36.13-1p36.12 (chr1:19077793-20081292 (GRCh37/hg19)) defining a new contiguous gene deletion syndrome. The characteristic features of this new syndrome are learning disability or mild intellectual disability, speech delay, behavioral abnormalities, and ptosis. The genes UBR4 and CAPZB are considered the most likely candidate genes for the features of this new syndrome.
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Affiliation(s)
| | | | - Helen Cox
- Clinical Genetics Unit, West Midlands Regional Clinical Genetics Unit Birmingham U.K., Birmingham, UK
| | - Farah Kanani
- Sheffield Clinical Genetics Service, Northern General Hospital, Sheffield, UK
| | - Michael Parker
- Sheffield Clinical Genetics Service, Northern General Hospital, Sheffield, UK
| | - Andrew E Fry
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Childrens' Hospital, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Childrens' Hospital, Rome, Italy
| | | | - Shelagh Joss
- Clinical Genetics, West of Scotland Genetic Services, the Queen Elisabeth University Hospital, Glasgow, UK
| | - Joan P Jørgensen
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
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10
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Abstract
Influenza A virus (IAV) is an enveloped virus of the Orthomyxoviridae with a negative-sense single-stranded RNA genome. During virus cell entry, viral and cellular cues are delivered in a stepwise manner within two distinct cellular compartments-the endosomes and the cytosol. Endosome maturation primes the viral core for uncoating by cytosolic host proteins and host-mediated virus disaggregation is essential for genome import and replication in the nucleus. Recent evidence shows that two well-known cellular proteins-histone deacetylase 6 (HDAC6) and karyopherin-β2 (kapβ2)-uncoat influenza virus. HDAC6 is 1 of 11 HDACs and an X-linked, cytosolic lysine deacetylase. Under normal cellular conditions HDAC6 is the tubulin deacetylase. Under proteasomal stress HDAC6 binds unanchored ubiquitin, dynein and myosin II to sequester misfolded protein aggregates for autophagy. Kapβ2 is a member of the importin β family that transports RNA-binding proteins into the nucleus by binding to disordered nuclear localization signals (NLSs) known as PY-NLS. Kapβ2 is emerging as a universal uncoating factor for IAV and human immunodeficiency virus type 1 (HIV-1). Kapβ2 can also reverse liquid-liquid phase separation (LLPS) of RNA-binding proteins by promoting their disaggregation. Thus, it is becoming evident that key players in the management of cellular condensates and membraneless organelles are potent virus uncoating factors. This emerging concept reveals implications in viral pathogenesis, as well as, the promise for cell-targeted therapeutic strategies to block universal virus uncoating pathways hijacked by enveloped RNA viruses.
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Affiliation(s)
- Yohei Yamauchi
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom.
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11
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Abstract
BACKGROUND Recently, pathogenic alleles within ubiquitin N-recognin domain-containing E3 ligase 4 (UBR4) gene have been shown to be associated with Hirschsprung disease (HSCR). We determined the UBR4 expressions in Indonesian HSCR patients. METHODS We analyzed the UBR4 expressions in the colons of HSCR patient and anorectal malformation (ARM) patient as control by real-time polymerase chain reaction (qPCR). RESULTS Thirty-seven patients with non-syndromic HSCR and eighteen controls were involved in this study. qPCR revealed that the UBR4 expression was strongly decreased (0.77-fold) in the ganglionic group of patients with HSCR compared to the control group with ARM (ΔCT 2.43 ± 0.36 vs. 2.05 ± 0.69; p = 0.009), whereas the UBR4 expression was also significantly reduced (0.79-fold) in the aganglionic group of patients with HSCR compared to the control group with ARM (ΔCT 2.39 ± 0.46 vs. 2.05 ± 0.69; p = 0.044). However, the UBR4 expression change was not associated with gender (p = 0.35 and 0.80), nor with degree of aganglionosis both in ganglionic and aganglionic colons (p = 0.72 and 0.73), respectively. CONCLUSION Our study demonstrates that expression of UBR4 is decreased in both aganglionic and ganglionic colon of HSCR patients.
