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Zanotta N, Panzeri E, Minghetti S, Citterio A, Giorda R, Marelli S, Bassi MT, Zucca C. A case of a childhood onset developmental encephalopathy with a novel de novo truncating variant in the Membrane Protein Palmitoylated 5 (MPP5) gene. Seizure 2024; 116:151-155. [PMID: 36710240 DOI: 10.1016/j.seizure.2023.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Membrane Protein Palmitoylated 5 (MPP5) is a highly conserved apical complex protein, essential for cell polarity. Defects in neuronal cell polarity are associated with neurologic disorders. Only three patients with heterozygous MPP5 de novo variants have been reported so far, with global developmental delay, behavioral changes and in only one case epileptic seizures. OBJECTIVE To describe a new patient with a novel truncating de novo mutation in MPP5 and to characterize in detail the epileptic phenotype and electroencephalographic features of the encephalopathy. METHODS We identified a novel truncating de novo mutation in MPP5 in a 44 year old patient by exome sequencing (p.Ser498Phefs*15). We retrospectively analyzed his clinical and instrumental data along a thirty-year follow up. RESULT Our patient presents with generalized tonic-clonic seizures, myoclonic and clonic seizures, non-epileptic myoclonus, tremor, severe intellectual disability, mild face dysmorphic traits, and psychosis. DISCUSSION AND CONCLUSION We present a case of a childhood onset developmental encephalopathy with a likely-pathogenic variant in the MPP5 gene.. This represents the first complete description of the epileptic syndrome associated with the MPP5 gene.
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Affiliation(s)
- Nicoletta Zanotta
- Clinical Neurophysiology Unit, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy.
| | - Elena Panzeri
- Molecular Biology Laboratory, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy
| | - Sara Minghetti
- Clinical Neurophysiology Unit, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy
| | - Andrea Citterio
- Molecular Biology Laboratory, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy
| | - Susan Marelli
- Medical Genetic Service, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy
| | - Maria Teresa Bassi
- Molecular Biology Laboratory, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy
| | - Claudio Zucca
- Clinical Neurophysiology Unit, Scientific Institute, IRCCS E. Medea Via don Luigi Monza, 20, Bosisio Parini, Lecco 23842, Italy
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Groh AC, Möller-Kerutt A, Gilhaus K, Höffken V, Nedvetsky P, Kleimann S, Behrens M, Ghosh S, Hansen U, Krahn MP, Ebnet K, Pavenstädt H, Ludwig A, Weide T. PALS1 is a key regulator of the lateral distribution of tight junction proteins in renal epithelial cells. J Cell Sci 2024; 137:jcs261303. [PMID: 38265145 DOI: 10.1242/jcs.261303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 12/04/2023] [Indexed: 01/25/2024] Open
Abstract
The evolutionarily conserved apical Crumbs (CRB) complex, consisting of the core components CRB3a (an isoform of CRB3), PALS1 and PATJ, plays a key role in epithelial cell-cell contact formation and cell polarization. Recently, we observed that deletion of one Pals1 allele in mice results in functional haploinsufficiency characterized by renal cysts. Here, to address the role of PALS1 at the cellular level, we generated CRISPR/Cas9-mediated PALS1-knockout MDCKII cell lines. The loss of PALS1 resulted in increased paracellular permeability, indicating an epithelial barrier defect. This defect was associated with a redistribution of several tight junction-associated proteins from bicellular to tricellular contacts. PALS1-dependent localization of tight junction proteins at bicellular junctions required its interaction with PATJ. Importantly, reestablishment of the tight junction belt upon transient F-actin depolymerization or upon Ca2+ removal was strongly delayed in PALS1-deficient cells. Additionally, the cytoskeleton regulator RhoA was redistributed from junctions into the cytosol under PALS1 knockout. Together, our data uncover a critical role of PALS1 in the coupling of tight junction proteins to the F-actin cytoskeleton, which ensures their correct distribution along bicellular junctions and the formation of tight epithelial barrier.
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Affiliation(s)
- Ann-Christin Groh
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Annika Möller-Kerutt
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Kevin Gilhaus
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Verena Höffken
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Pavel Nedvetsky
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Medical Cell Biology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Simon Kleimann
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Malina Behrens
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Sujasha Ghosh
- School of Biological Sciences and NTU Institute of Structural Biology (NISB), Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore City, Singapore
| | - Uwe Hansen
- University Hospital of Münster, Institute of Musculoskeletal Medicine (IMM), Head Core Facility Electron Microscopy, Domagkstraße 3, 48149 Münster, Germany
| | - Michael P Krahn
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Medical Cell Biology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Klaus Ebnet
- Institute-associated Research Group "Cell adhesion and cell polarity", Institute of Medical Biochemistry, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Von-Esmarch-Straße 56, 48149 Münster, Germany
| | - Hermann Pavenstädt
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Alexander Ludwig
- School of Biological Sciences and NTU Institute of Structural Biology (NISB), Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore City, Singapore
| | - Thomas Weide
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
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Liu C, Hou L, Zhao Q, Zhou W, Liu K, Liu Q, Zhou T, Xu B, Li P, Huang R. The selected genes NR6A1, RSAD2-CMPK2, and COL3A1 contribute to body size variation in Meishan pigs through different patterns. J Anim Sci 2023; 101:skad304. [PMID: 37703114 PMCID: PMC10548407 DOI: 10.1093/jas/skad304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023] Open
Abstract
The high-fertility Meishan pig is currently categorized into medium sized (MMS) and small sized (SMS) based on body size. To identify causal genes responsible for the variation in body size within the two categories, we sequenced individuals representing the entire consanguinity of the existing Meishan pig. This enabled us to conduct genome selective signal analysis. Our findings revealed the genomes of MMS and SMS are stratified, with selective sweep regions formed by differential genomic intervals between the two categories enriched in multiple pig body size related quantitative trait loci (QTLs). Furthermore, the missense mutation c.575T > C of candidate causal gene NR6A1, accounting for the variation in lumbar vertebrae number in pigs, was positively selected in MMS only, leading to an increase in body length of MMS at 6 months of age. To precisely identify causal genes accounting for body size variation through multi-omics, we collected femoral cartilage and liver transcription data from MMS and SMS respectively, and re-sequencing data from pig breeds exhibiting varying body sizes. We found that two selected regions where the RSAD2-CMPK2 and COL3A1 genes are located, respectively, showed different haplotypes in pig breeds of varying body size, and was associated with body or carcass length in hybridized Suhuai pig. Additionally, the above three hub genes, were significantly greater expressed in SMS femoral cartilage and liver tissues compared to MMS. These three genes could strengthen the pathways related to bone resorption and metabolism in SMS, potentially hindering bone and skeletal development and resulting in a smaller body size in SMS. These findings provide valuable insights into the genetic mechanism of body size variation in Meishan pig population.