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Zhang RX, Ge S, He J, Li S, Hao Y, Du H, Liu Z, Cheng R, Feng YQ, Xiong L, Li C, Hetherington AM, Liang YK. BIG regulates stomatal immunity and jasmonate production in Arabidopsis. THE NEW PHYTOLOGIST 2019; 222:335-348. [PMID: 30372534 DOI: 10.1111/nph.15568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/19/2018] [Indexed: 05/26/2023]
Abstract
Plants have evolved an array of responses that provide them with protection from attack by microorganisms and other predators. Many of these mechanisms depend upon interactions between the plant hormones jasmonate (JA) and ethylene (ET). However, the molecular basis of these interactions is insufficiently understood. Gene expression and physiological assays with mutants were performed to investigate the role of Arabidopsis BIG gene in stress responses. BIG transcription is downregulated by methyl JA (MeJA), necrotrophic infection or mechanical injury. BIG deficiency promotes JA-dependent gene induction, increases JA production but restricts the accumulation of both ET and salicylic acid. JA-induced anthocyanin accumulation and chlorophyll degradation are enhanced and stomatal immunity is impaired by BIG disruption. Bacteria- and lipopolysaccaride (LPS)-induced stomatal closure is reduced in BIG gene mutants, which are hyper-susceptible to microbial pathogens with different lifestyles, but these mutants are less attractive to phytophagous insects. Our results indicate that BIG negatively and positively regulate the MYC2 and ERF1 arms of the JA signalling pathway. BIG warrants recognition as a new and distinct regulator that regulates JA responses, the synergistic interactions of JA and ET, and other hormonal interactions that reconcile the growth and defense dilemma in Arabidopsis.
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Affiliation(s)
- Ruo-Xi Zhang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shengchao Ge
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jingjing He
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shuangchen Li
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanhong Hao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Hao Du
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant, Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongming Liu
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Cheng
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant, Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Alistair M Hetherington
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Yun-Kuan Liang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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13
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Cheng R, Gong L, Li Z, Liang YK. Rice BIG gene is required for seedling viability. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:39-50. [PMID: 30530202 DOI: 10.1016/j.jplph.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/04/2018] [Accepted: 11/04/2018] [Indexed: 05/07/2023]
Abstract
Arabidopsis BIG (AtBIG) gene encodes an enormous protein that is required for auxin transport. Loss of AtBIG function not only profoundly changes plant architecture but also alters plant adaptability to environmental stimuli. A putative homolog of AtBIG exists in the rice genome, but no function has been ascribed to it. In this study, we focus on the characterization of the gene structure and function of OsBIG. Sequence and phylogenetic analysis shows that the homologs of OsBIG have high amino acid conservation in several domains across species. Transgenic rice plants in which the expression of OsBIG was disrupted through the CRISPR/Cas9 system-mediated genome editing were used for phenotypic analysis. The Osbig/- plants show high levels of cell death, enhanced electrolyte leakage and membrane lipid peroxidation, and reduced chlorophyll content, which likely accounted for the seedling lethality. Moreover, gene expression between Osbig/- and wild-type plants analyzed by RNA-seq indicates that a number of metabolic and hormonal pathways including ribosome, DNA replication, photosynthesis, and chlorophyll metabolism were significantly perturbed by OsBIG deficiency. In summary, OsBIG gene is integral to the normal growth and development in rice.
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Affiliation(s)
- Rui Cheng
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Luping Gong
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhengzheng Li
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yun-Kuan Liang
- State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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14
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Gunz P, Tilot AK, Wittfeld K, Teumer A, Shapland CY, van Erp TGM, Dannemann M, Vernot B, Neubauer S, Guadalupe T, Fernández G, Brunner HG, Enard W, Fallon J, Hosten N, Völker U, Profico A, Di Vincenzo F, Manzi G, Kelso J, St Pourcain B, Hublin JJ, Franke B, Pääbo S, Macciardi F, Grabe HJ, Fisher SE. Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity. Curr Biol 2018; 29:120-127.e5. [PMID: 30554901 PMCID: PMC6380688 DOI: 10.1016/j.cub.2018.10.065] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022]
Abstract
One of the features that distinguishes modern humans from our extinct relatives and ancestors is a globular shape of the braincase [1-4]. As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture [4, 5]. However, in the absence of fossil brain tissue, the underlying neuroanatomical changes as well as their genetic bases remain elusive. To better understand the biological foundations of modern human endocranial shape, we turn to our closest extinct relatives: the Neandertals. Interbreeding between modern humans and Neandertals has resulted in introgressed fragments of Neandertal DNA in the genomes of present-day non-Africans [6, 7]. Based on shape analyses of fossil skull endocasts, we derive a measure of endocranial globularity from structural MRI scans of thousands of modern humans and study the effects of introgressed fragments of Neandertal DNA on this phenotype. We find that Neandertal alleles on chromosomes 1 and 18 are associated with reduced endocranial globularity. These alleles influence expression of two nearby genes, UBR4 and PHLPP1, which are involved in neurogenesis and myelination, respectively. Our findings show how integration of fossil skull data with archaic genomics and neuroimaging can suggest developmental mechanisms that may contribute to the unique modern human endocranial shape.
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Affiliation(s)
- Philipp Gunz
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Amanda K Tilot
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, P.O. Box 310, 6500 AH, Nijmegen, the Netherlands
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University of Greifswald, Ellernholzstr. 1-2, 17489 Greifswald, Germany; German Center for Neurodegenerative Diseases (DZNE), Partner Site Rostock/Greifswald, Ellernholzstr. 1-2, 17489 Greifswald, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Walter-Rathenau Str. 48, 17475 Greifswald, Germany
| | - Chin Yang Shapland
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, P.O. Box 310, 6500 AH, Nijmegen, the Netherlands
| | - Theo G M van Erp
- Clinical and Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California, Irvine, 5251 California Ave, Irvine, CA 92617, USA
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Simon Neubauer
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Tulio Guadalupe
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, P.O. Box 310, 6500 AH, Nijmegen, the Netherlands
| | - Guillén Fernández
- Department of Cognitive Neuroscience, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, 6500 GA, Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, 6500 GA, Nijmegen, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, the Netherlands
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department Biology II, Ludwig Maximilians University Munich, Grosshaderner Str. 2, D-82152 Martinsried, Germany
| | - James Fallon
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Norbert Hosten
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine, Ernst-Moritz-Arndt-University Greifswald, Ferdinand-Sauerbruch-Str. 1, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Antonio Profico
- Università degli Studi di Roma La Sapienza, Department of Environmental Biology, Piazzale Aldo Moro, 5, 00185, Roma, Italy
| | - Fabio Di Vincenzo
- Università degli Studi di Roma La Sapienza, Department of Environmental Biology, Piazzale Aldo Moro, 5, 00185, Roma, Italy; Istituto Italiano di Paleontologia Umana, Via Ulisse Aldrovandi, 18, 00197, Roma, Italy
| | - Giorgio Manzi
- Università degli Studi di Roma La Sapienza, Department of Environmental Biology, Piazzale Aldo Moro, 5, 00185, Roma, Italy
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, P.O. Box 310, 6500 AH, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Barbara Franke
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands; Departments of Human Genetics and Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California, Irvine, Sprague Hall - Room 312, Gillespie Neuroscience - Laboratory, Mail Code: 3960, Irvine, CA 92697, USA
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University of Greifswald, Ellernholzstr. 1-2, 17489 Greifswald, Germany
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, P.O. Box 310, 6500 AH, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands.