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Affiliation(s)
- Chenxi Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Liming Hou
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Qingbo Zhao
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Wuduo Zhou
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Kaiyue Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
| | - Tengbin Zhou
- Kunshan Animal Disease Prevention and Control Center, Suzhou 215000, China
| | - Binbin Xu
- Kunshan Meishan Pig Breeding Co., Ltd., Suzhou 215000, China
| | - Pinghua Li
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
- Huaian Academy, Nanjing Agricultural University, Huaian 223001, China
| | - Ruihua Huang
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing 210095, China
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Chen Y, Wu L, Shi M, Zeng D, Hu R, Wu X, Han S, He K, Xu H, Shao X, Ma R. Electroacupuncture Inhibits NLRP3 Activation by Regulating CMPK2 After Spinal Cord Injury. Front Immunol 2022; 13:788556. [PMID: 35401582 PMCID: PMC8987202 DOI: 10.3389/fimmu.2022.788556] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives This study aimed to evaluate the expression of cytosine monophosphate kinase 2 (CMPK2) and activation of the NLRP3 inflammasome in rats with spinal cord injury (SCI) and to characterize the effects of electroacupuncture on CMPK2-associated regulation of the NLRP3 inflammasome. Methods An SCI model was established in Sprague–Dawley (SD) rats. The expression levels of NLRP3 and CMPK2 were measured at different time points following induction of SCI. The rats were randomly divided into a sham group (Sham), a model group (Model), an electroacupuncture group (EA), an adeno-associated virus (AAV) CMPK2 group, and an AAV NC group. Electroacupuncture was performed at jiaji points on both sides of T9 and T11 for 20 min each day for 3 consecutive days. In the AAV CMPK2 and AAV NC groups, the viruses were injected into the T9 spinal cord via a microneedle using a microscope and a stereotactic syringe. The Basso–Beattie–Bresnahan (BBB) score was used to evaluate the motor function of rats in each group. Histopathological changes in spinal cord tissue were detected using H&E staining, and the expression levels of NLRP3, CMPK2, ASC, caspase-1, IL-18, and IL-1β were quantified using Western blotting (WB), immunofluorescence (IF), and RT-PCR. Results The expression levels of NLRP3 and CMPK2 in the spinal cords of the model group were significantly increased at day 1 compared with those in the sham group (p < 0.05). The expression levels of NLRP3 and CMPK2 decreased gradually over time and remained low at 14 days post-SCI. We successfully constructed AAV CMPK2 and showed that CMPK2 was significantly knocked down following 2 dilutions. Finally, treatment with EA or AAV CMPK2 resulted in significantly increased BBB scores compared to those in the model group and the AAV NC group (p < 0.05). The histomorphology of the spinal cord in the EA and AAV CMPK2 groups was significantly different than that in the model and AAV NC groups. WB, IF, and PCR analyses showed that the expression levels of CMPK2, NLRP3, ASC, caspase-1, IL-18, and IL-1β were significantly lower in the EA and AAV CMPK2 groups compared with those in the model and AAV NC groups (p < 0.05). Conclusion Our study showed that CMPK2 regulated NLRP3 expression in rats with SCI. Activation of NLRP3 is a critical mechanism of inflammasome activation and the inflammatory response following SCI. Electroacupuncture downregulated the expression of CMPK2 and inhibited activation of NLRP3, which could improve motor function in rats with SCI.
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Affiliation(s)
- Yi Chen
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Lei Wu
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
- Department of Acupuncture, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Mengting Shi
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Danyi Zeng
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Rong Hu
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Xingying Wu
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Shijun Han
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Kelin He
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
- Department of Acupuncture, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Haipeng Xu
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - XiaoMei Shao
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Ruijie Ma
- Department of Neurobiology and Acupuncture Research, The Third School of Clinical Medicine (School of Rehabilitation Medicine), Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
- Department of Acupuncture, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Ruijie Ma,
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Vanoevelen JM, Bierau J, Grashorn JC, Lambrichs E, Kamsteeg EJ, Bok LA, Wevers RA, van der Knaap MS, Bugiani M, Frisk JH, Colnaghi R, O'Driscoll M, Hellebrekers DMEI, Rodenburg R, Ferreira CR, Brunner HG, van den Wijngaard A, Abdel-Salam GMH, Wang L, Stumpel CTRM. DTYMK is essential for genome integrity and neuronal survival. Acta Neuropathol 2022; 143:245-262. [PMID: 34918187 PMCID: PMC8742820 DOI: 10.1007/s00401-021-02394-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Nucleotide metabolism is a complex pathway regulating crucial cellular processes such as nucleic acid synthesis, DNA repair and proliferation. This study shows that impairment of the biosynthesis of one of the building blocks of DNA, dTTP, causes a severe, early-onset neurodegenerative disease. Here, we describe two unrelated children with bi-allelic variants in DTYMK, encoding dTMPK, which catalyzes the penultimate step in dTTP biosynthesis. The affected children show severe microcephaly and growth retardation with minimal neurodevelopment. Brain imaging revealed severe cerebral atrophy and disappearance of the basal ganglia. In cells of affected individuals, dTMPK enzyme activity was minimal, along with impaired DNA replication. In addition, we generated dtymk mutant zebrafish that replicate this phenotype of microcephaly, neuronal cell death and early lethality. An increase of ribonucleotide incorporation in the genome as well as impaired responses to DNA damage were observed in dtymk mutant zebrafish, providing novel pathophysiological insights. It is highly remarkable that this deficiency is viable as an essential component for DNA cannot be generated, since the metabolic pathway for dTTP synthesis is completely blocked. In summary, by combining genetic and biochemical approaches in multiple models we identified loss-of-function of DTYMK as the cause of a severe postnatal neurodegenerative disease and highlight the essential nature of dTTP synthesis in the maintenance of genome stability and neuronal survival.
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Affiliation(s)
- Jo M Vanoevelen
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands.
- GROW-School for Oncology and Developmental Biology, 6229 ER, Maastricht, The Netherlands.
| | - Jörgen Bierau
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands
| | - Janine C Grashorn
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands
| | - Ellen Lambrichs
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud UMC, 6525 GA, Nijmegen, The Netherlands
| | - Levinus A Bok
- Department of Pediatrics, Màxima Medical Center, 5504 DB, Veldhoven, The Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Radboud UMC, 6525 GA, Nijmegen, The Netherlands
| | | | - Marianna Bugiani
- Department of Neuropathology, VUMC, 1105 AZ, Amsterdam, The Netherlands
| | - Junmei Hu Frisk
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Rita Colnaghi
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RH, UK
| | - Mark O'Driscoll
- Genome Damage and Stability Centre, University of Sussex, Brighton, BN1 9RH, UK
| | - Debby M E I Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands
| | - Richard Rodenburg
- Translational Metabolic Laboratory, Radboud UMC, 6525 GA, Nijmegen, The Netherlands
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands
- Department of Human Genetics, Radboud UMC, 6525 GA, Nijmegen, The Netherlands
- GROW-School for Oncology and Developmental Biology, 6229 ER, Maastricht, The Netherlands
- MHENS School of Neuroscience, 6229 ER, Maastricht, The Netherlands
- Donders Institute of Neuroscience, Radboud UMC, 6525 GA, Nijmegen, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Centre+, 6229 ER, Maastricht, The Netherlands.