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15
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Kim ST, Lee YJ, Tasaki T, Mun SR, Hwang J, Kang MJ, Ganipisetti S, Yi EC, Kim BY, Kwon YT. The N-recognin UBR4 of the N-end rule pathway is targeted to and required for the biogenesis of the early endosome. J Cell Sci 2018; 131:jcs.217646. [PMID: 30111582 DOI: 10.1242/jcs.217646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/30/2018] [Indexed: 12/26/2022] Open
Abstract
The N-end rule pathway is a proteolytic system in which single N-terminal residues of proteins act as N-degrons. These degrons are recognized by N-recognins, facilitating substrate degradation via the ubiquitin (Ub) proteasome system (UPS) or autophagy. We have previously identified a set of N-recognins [UBR1, UBR2, UBR4 (also known as p600) and UBR5 (also known as EDD)] that bind N-degrons through their UBR boxes to promote proteolysis by the proteasome. Here, we show that the 570 kDa N-recognin UBR4 is associated with maturing endosomes through an interaction with Ca2+-bound calmodulin. The endosomal recruitment of UBR4 is essential for the biogenesis of early endosomes (EEs) and endosome-related processes, such as the trafficking of endocytosed protein cargos and degradation of extracellular cargos by endosomal hydrolases. In mouse embryos, UBR4 marks and plays a role in the endosome-lysosome pathway that mediates the heterophagic proteolysis of endocytosed maternal proteins into amino acids. By screening 9591 drugs through the DrugBank database, we identify picolinic acid as a putative ligand for UBR4 that inhibits the biogenesis of EEs. Our results suggest that UBR4 is an essential modulator in the endosome-lysosome system.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sung Tae Kim
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, United States
| | - Yoon Jee Lee
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Takafumi Tasaki
- Division of Protein Regulation Research, Medical Research Institute, Kanazawa Medical University, Ishikawa, 920-0293, Japan.,Department of Medical Zoology, Kanazawa Medical University, Ishikawa, 920-0293, Japan
| | - Su Ran Mun
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Joonsung Hwang
- World Class Institute, Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, 28116, Republic of Korea
| | - Min Jueng Kang
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, 03080, Republic of Korea
| | - Srinivasrao Ganipisetti
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, 03080, Republic of Korea
| | - Bo Yeon Kim
- World Class Institute, Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, 28116, Republic of Korea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea .,Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
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16
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He J, Zhang R, Peng K, Tagliavia C, Li S, Xue S, Liu A, Hu H, Zhang J, Hubbard KE, Held K, McAinsh MR, Gray JE, Kudla J, Schroeder JI, Liang Y, Hetherington AM. The BIG protein distinguishes the process of CO 2 -induced stomatal closure from the inhibition of stomatal opening by CO 2. THE NEW PHYTOLOGIST 2018; 218:232-241. [PMID: 29292834 PMCID: PMC5887946 DOI: 10.1111/nph.14957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 11/12/2017] [Indexed: 05/09/2023]
Abstract
We conducted an infrared thermal imaging-based genetic screen to identify Arabidopsis mutants displaying aberrant stomatal behavior in response to elevated concentrations of CO2 . This approach resulted in the isolation of a novel allele of the Arabidopsis BIG locus (At3g02260) that we have called CO2 insensitive 1 (cis1). BIG mutants are compromised in elevated CO2 -induced stomatal closure and bicarbonate activation of S-type anion channel currents. In contrast with the wild-type, they fail to exhibit reductions in stomatal density and index when grown in elevated CO2 . However, like the wild-type, BIG mutants display inhibition of stomatal opening when exposed to elevated CO2 . BIG mutants also display wild-type stomatal aperture responses to the closure-inducing stimulus abscisic acid (ABA). Our results indicate that BIG is a signaling component involved in the elevated CO2 -mediated control of stomatal development. In the control of stomatal aperture by CO2 , BIG is only required in elevated CO2 -induced closure and not in the inhibition of stomatal opening by this environmental signal. These data show that, at the molecular level, the CO2 -mediated inhibition of opening and promotion of stomatal closure signaling pathways are separable and BIG represents a distinguishing element in these two CO2 -mediated responses.
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Affiliation(s)
- Jingjing He
- State Key Laboratory of Hybrid RiceDepartment of Plant SciencesCollege of Life SciencesWuhan UniversityWuhan430072China
| | - Ruo‐Xi Zhang
- State Key Laboratory of Hybrid RiceDepartment of Plant SciencesCollege of Life SciencesWuhan UniversityWuhan430072China
| | - Kai Peng
- School of Biological SciencesLife Sciences Building24 Tyndall AvenueBristolBS8 1TQUK
| | | | - Siwen Li
- State Key Laboratory of Hybrid RiceDepartment of Plant SciencesCollege of Life SciencesWuhan UniversityWuhan430072China
| | - Shaowu Xue
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Amy Liu
- Cell and Developmental Biology SectionDivision of Biological SciencesUniversity of California at San DiegoLa JollaCA92093USA
| | - Honghong Hu
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- Cell and Developmental Biology SectionDivision of Biological SciencesUniversity of California at San DiegoLa JollaCA92093USA
| | - Jingbo Zhang
- Cell and Developmental Biology SectionDivision of Biological SciencesUniversity of California at San DiegoLa JollaCA92093USA
| | - Katharine E. Hubbard
- Cell and Developmental Biology SectionDivision of Biological SciencesUniversity of California at San DiegoLa JollaCA92093USA
- School of Environmental SciencesUniversity of HullHullHU6 7RXUK
| | - Katrin Held
- Institut für Biologie und Biotechnologie der PflanzenUniversität MünsterSchlossplatz 7Münster48149Germany
| | | | - Julie E. Gray
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth Court, Western BankSheffieldS10 2TNUK
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der PflanzenUniversität MünsterSchlossplatz 7Münster48149Germany
| | - Julian I. Schroeder
- Cell and Developmental Biology SectionDivision of Biological SciencesUniversity of California at San DiegoLa JollaCA92093USA
| | - Yun‐Kuan Liang
- State Key Laboratory of Hybrid RiceDepartment of Plant SciencesCollege of Life SciencesWuhan UniversityWuhan430072China
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17
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Maffioli E, Schulte C, Nonnis S, Grassi Scalvini F, Piazzoni C, Lenardi C, Negri A, Milani P, Tedeschi G. Proteomic Dissection of Nanotopography-Sensitive Mechanotransductive Signaling Hubs that Foster Neuronal Differentiation in PC12 Cells. Front Cell Neurosci 2018; 11:417. [PMID: 29354032 PMCID: PMC5758595 DOI: 10.3389/fncel.2017.00417] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Neuronal cells are competent in precisely sensing nanotopographical features of their microenvironment. The perceived microenvironmental information will be “interpreted” by mechanotransductive processes and impacts on neuronal functioning and differentiation. Attempts to influence neuronal differentiation by engineering substrates that mimic appropriate extracellular matrix (ECM) topographies are hampered by the fact that profound details of mechanosensing/-transduction complexity remain elusive. Introducing omics methods into these biomaterial approaches has the potential to provide a deeper insight into the molecular processes and signaling cascades underlying mechanosensing/-transduction but their exigence in cellular material is often opposed by technical limitations of major substrate top-down fabrication methods. Supersonic cluster beam deposition (SCBD) allows instead the bottom-up fabrication of nanostructured substrates over large areas characterized by a quantitatively controllable ECM-like nanoroughness that has been recently shown to foster neuron differentiation and maturation. Exploiting this capacity of SCBD, we challenged mechanosensing/-transduction and differentiative behavior of neuron-like PC12 cells with diverse nanotopographies and/or changes of their biomechanical status, and analyzed their phosphoproteomic profiles in these settings. Versatile proteins that can be associated to significant processes along the mechanotransductive signal sequence, i.e., cell/cell interaction, glycocalyx and ECM, membrane/f-actin linkage and integrin activation, cell/substrate interaction, integrin adhesion complex, actomyosin organization/cellular mechanics, nuclear organization, and transcriptional regulation, were affected. The phosphoproteomic data suggested furthermore an involvement of ILK, mTOR, Wnt, and calcium signaling in these nanotopography- and/or cell mechanics-related processes. Altogether, potential nanotopography-sensitive mechanotransductive signaling hubs participating in neuronal differentiation were dissected.