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Yuan XL, Zhang R, Zheng Y, Sun L, Wang G, Chen S, Xu Y, Chen SL, Qiu K, Ng TK. Corneal curvature-associated MTOR variant differentiates mild myopia from high myopia in Han Chinese population. Ophthalmic Genet 2021; 42:446-457. [PMID: 33979260 DOI: 10.1080/13816810.2021.1923035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/27/2021] [Accepted: 04/18/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Myopia is the most prevalent ocular disorder in the world, and corneal parameters have been regarded as key ocular biometric parameters determining the refractive status. Here, we aimed to determine the association of genome-wide association study-identified corneal curvature (CC)-related gene variants with different severity of myopia and ocular biometric parameters in Chinese population. METHODS Total 2,101 unrelated Han Chinese subjects were recruited, including 1,649 myopia and 452 control subjects. Five previously reported CC-associated gene variants (PDGFRA, MTOR, WNT7B, CMPK1 and RBP3) were genotyped by TaqMan assay, and their association with different myopia severity and ocular biometric parameters were evaluated. RESULTS Joint additive effect analysis showed that MTOR rs74225573 paired with PDGFRA rs2114039 (P = .009, odds ratio (OR) = 4.91) or CMPK1 rs17103186 (P = .002, OR = 13.03) were significantly associated with higher risk in mild myopia. Critically, mild myopia subjects had significantly higher frequency in MTOR rs74225573 C allele than high myopia subjects (P = .003), especially in male subjects (P = .001, OR = 0.49). High myopia subjects carrying MTOR rs74225573 C allele have significant flatter CC (P = .035) and longer corneal radius (P = .044) than those carrying TT genotype. CONCLUSION This study revealed that male high myopia subjects are more prone to carry CC-related MTOR rs74225573 T allele, whereas mild myopia subjects are prone to carry the C allele. MTOR rs7422573 variant could be a genetic marker to differentiate mild from high myopia in risk assessment. ABBREVIATIONS ACD: anterior chamber depth; AL: axial length; AL/CR: axial length/corneal radius ratio; ANOVA: analysis of variance; CC: corneal curvature; CCT: central corneal thickness; C.I.: confidence interval; CMPK1: cytidine/uridine monophosphate kinase 1; CR: corneal radius; D: diopter; GWAS: genome-wide association studies; HWE: Hardy-Weinberg equilibrium; LT: lens thickness; MIPEP: mitochondrial intermediate peptidase; MTOR: mechanistic target of rapamycin kinase; OR: odds ratio; PDGFRA: platelet-derived growth factor receptor-α; RBP3: retinol-binding protein 3; SD: standard deviation; SE: spherical equivalence; SNTB1: syntrophin beta 1; VCD: vitreous chamber depth; VIPR2: vasoactive intestinal peptide receptor 2; WNT7B: wingless/integrated family member 7B.
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Affiliation(s)
- Xiang-Ling Yuan
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | - Riping Zhang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yuqian Zheng
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Lixia Sun
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Geng Wang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Shaowan Chen
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yanxuan Xu
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Shao-Lang Chen
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Kunliang Qiu
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
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7
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Feng C, Tang Y, Liu X, Zhou Z. CMPK2 of triploid crucian carp is involved in immune defense against bacterial infection. Dev Comp Immunol 2021; 116:103924. [PMID: 33186560 DOI: 10.1016/j.dci.2020.103924] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Cytidine/uridine monophosphate kinase 2 (CMPK2) is a thymidylate kinase and in mammals is known to be involved in mitochondrial DNA (mtDNA) synthesis and antiviral immunity. However, very little is known about the function of CMPK2 in fish. With an aim to elucidate the antimicrobial mechanism of CMPK2 in fish, we in this study examined the function of CMPK2 from triploid crucian carp (3nCmpk2). 3nCmpk2 is 426 residues in length and possesses the conserved thymidylate kinase domain. The deduced amino acid sequence of 3nCmpk2 shares 53.2%-99.1% overall identities with the CMPK2 of several fish species. Quantitative real time RT-PCR (qRT-PCR) analysis showed that 3nCmpk2 expression occurred in multiple tissues and was upregulated by bacterial infection in a time-dependent manner. Recombinant 3nCmpk2 (r3nCmpk2) induced mtDNA synthesis and NLRP3 activation. Overexpression of 3nCmpk2 protects the intestinal barrier and hampers the bacterial colonization in fish tissues. These results provide the first evidence that 3nCmpk2 is involved in host innate immunity and plays a protective role in antimicrobial responses during bacterial infection.
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Affiliation(s)
- Chen Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yiyang Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiaofeng Liu
- Department of Nutrition, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zejun Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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8
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Liu W, Chen B, Yao J, Liu J, Kuang M, Wang F, Wang Y, Elkady G, Lu Y, Zhang Y, Liu X. Identification of fish CMPK2 as an interferon stimulated gene against SVCV infection. Fish Shellfish Immunol 2019; 92:125-132. [PMID: 31125665 DOI: 10.1016/j.fsi.2019.05.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/09/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Cytidine/uridine monophosphate kinase 2 (CMPK2) is known as a nucleoside monophosphate kinase in mitochondria to maintains intracellular UTP/CTP, and could be induced by immunostimulants LPS and Poly (I:C) in mammals, suggesting its potential antiviral and antibacterial role. In this study, CMPK2 was cloned and characterized in Fathead minnow (FHM) cells. In vivo analysis of tissue distribution revealed that CMPK2 transcript was detected in all the tissues of zebrafish (Danio rerio) examined in this study, particularly abundant in liver, spleen and kidney. In addition, indirect immunofluorescence showed that CMPK2 was localized in the cytoplasm of FHM cells. Expression of CMPK2 mRNA was significantly up-regulated following challenge with Spring viraemia of carp virus (SVCV), poly(I:C), or zebrafish IFN1 and IFN3 both in vitro and in vivo. Furthermore, overexpression and RNA interference of CMPK2 in SVCV-infected FHM cells showed significantly antiviral effect. In summary, this study for the first time shows the presence and distribution of CMPK2 in different tissues of zebrafish, but also demonstrates its antiviral potential against SVCV infection in vivo. These new findings could contribute to explain the molecular mechanism of the CMPK2 mediated antiviral function.
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Affiliation(s)
- Wanmeng Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Bo Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Jian Yao
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Jiaoyun Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Ming Kuang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Fang Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Yeda Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Gehad Elkady
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Yuanan Lu
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Yongan Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Xueqin Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China.
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9
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Kikuchi M, Kizaki K, Shigeno S, Toji N, Ishiguro-Oonuma T, Koshi K, Takahashi T, Hashizume K. Newly identified interferon tau-responsive Hes family BHLH transcription factor 4 and cytidine/uridine monophosphate kinase 2 genes in peripheral blood granulocytes during early pregnancy in cows. Domest Anim Endocrinol 2019; 68:64-72. [PMID: 30870785 DOI: 10.1016/j.domaniend.2019.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/14/2019] [Accepted: 01/22/2019] [Indexed: 11/16/2022]
Abstract
In cattle, interferon-stimulated genes (ISGs) such as ISG15, MX1, MX2, and OAS1 are known as classic ISGs that are highly involved in the implantation process. Various molecules play a crucial role in the mechanisms underlying ISG effects. Although microarray analyses have highlighted the expression of various molecules during the implantation period, these molecules remain incompletely characterized. In the present study, various specifically expressed genes were selected and their characteristics were examined. The microarray data from peripheral blood leukocytes derived from artificially inseminated cows and granulocytes obtained from embryo-transferred cows, respectively, were used to identify new ISG candidates. Seven common genes, including ISG15 and OAS1, were confirmed, but only 4 of the 5 genes were amplified by reverse transcription quantitative polymerase chain reaction. In addition, 3 expressed sequence tags (ESTs) exhibited significantly greater expression in granulocytes from pregnant cows than that observed in bred nonpregnant cows, and the expression in granulocytes increased after interferon-tau stimulation. Sequence alignment revealed similar sequences within 2 ESTs on the Hairy and enhancer of split (Hes) family basic helix-loop-helix transcription factor 4 (HES4) gene. An additional EST was identified as cytidine/uridine monophosphate kinase 2 (CMPK2). In silico analysis facilitated the identification of transcription factor-binding sequences, including an interferon-stimulated response element and interferon regulatory factor-binding sites, within the promoter region of HES4 and CMPK2. These genes may function as new ISGs in the context of implantation and may participate in the coordination of the feto-maternal interface in cows.
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Affiliation(s)
- M Kikuchi
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Physiology, Iwate University, Morioka, Iwate 020-8550, Japan
| | - K Kizaki
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Physiology, Iwate University, Morioka, Iwate 020-8550, Japan.
| | - S Shigeno
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Physiology, Iwate University, Morioka, Iwate 020-8550, Japan
| | - N Toji
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Physiology, Iwate University, Morioka, Iwate 020-8550, Japan
| | - T Ishiguro-Oonuma
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Physiology, Iwate University, Morioka, Iwate 020-8550, Japan
| | - K Koshi
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Physiology, Iwate University, Morioka, Iwate 020-8550, Japan
| | - T Takahashi
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Theriogenology, Iwate University, Morioka, Iwate 020-8550, Japan
| | - K Hashizume
- Cooperative Department of Veterinary Medicine, Laboratory of Veterinary Physiology, Iwate University, Morioka, Iwate 020-8550, Japan
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10
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Dong Q, Zhang YX, Zhou Q, Liu QE, Chen DB, Wang H, Cheng SH, Cao LY, Shen XH. UMP Kinase Regulates Chloroplast Development and Cold Response in Rice. Int J Mol Sci 2019; 20:E2107. [PMID: 31035645 PMCID: PMC6539431 DOI: 10.3390/ijms20092107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 02/04/2023] Open
Abstract
Pyrimidine nucleotides are important metabolites that are building blocks of nucleic acids, which participate in various aspects of plant development. Only a few genes involved in pyrimidine metabolism have been identified in rice and the majority of their functions remain unclear. In this study, we used a map-based cloning strategy to isolate a UMPK gene in rice, encoding the UMP kinase that phosphorylates UMP to form UDP, from a recessive mutant with pale-green leaves. In the mutant, UDP content always decreased, while UTP content fluctuated with the development of leaves. Mutation of UMPK reduced chlorophyll contents and decreased photosynthetic capacity. In the mutant, transcription of plastid-encoded RNA polymerase-dependent genes, including psaA, psbB, psbC and petB, was significantly reduced, whereas transcription of nuclear-encoded RNA polymerase-dependent genes, including rpoA, rpoB, rpoC1, and rpl23, was elevated. The expression of UMPK was significantly induced by various stresses, including cold, heat, and drought. Increased sensitivity to cold stress was observed in the mutant, based on the survival rate and malondialdehyde content. High accumulation of hydrogen peroxide was found in the mutant, which was enhanced by cold treatment. Our results indicate that the UMP kinase gene plays important roles in regulating chloroplast development and stress response in rice.
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Affiliation(s)
- Qing Dong
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Ying-Xin Zhang
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Quan Zhou
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Qun-En Liu
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Dai-Bo Chen
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Hong Wang
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shi-Hua Cheng
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Li-Yong Cao
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
| | - Xi-Hong Shen
- State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China.
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11
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Zhong Z, Liang S, Sanchez-Lopez E, He F, Shalapour S, Lin XJ, Wong J, Ding S, Seki E, Schnabl B, Hevener AL, Greenberg HB, Kisseleva T, Karin M. New mitochondrial DNA synthesis enables NLRP3 inflammasome activation. Nature 2018; 560:198-203. [PMID: 30046112 PMCID: PMC6329306 DOI: 10.1038/s41586-018-0372-z] [Citation(s) in RCA: 650] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 06/13/2018] [Indexed: 02/06/2023]
Abstract
Dysregulated NLRP3 inflammasome activity results in uncontrolled inflammation, which underlies many chronic diseases. Although mitochondrial damage is needed for the assembly and activation of the NLRP3 inflammasome, it is unclear how macrophages are able to respond to structurally diverse inflammasome-activating stimuli. Here we show that the synthesis of mitochondrial DNA (mtDNA), induced after the engagement of Toll-like receptors, is crucial for NLRP3 signalling. Toll-like receptors signal via the MyD88 and TRIF adaptors to trigger IRF1-dependent transcription of CMPK2, a rate-limiting enzyme that supplies deoxyribonucleotides for mtDNA synthesis. CMPK2-dependent mtDNA synthesis is necessary for the production of oxidized mtDNA fragments after exposure to NLRP3 activators. Cytosolic oxidized mtDNA associates with the NLRP3 inflammasome complex and is required for its activation. The dependence on CMPK2 catalytic activity provides opportunities for more effective control of NLRP3 inflammasome-associated diseases.