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Affiliation(s)
- Elisa Maffioli
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Carsten Schulte
- Centre for Nanostructured Materials and Interfaces, Università degli Studi di Milano, Milan, Italy.,Fondazione Filarete, Milan, Italy
| | - Simona Nonnis
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy.,Fondazione Filarete, Milan, Italy
| | - Francesca Grassi Scalvini
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy.,Fondazione Filarete, Milan, Italy
| | - Claudio Piazzoni
- Centre for Nanostructured Materials and Interfaces, Università degli Studi di Milano, Milan, Italy
| | - Cristina Lenardi
- Centre for Nanostructured Materials and Interfaces, Università degli Studi di Milano, Milan, Italy
| | - Armando Negri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy.,Fondazione Filarete, Milan, Italy
| | - Paolo Milani
- Centre for Nanostructured Materials and Interfaces, Università degli Studi di Milano, Milan, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy.,Fondazione Filarete, Milan, Italy
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18
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Influenza A Virus M2 Protein: Roles from Ingress to Egress. Int J Mol Sci 2017; 18:ijms18122649. [PMID: 29215568 PMCID: PMC5751251 DOI: 10.3390/ijms18122649] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 11/17/2022] Open
Abstract
Influenza A virus (IAV) matrix protein 2 (M2) is among the smallest bona fide, hence extensively studied, ion channel proteins. The M2 ion channel activity is not only essential for virus replication, but also involved in modulation of cellular homeostasis in a variety of ways. It is also the target for ion channel inhibitors, i.e., anti-influenza drugs. Thus far, several studies have been conducted to elucidate its biophysical characteristics, structure-function relationships of the ion channel, and the M2-host interactome. In this review, we discuss M2 protein synthesis and assembly into an ion channel, its roles in IAV replication, and the pathophysiological impact on the host cell.
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19
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Keo A, Aziz NA, Dzyubachyk O, van der Grond J, van Roon-Mom WMC, Lelieveldt BPF, Reinders MJT, Mahfouz A. Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington's Disease. Front Mol Neurosci 2017; 10:399. [PMID: 29249939 PMCID: PMC5714896 DOI: 10.3389/fnmol.2017.00399] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/15/2017] [Indexed: 02/04/2023] Open
Abstract
Cytosine-adenine-guanine (CAG) repeat expansions in the coding regions of nine polyglutamine (polyQ) genes (HTT, ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATN1, AR, and TBP) are the cause of several neurodegenerative diseases including Huntington’s disease (HD), six different spinocerebellar ataxias (SCAs), dentatorubral-pallidoluysian atrophy, and spinobulbar muscular atrophy. The expanded CAG repeat length in the causative gene is negatively related to the age-at-onset (AAO) of clinical symptoms. In addition to the expanded CAG repeat length in the causative gene, the normal CAG repeats in the other polyQ genes can affect the AAO, suggesting functional interactions between the polyQ genes. However, there is no detailed assessment of the relationships among polyQ genes in pathologically relevant brain regions. We used gene co-expression analysis to study the functional relationships among polyQ genes in different brain regions using the Allen Human Brain Atlas (AHBA), a spatial map of gene expression in the healthy brain. We constructed co-expression networks for seven anatomical brain structures, as well as a region showing a specific pattern of atrophy in HD patients detected by magnetic resonance imaging (MRI) of the brain. In this HD-associated region, we found that ATN1 and ATXN2 were co-expressed and shared co-expression partners which were enriched for DNA repair genes. We observed a similar co-expression pattern in the frontal lobe, parietal lobe, and striatum in which this relation was most pronounced. Given that the co-expression patterns for these anatomical structures were similar to those for the HD-associated region, our results suggest that their disruption is likely involved in HD pathology. Moreover, ATN1 and ATXN2 also shared many co-expressed genes with HTT, the causative gene of HD, across the brain. Although this triangular relationship among these three polyQ genes may also be dysregulated in other polyQ diseases, stronger co-expression patterns between ATN1 and ATXN2 observed in the HD-associated region, especially in the striatum, may be more specific to HD.