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Affiliation(s)
- Zhenyu Zhong
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shuang Liang
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Elsa Sanchez-Lopez
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Feng He
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shabnam Shalapour
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xue-Jia Lin
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Biomedical Translational Research Institute and the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jerry Wong
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Siyuan Ding
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Ekihiro Seki
- Department of Medicine, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bernd Schnabl
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrea L Hevener
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Harry B Greenberg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Tatiana Kisseleva
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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12
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Chen F, Dong G, Ma X, Wang F, Zhang Y, Xiong E, Wu J, Wang H, Qian Q, Wu L, Yu Y. UMP kinase activity is involved in proper chloroplast development in rice. Photosynth Res 2018; 137:53-67. [PMID: 29392476 PMCID: PMC5999181 DOI: 10.1007/s11120-017-0477-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/27/2017] [Indexed: 05/23/2023]
Abstract
Isolation of leaf-color mutants is important in understanding the mechanisms of chloroplast biogenesis and development. In this study, we identified and characterized a rice (Oryza sativa) mutant, yellow leaf 2 (yl2), exhibiting pale yellow leaves with a few longitudinal white stripes at the early seedling stage then gradually turning yellow. Genetic analyses revealed that YL2 encodes a thylakoid membrane-localized protein with significant sequence similarity to UMP kinase proteins in prokaryotes and eukaryotes. Prokaryotic UMP kinase activity was subsequently confirmed, with YL2 deficiency causing a significant reduction in chlorophyll accumulation and photochemical efficiency. Moreover, YL2 is also light dependent and preferentially expressed in green tissues. Chloroplast development was abnormal in the yl2 mutant, possibly due to reduced accumulation of thylakoid membranes and a lack of normal stroma lamellae. 2D Blue-Native SDS-PAGE and immunoblot analyses revealed a reduction in several subunits of photosynthetic complexes, in particular, the AtpB subunit of ATP synthase, while mRNA levels of corresponding genes were unchanged or increased compared with the wild type. In addition, we observed a significant decrease (ca. 36.3%) in cpATPase activity in the yl2 mutant compared with the wild type. Taken together, our results suggest that UMP kinase activity plays an essential role in chloroplast development and regulating cpATPase biogenesis in rice.
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Affiliation(s)
- Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Guojun Dong
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Zhejiang, China
| | - Xiaohui Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Fang Wang
- Institute of Insect Sciences, Zhejiang University, Zhejiang, China
| | - Yanli Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Erhui Xiong
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Jiahuan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China
| | - Qian Qian
- State Key Laboratory for Rice Biology, China National Rice Research Institute, Zhejiang, China
| | - Limin Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China.
| | - Yanchun Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, China.
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13
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Zhu X, Guo S, Wang Z, Du Q, Xing Y, Zhang T, Shen W, Sang X, Ling Y, He G. Map-based cloning and functional analysis of YGL8, which controls leaf colour in rice (Oryza sativa). BMC Plant Biol 2016; 16:134. [PMID: 27297403 PMCID: PMC4907030 DOI: 10.1186/s12870-016-0821-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 05/25/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND As the indispensable part of plant, leaf blade mainly functions as the production workshops where organic substance is produced by photosynthesis. Leaf colour mutation is a genetic phenomenon that has a high frequency and is easily identified. The mutations always exhibit negative impact on the development of plants in any of the different stages of growth. Up to now, numerous genes involved in leaf colour mutations have been cloned. RESULTS In this study, a yellow-green leaf mutant, yellow-green leaf 8 (ygl8), with stable genetic phenotype, has been screened out in the progeny of an excellent indica restorer line Jinhui 10 with seeds treated by EMS. The levels of Chl a, Chl b and total chlorophyll were significantly lower in ygl8 than those in the WT throughout the whole growth period, while no clear change was noted in the Chl a/b ratio. Transmission electron microscopy demonstrated that the lamellae were clearly intumescent and intricately stacked in ygl8. Furthermore, compared with those of the WT, the stomatal conductance, intercellular CO2 concentration, photosynthetic rate and transpiration rate of ylg8 were all significantly lower. Map-based cloning results showed that Loc_Os01g73450, encoding a chloroplast-targeted UMP kinase, corresponded to Ygl8 and played an important role in regulating leaf colour in rice (Oryza sativa). Complementation of ygl8 with the WT DNA sequence of Loc_Os01g73450 led to restoration of the normal phenotype, and transgenic RNA interference plants showed a yellow-green colour. Analysis of the spatial and temporal expression of Ygl8 indicated that it was highly expressed in leaf blades and weakly expressed in other tissues. qRT-PCR also showed that the expression levels of the major Photosystem I core subunits plastome-encoded PsaA, PsaB and PsbC were significantly reduced in ygl8. The expression levels of nuclear-encoded gene involved in Chl biosynthesis HEMC, HEME, and PORA were also decreased when compared with the wild-type. CONCLUSIONS Independent of Chl biosynthesis and photosystem, YGL8 may affect the structure and function of chloroplasts grana lamellae by regulating plastid genome encoded thylakoid membrane constitutive gene expression and indirectly influences Chl biosynthesis.
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Affiliation(s)
- Xiaoyan Zhu
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
| | - Shuang Guo
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
- Institute of Rice, Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Zhongwei Wang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
| | - Qing Du
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
- Forestry Bureau of Chuanshan District, Suining, Sichuan, 629000, China
| | - Yadi Xing
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
| | - Tianquan Zhang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
| | - Wenqiang Shen
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
| | - Xianchun Sang
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
| | - Yinghua Ling
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China
| | - Guanghua He
- Key Laboratory of Application and Safety Control of Genetically Modified Crops, Rice Research Institute of Southwest University, Chongqing, 400716, China.
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14
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Singh VK, Doharey PK, Kumar V, Saxena JK, Siddiqi MI, Rathaur S, Narender T. Synthesis, molecular docking and Brugia malayi thymidylate kinase (BmTMK) enzyme inhibition study of novel derivatives of [6]-shogaol. Eur J Med Chem 2015; 93:74-82. [PMID: 25659753 DOI: 10.1016/j.ejmech.2015.01.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/03/2023]
Abstract
[6]-Shogaol (1) was isolated from Zingiber officinale. Twelve novel compounds have been synthesized and evaluated for their Brugia malayi thymidylate kinase (BmTMK) inhibition activity, which plays important role for the DNA synthesis in parasite. [6]-Shogaol (1) and shogaol with thymine head group (2), 5-bromouracil head group (3), adenine head group (4) and 2-amino-3-methylpyridine head group (5) showed potential inhibitory effect on BmTMK activity. Further molecular docking studies were carried out to explore the putative binding mode of compounds 1-5.
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Affiliation(s)
- Vinay Kr Singh
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, (CSIR-CDRI), BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - Pawan K Doharey
- Biochemistry Division, CSIR-Central Drug Research Institute, (CSIR-CDRI), BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - Vikash Kumar
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, (CSIR-CDRI), BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - J K Saxena
- Biochemistry Division, CSIR-Central Drug Research Institute, (CSIR-CDRI), BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - M I Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, (CSIR-CDRI), BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - Sushma Rathaur
- Department of Biochemistry, Banaras Hindu University, Varanasi 221005, India
| | - Tadigoppula Narender
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, (CSIR-CDRI), BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India.
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15
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Ivanova ME, Fletcher GC, O’Reilly N, Purkiss AG, Thompson BJ, McDonald NQ. Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove. Acta Crystallogr D Biol Crystallogr 2015; 71:555-64. [PMID: 25760605 PMCID: PMC4356366 DOI: 10.1107/s139900471402776x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/19/2014] [Indexed: 12/21/2022]
Abstract
Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein-protein interaction.
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Affiliation(s)
- Marina E. Ivanova
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Georgina C. Fletcher
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Nicola O’Reilly
- Peptide Chemistry Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Andrew G. Purkiss
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Barry J. Thompson
- Epithelial Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
| | - Neil Q. McDonald
- Structural Biology Laboratories, Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY, England
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England
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16
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Sato T, Neschadim A, Lavie A, Yanagisawa T, Medin JA. The engineered thymidylate kinase (TMPK)/AZT enzyme-prodrug axis offers efficient bystander cell killing for suicide gene therapy of cancer. PLoS One 2013; 8:e78711. [PMID: 24194950 PMCID: PMC3806853 DOI: 10.1371/journal.pone.0078711] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 09/16/2013] [Indexed: 11/22/2022] Open
Abstract
We previously described a novel suicide (or ‘cell fate control’) gene therapy enzyme/prodrug system based on an engineered variant of human thymidylate kinase (TMPK) that potentiates azidothymidine (AZT) activation. Delivery of a suicide gene sequence into tumors by lentiviral transduction embodies a cancer gene therapy that could employ bystander cell killing as a mechanism driving significant tumor regression in vivo. Here we present evidence of a significant bystander cell killing in vitro and in vivo mediated by the TMPK/AZT suicide gene axis that is reliant on the formation of functional gap-junctional intercellular communications (GJICs). Potentiation of AZT activation by the engineered TMPK expressed in the human prostate cancer cell line, PC-3, resulted in effective bystander killing of PC-3 cells lacking TMPK expression – an effect that could be blocked by the GJIC inhibitor, carbenoxolone. Although GJICs are mainly formed by connexins, a new family of GJIC molecules designated pannexins has been recently identified. PC-3 cells expressed both connexin43 (Cx43) and Pannexin1 (Panx1), but Panx1 expression predominated at the plasma membrane, whereas Cx43 expression was primarily localized to the cytosol. The contribution of bystander effects to the reduction of solid tumor xenografts established by the PC-3 cell line was evaluated in an animal model. We demonstrate the contribution of bystander cell killing to tumor regression in a xenograft model relying on the delivery of expression of the TMPK suicide gene into tumors via direct intratumoral injection of recombinant therapeutic lentivirus. Taken together, our data underscore that the TMPK/AZT enzyme-prodrug axis can be effectively utilized in suicide gene therapy of solid tumors, wherein significant tumor regression can be achieved via bystander effects mediated by GJICs.
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Affiliation(s)
- Takeya Sato
- Molecular Pharmacology, Tohoku University, Sendai, Miyagi, Japan
- * E-mail:
| | - Anton Neschadim
- Research & Development, Canadian Blood Services, Toronto, Ontario, Canada
| | - Arnon Lavie
- Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | | | - Jeffrey A. Medin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- University Health Network, Toronto, Ontario, Canada
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17
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Ma J, Rahlfs S, Jortzik E, Schirmer RH, Przyborski JM, Becker K. Subcellular localization of adenylate kinases in Plasmodium falciparum. FEBS Lett 2012; 586:3037-43. [PMID: 22819813 DOI: 10.1016/j.febslet.2012.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/14/2012] [Accepted: 07/02/2012] [Indexed: 11/18/2022]
Abstract
Adenylate kinases (AK) play a key role in nucleotide signaling processes and energy metabolism by catalyzing the reversible conversion of ATP and AMP to 2 ADP. In the malaria parasite Plasmodium falciparum this reaction is mediated by AK1, AK2, and a GTP:AMP phosphotransferase (GAK). Here, we describe two additional adenylate kinase-like proteins: PfAKLP1, which is homologous to human AK6, and PfAKLP2. Using GFP-fusion proteins and life cell imaging, we demonstrate a cytosolic localization for PfAK1, PfAKLP1, and PfAKLP2, whereas PfGAK is located in the mitochondrion. PfAK2 is located at the parasitophorous vacuole membrane, and this localization is driven by N-myristoylation.
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Affiliation(s)
- Jipeng Ma
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, 35392 Giessen, Germany
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18
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Penpassakarn P, Chaiyen P, Palittapongarnpim P. Efficient heterologous expression and one-step purification of fully active c-terminal histidine-tagged uridine monophosphate kinase from Mycobacterium tuberculosis. Southeast Asian J Trop Med Public Health 2011; 42:1452-1459. [PMID: 22299415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Tuberculosis has long been recognized as one of the most significant public health problems. Finding novel antituberculous drugs is always a necessary approach for controlling the disease. Mycobacterium tuberculosis pyrH gene (Rv2883c) encodes for uridine monophosphate kinase (UMK), which is a key enzyme in the uridine nucleotide interconversion pathway. The enzyme is essential for M. tuberculosis to sustain growth and hence is a potential drug target. In this study, we have developed a rapid protocol for production and purification of M. tuberculosis UMK by cloning pyrH (Rv2883c) of M. tuberculosis H37Rv with the addition of 6-histidine residues to the C-terminus of the protein, and expressing in E. coli BL21-CodonPlus (DE3)-RIPL using an auto-induction medium. The enzyme was efficiently purified by a single-step TALON cobalt affinity chromatography with about 8 fold increase in specific activity, which was determined by a coupled assay with the pyruvate kinase and lactate dehydrogenase. The molecular mass of monomeric UMK was 28.2 kDa and that of the native enzyme was 217 kDa. The enzyme uses UMP as a substrate but not CMP and TMP and activity was enhanced by GTP. Measurements of enzyme kinetics revealed the kcat value of 7.6 +/- 0.4 U mg(-1) or 0.127 +/- 0.006 sec(-1).The protocol reported here can be used for expression of M. tuberculosis UMK in large quantity for formulating a high throughput target-based assay for screening anti-tuberculosis UMK compounds.
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Mascia T, Santovito E, Gallitelli D, Cillo F. Evaluation of reference genes for quantitative reverse-transcription polymerase chain reaction normalization in infected tomato plants. Mol Plant Pathol 2010. [PMID: 21029324 DOI: 10.1111/j.1365-3059.2009.02239.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The quantification of messenger RNA expression levels by real-time reverse-transcription polymerase chain reaction requires the availability of reference genes that are stably expressed regardless of the experimental conditions under study. We examined the expression variations of a set of eight candidate reference genes in tomato leaf and root tissues subjected to the infection of five taxonomically and molecularly different plant viruses and a viroid, inducing diverse pathogenic effects on inoculated plants. Parallel analyses by three commonly used dedicated algorithms, geNorm, NormFinder and BestKeeper, showed that different viral infections and tissues of origin influenced, to some extent, the expression levels of these genes. However, all algorithms showed high levels of stability for glyceraldehyde 3-phosphate dehydrogenase and ubiquitin, indicated as the most suitable endogenous transcripts for normalization in both tissue types. Actin and uridylate kinase were also stably expressed throughout the infected tissues, whereas cyclophilin showed tissue-specific expression stability only in root samples. By contrast, two widely employed reference genes, 18S ribosomal RNA and elongation factor 1α, demonstrated highly variable expression levels that should discourage their use for normalization. In addition, expression level analysis of ascorbate peroxidase and superoxide dismutase showed the modulation of the two genes in virus-infected tomato leaves and roots. The relative quantification of the two genes varied according to the reference genes selected, thus highlighting the importance of the choice of the correct normalization method in such experiments.