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Affiliation(s)
- Arlin Keo
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - N Ahmad Aziz
- Department of Neurology, Leiden University Medical Center, Leiden, Netherlands
| | - Oleh Dzyubachyk
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Boudewijn P F Lelieveldt
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marcel J T Reinders
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - Ahmed Mahfouz
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
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20
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Abstract
Episodic ataxia (EA) is a rare neurological condition characterized by recurrent spells of truncal ataxia and incoordination. Five genes (KCNA1, CACNA1A, CACNB4, SLC1A3, and UBR4) have been linked to EA. Despite extensive efforts to genetically diagnose EA, many patients remain still undiagnosed. Whole-exome sequencing was carried out in 39 Korean patients with EA to identify pathogenic mutations of the five known EA genes. We also evaluated 40 candidate genes that cause EA as a secondary phenotype or cerebellar ataxia. Eighteen patients (46%) revealed genetic information useful for establishing a molecular diagnosis of EA. In 11 patients, 16 pathogenic mutations were detected in three EA genes. These included nine mutations in CACNA1A, three in SLC1A3, and four in UBR4. Three patients had mutations in two genes, either CACNA1A and SLC1A3 or CACNA1A and UBR4, suggesting that SLC1A3 and UBR4 may act as genetic modifiers with synergic effects on the abnormal presynaptic activity caused by CACNA1A mutations. In seven patients with negative results for screening of EA genes, potential pathogenic mutations were identified in the candidate genes ATP1A2, SCN1A, TTBK2, TGM6, FGF14, and KCND3. This study demonstrates the genetic heterogeneity of Korean EA, and indicates that whole-exome sequencing may be useful for molecular genetic diagnosis of EA.
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21
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The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes. Hum Genet 2017; 136:921-939. [PMID: 28600779 PMCID: PMC5502059 DOI: 10.1007/s00439-017-1821-8] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/05/2017] [Indexed: 12/13/2022]
Abstract
In this study, we report the experience of the only reference clinical next-generation sequencing lab in Saudi Arabia with the first 1000 families who span a wide-range of suspected Mendelian phenotypes. A total of 1019 tests were performed in the period of March 2016–December 2016 comprising 972 solo (index only), 14 duo (parents or affected siblings only), and 33 trio (index and parents). Multigene panels accounted for 672 tests, while whole exome sequencing (WES) represented the remaining 347 tests. Pathogenic or likely pathogenic variants that explain the clinical indications were identified in 34% (27% in panels and 43% in exomes), spanning 279 genes and including 165 novel variants. While recessive mutations dominated the landscape of solved cases (71% of mutations, and 97% of which are homozygous), a substantial minority (27%) were solved on the basis of dominant mutations. The highly consanguineous nature of the study population also facilitated homozygosity for many private mutations (only 32.5% of the recessive mutations are founder), as well as the first instances of recessive inheritance of previously assumed strictly dominant disorders (involving ITPR1, VAMP1, MCTP2, and TBP). Surprisingly, however, dual molecular diagnosis was only observed in 1.5% of cases. Finally, we have encountered candidate variants in 75 genes (ABHD6, ACY3, ADGRB2, ADGRG7, AGTPBP1, AHNAK2, AKAP6, ASB3, ATXN1L, C17orf62, CABP1, CCDC186, CCP110, CLSTN2, CNTN3, CNTN5, CTNNA2, CWC22, DMAP1, DMKN, DMXL1, DSCAM, DVL2, ECI1, EP400, EPB41L5, FBXL22, GAP43, GEMIN7, GIT1, GRIK4, GRSF1, GTRP1, HID1, IFNL1, KCNC4, LRRC52, MAP7D3, MCTP2, MED26, MPP7, MRPS35, MTDH, MTMR9, NECAP2, NPAT, NRAP, PAX7, PCNX, PLCH2, PLEKHF1, PTPN12, QKI, RILPL2, RIMKLA, RIMS2, RNF213, ROBO1, SEC16A, SIAH1, SIRT2, SLAIN2, SLC22A20, SMDT1, SRRT, SSTR1, ST20, SYT9, TSPAN6, UBR4, VAMP4, VPS36, WDR59, WDYHV1, and WHSC1) not previously linked to human phenotypes and these are presented to accelerate post-publication matchmaking. Two of these genes were independently mutated in more than one family with similar phenotypes, which substantiates their link to human disease (AKAP6 in intellectual disability and UBR4 in early dementia). If the novel candidate disease genes in this cohort are independently confirmed, the yield of WES will have increased to 83%, which suggests that most “negative” clinical exome tests are unsolved due to interpretation rather than technical limitations.