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Affiliation(s)
- Tiziana Mascia
- Istituto di Virologia Vegetale, CNR, Via Amendola 165/A, 70126 Bari, Italy
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20
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Mascia T, Santovito E, Gallitelli D, Cillo F. Evaluation of reference genes for quantitative reverse-transcription polymerase chain reaction normalization in infected tomato plants. Mol Plant Pathol 2010. [PMID: 21029324 DOI: 10.1111/j.1364-3703.2010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The quantification of messenger RNA expression levels by real-time reverse-transcription polymerase chain reaction requires the availability of reference genes that are stably expressed regardless of the experimental conditions under study. We examined the expression variations of a set of eight candidate reference genes in tomato leaf and root tissues subjected to the infection of five taxonomically and molecularly different plant viruses and a viroid, inducing diverse pathogenic effects on inoculated plants. Parallel analyses by three commonly used dedicated algorithms, geNorm, NormFinder and BestKeeper, showed that different viral infections and tissues of origin influenced, to some extent, the expression levels of these genes. However, all algorithms showed high levels of stability for glyceraldehyde 3-phosphate dehydrogenase and ubiquitin, indicated as the most suitable endogenous transcripts for normalization in both tissue types. Actin and uridylate kinase were also stably expressed throughout the infected tissues, whereas cyclophilin showed tissue-specific expression stability only in root samples. By contrast, two widely employed reference genes, 18S ribosomal RNA and elongation factor 1α, demonstrated highly variable expression levels that should discourage their use for normalization. In addition, expression level analysis of ascorbate peroxidase and superoxide dismutase showed the modulation of the two genes in virus-infected tomato leaves and roots. The relative quantification of the two genes varied according to the reference genes selected, thus highlighting the importance of the choice of the correct normalization method in such experiments.
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Affiliation(s)
- Tiziana Mascia
- Istituto di Virologia Vegetale, CNR, Via Amendola 165/A, 70126 Bari, Italy
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21
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Mascia T, Santovito E, Gallitelli D, Cillo F. Evaluation of reference genes for quantitative reverse-transcription polymerase chain reaction normalization in infected tomato plants. Mol Plant Pathol 2010; 11:805-16. [PMID: 21029324 PMCID: PMC6640390 DOI: 10.1111/j.1364-3703.2010.00646.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The quantification of messenger RNA expression levels by real-time reverse-transcription polymerase chain reaction requires the availability of reference genes that are stably expressed regardless of the experimental conditions under study. We examined the expression variations of a set of eight candidate reference genes in tomato leaf and root tissues subjected to the infection of five taxonomically and molecularly different plant viruses and a viroid, inducing diverse pathogenic effects on inoculated plants. Parallel analyses by three commonly used dedicated algorithms, geNorm, NormFinder and BestKeeper, showed that different viral infections and tissues of origin influenced, to some extent, the expression levels of these genes. However, all algorithms showed high levels of stability for glyceraldehyde 3-phosphate dehydrogenase and ubiquitin, indicated as the most suitable endogenous transcripts for normalization in both tissue types. Actin and uridylate kinase were also stably expressed throughout the infected tissues, whereas cyclophilin showed tissue-specific expression stability only in root samples. By contrast, two widely employed reference genes, 18S ribosomal RNA and elongation factor 1α, demonstrated highly variable expression levels that should discourage their use for normalization. In addition, expression level analysis of ascorbate peroxidase and superoxide dismutase showed the modulation of the two genes in virus-infected tomato leaves and roots. The relative quantification of the two genes varied according to the reference genes selected, thus highlighting the importance of the choice of the correct normalization method in such experiments.
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Affiliation(s)
- Tiziana Mascia
- Istituto di Virologia Vegetale, CNR, Via Amendola 165/A, 70126 Bari, Italy
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22
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Hein P, Stöckel J, Bennewitz S, Oelmüller R. A protein related to prokaryotic UMP kinases is involved in psaA/B transcript accumulation in Arabidopsis. Plant Mol Biol 2009; 69:517-28. [PMID: 19037728 DOI: 10.1007/s11103-008-9433-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 11/10/2008] [Indexed: 05/06/2023]
Abstract
Dpt1 (defect in p saA/B transcript accumulation 1) is a novel photosystem (PS) I mutant in Arabidopsis. dpt1 mutants fail to grow photoautotrophically, and are impaired in the accumulation of psaA/B transcripts while the transcript levels for the remaining PSI subunits, for subunits of the PSII, the cyt-b ( 6 )/f-complex, and the ribulose-1,5-bisphosphate carboxylase are comparable to the wild type. In-organello run-on transcription assays demonstrate that the lower psaA/B transcript abundance in dpt1-1 is not caused by the inability to transcribe the psaA/psaB/rps14 operon. psaA/B transcripts in the mutant are associated with polyribosomes and translated. Thus, the mutation affects post-transcriptional processes specific for psaA/B. The dpt1 gene was isolated by map-based cloning. The protein is localized in the stroma of the chloroplast and exhibits striking similarities to UMP kinases of prokaryotic origin. Our results show that the nuclear encoded protein Dpt1 is essential for retaining photosynthetic activity in higher plant chloroplasts and involved in post-transcriptional steps of psaA/B transcript accumulation. We discuss that Dpt1 may be a bifunctional protein that couples the pyrimidine metabolism to the photosynthetic electron transport.
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Affiliation(s)
- Paul Hein
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-Universität Jena, Dornburgerstr. 159, 07743, Jena, Germany
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23
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Li B, Ji L, Wu Y, Hao X. [Isolation, prokaryotic expression and activity analysis of thymidylate kinase (tmk) gene from Phytoplasma of wheat blue dwarf]. Wei Sheng Wu Xue Bao 2008; 48:739-744. [PMID: 18720837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
OBJECTIVE Wheat blue dwarf (WBD) is an important disease in winter wheat district, which causes serious losses in wheat production. Thymidylate kinase (TMK) catalyses the phosphorylation of dTMP to dTDP in the de novo and salvage pathways of dTTP synthesis in both prokaryotes and eukaryotes. In order effectively control this phytoplasma, we isolated the thymidylate kinase gene of WBD phytoplasma, and analyzed the catalytic activity of TMK protein. METHODS tmk gene was amplified from the phytoplasma of WBD, the amplicons were digested with EcoR I and Hind III and then inserted into expression vector pET-30a(+). The polyHis-tagged TMK was expressed in E. coli BL21 (DE3) and fusion protein was obtained and purified by Ni-NTA column. The TMK activities were measured by the method of en-zyme-coupled assay involving Mg2+, dTMP and ATP. RESULTS Two genes, tmk-1 and tmk-2 were obtained, with the molecular weight of 630 bp and 624 bp. Both of them encoded an amino acid sequence with three conserved functional motifs which related with binding NTP/NMP. The fusion protein, TMK-2 had a higher catalytic activity (112.41 U/mg) than TMK-1 (16.4 U/mg), and its optimum catalytic conditions were 32 degrees C, pH7.3, 1.5 mmol/L Mg2+ and 1 mmol/L ATP. CONCLUSION TMK-1 and TMK-2 had conserved functional motifs in their primary sequence, and suggested that they may function as TMK enzymes. But, the TMK-1-polyHis fusion protein had very low catalytic activity, the possible reason was that two highly conserved regions were absent in TMK-1, and it might function as another type of kinase in WBD phytoplasma. This experiment lay a foundation for further study of the TMK function in infection and reproduction of WBD phytoplasma.