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Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. Cell Host Microbe 2016; 18:723-35. [PMID: 26651948 DOI: 10.1016/j.chom.2015.11.002] [Citation(s) in RCA: 669] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/06/2015] [Accepted: 11/10/2015] [Indexed: 12/24/2022]
Abstract
Several systems-level datasets designed to dissect host-pathogen interactions during influenza A infection have been reported. However, apparent discordance among these data has hampered their full utility toward advancing mechanistic and therapeutic knowledge. To collectively reconcile these datasets, we performed a meta-analysis of data from eight published RNAi screens and integrated these data with three protein interaction datasets, including one generated within the context of this study. Further integration of these data with global virus-host interaction analyses revealed a functionally validated biochemical landscape of the influenza-host interface, which can be queried through a simplified and customizable web portal (http://www.metascape.org/IAV). Follow-up studies revealed that the putative ubiquitin ligase UBR4 associates with the viral M2 protein and promotes apical transport of viral proteins. Taken together, the integrative analysis of influenza OMICs datasets illuminates a viral-host network of high-confidence human proteins that are essential for influenza A virus replication.
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Rinschen MM, Bharill P, Wu X, Kohli P, Reinert MJ, Kretz O, Saez I, Schermer B, Höhne M, Bartram MP, Aravamudhan S, Brooks BR, Vilchez D, Huber TB, Müller RU, Krüger M, Benzing T. The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes. Hum Mol Genet 2016; 25:1328-44. [PMID: 26792178 DOI: 10.1093/hmg/ddw016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/16/2016] [Indexed: 11/13/2022] Open
Abstract
The PHB-domain protein podocin maintains the renal filtration barrier and its mutation is an important cause of hereditary nephrotic syndrome. Podocin and its Caenorhabditis elegans orthologue MEC-2 have emerged as key components of mechanosensitive membrane protein signalling complexes. Whereas podocin resides at a specialized cell junction at the podocyte slit diaphragm, MEC-2 is found in neurons required for touch sensitivity. Here, we show that the ubiquitin ligase Ubr4 is a key component of the podocin interactome purified both from cultured podocytes and native glomeruli. It colocalizes with podocin and regulates its stability. In C. elegans, this process is conserved. Here, Ubr4 is responsible for the degradation of mislocalized MEC-2 multimers. Ubiquitylomic analysis of mouse glomeruli revealed that podocin is ubiquitylated at two lysine residues. These sites were Ubr4-dependent and were conserved across species. Molecular dynamics simulations revealed that ubiquitylation of one site, K301, do not only target podocin/MEC-2 for proteasomal degradation, but may also affect stability and disassembly of the multimeric complex. We suggest that Ubr4 is a key regulator of podocyte foot process proteostasis.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany,
| | - Puneet Bharill
- Department II of Internal Medicine, Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Priyanka Kohli
- Department II of Internal Medicine, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | | | - Oliver Kretz
- Renal Division, University Hospital Freiburg, Freiburg, Germany, Neuroanatomy, University of Freiburg, Freiburg, Germany
| | - Isabel Saez
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Bernhard Schermer
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | | | - Sriram Aravamudhan
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany and
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Vilchez
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Tobias B Huber
- Renal Division, University Hospital Freiburg, Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Marcus Krüger
- Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and
| | - Thomas Benzing
- Department II of Internal Medicine, Center for Molecular Medicine Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany,
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