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Affiliation(s)
- Bei Li
- Northwest Agriculture and Forestry University, Shaanxi Key Laboratory for Agriculture Molecular Biotechnology, Yangling 712100.
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24
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Ronceret A, Gadea-Vacas J, Guilleminot J, Lincker F, Delorme V, Lahmy S, Pelletier G, Chabouté ME, Devic M. The first zygotic division in Arabidopsis requires de novo transcription of thymidylate kinase. Plant J 2008; 53:776-89. [PMID: 18036198 DOI: 10.1111/j.1365-313x.2007.03372.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Re-activation of cell division after fertilization involves the specific regulation of a set of genes. To identify genes involved in the gametophytic to sporophytic transition, we screened Arabidopsis T-DNA insertion lines for early seed abortion at the zygote (zeus) or one-cell embryo stages (cyclops), and characterized a sporophytic zygote-lethal mutation, zeus1. ZEUS1 encodes a thymidylate kinase (AtTMPK) that synthesizes dTDP and is involved in the regulation of DNA replication. Unlike in yeast and animals, the single AtTMPK gene is capable of producing two proteins by alternative splicing; the longer isoform is targeted to the mitochondria, the shorter to the cytosol. Transcription of AtTMPK is activated during the G(1)/S-phase transition of the cell cycle, similarly to yeast and mammalian orthologues. In AtTMPK:GUS plants, the reporter gene was preferentially expressed in cells undergoing division, but was not detected during the male and female gametophytic mitoses. GUS expression was observed in mature embryo sacs prior to fertilization, and this expression may indicate the time of synchronization of the gamete cell-cycle phases. Identification of ZEU1 emphasizes the importance of control of the metabolism of DNA in the regulation of the G(1)/S-phase transition at fertilization.
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Affiliation(s)
- Arnaud Ronceret
- Laboratoire Génome et Développement des Plantes, UMR-CNRS-IRD-Université 5096, 52 Avenue Paul Alduy, 66 860 Perpignan-cedex, France
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25
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Abstract
Intense investigation has identified an elaborate protein network controlling epithelial polarity. Although precise subcellular targeting of apical and basolateral determinants is required for epithelial architecture, little is known about how the individual determinant proteins become localized within the cell. Through a genetic screen for epithelial defects in the Drosophila follicle cells, we have found that the cytoplasmic Dynein motor is an essential regulator of apico–basal polarity. Our data suggest that Dynein acts through the cytoplasmic scaffolding protein Stardust (Sdt) to localize the transmembrane protein Crumbs, in part through the apical targeting of specific sdt mRNA isoforms. We have mapped the sdt mRNA localization signal to an alternatively spliced coding exon. Intriguingly, the presence or absence of this exon corresponds to a developmental switch in sdt mRNA localization in which apical transcripts are only found during early stages of epithelial development, while unlocalized transcripts predominate in mature epithelia. This work represents the first demonstration that Dynein is required for epithelial polarity and suggests that mRNA localization may have a functional role in the regulation of apico–basal organization. Moreover, we introduce a unique mechanism in which alternative splicing of a coding exon is used to control mRNA localization during development. Cells within epithelial sheets are highly polarized with distinct apical and basolateral membrane domains. This cellular organization is critical to both epithelial form and function, and a failure to maintain epithelial polarity is often linked to tumor progression. The protein network that establishes and maintains the two membrane domains relies on the precise subcellular localization of its molecular components, but little is known about how these proteins are targeted to their sites of action. We have shown that the localization of the apical determinant protein Stardust depends on the microtubule motor Dynein. While investigating the relationship between Dynein and Stardust, we also made two unexpected observations about stardust mRNA regulation. First, the mechanism by which Dynein localizes Stardust may depend, in part, on the apical targeting of the stardust mRNA. Second, some stardust mRNA is apically localized during early stages of epithelial development, but the selective removal of the apical localization signal leads to the sole production of uniformly localized transcripts in mature epithelial cells. Together, these results introduce roles for Dynein in apico–basal polarity regulation and raise important questions about the role of mRNA localization in the targeting of polarity determinant proteins and epithelial maturation.
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Affiliation(s)
- Sally Horne-Badovinac
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - David Bilder
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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26
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Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E. Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families. J Bioinform Comput Biol 2007; 5:693-715. [PMID: 17688312 DOI: 10.1142/s0219720007002709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2006] [Accepted: 02/06/2007] [Indexed: 11/18/2022]
Abstract
In this study, we address the issue of performing meaningful pK(a) calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pK(a) values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pK(a) calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pK(a) values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pK(a) calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pK(a) fluctuations among the models or have pK(a) values shifted by several pH units with respect to the pK(a) calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pK(a) calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pK(a) values for highly conserved titratable residues within large sets of homologous proteins.
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Affiliation(s)
- Petras Kundrotas
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
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27
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Collins CM, Olstad K, Sterud E, Jones CS, Noble LR, Mo TA, Cunningham CO. Isolation of a novel fish thymidylate kinase gene, upregulated in Atlantic salmon (Salmo salar L.) following infection with the monogenean parasite Gyrodactylus salaris. Fish Shellfish Immunol 2007; 23:793-807. [PMID: 17467294 DOI: 10.1016/j.fsi.2007.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 03/03/2007] [Accepted: 03/05/2007] [Indexed: 05/15/2023]
Abstract
Analysis of differential gene expression in salmon (Salmo salar) blood following infection with the monogenean parasite Gyrodactylus salaris, resulted in the isolation of a thymidylate kinase gene not previously described from fish and which showed similarity to an LPS-inducible thymidylate kinase gene isolated from mouse macrophages. This salmon TYKi-like gene may play a role in an innate generalised response to pathogen infection as it was upregulated in salmon following infection with the parasite, and also in response to injection with the immunostimulants LPS and Poly I:C, used to emulate bacterial and viral infections, respectively. The possible role of this gene in the biosynthesis of mitochondrial DNA in activated macrophages, in response to G. salaris infection is discussed.
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Affiliation(s)
- Catherine M Collins
- FRS Marine Laboratory, Molecular Genetics, Victoria Road, Torry, Aberdeen, Scotland, UK.
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28
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Abstract
l-Nucleoside analogues such as lamivudine are active for treating viral infections. Like d-nucleosides, the biological activity of the l-enantiomers requires their stepwise phosphorylation by cellular or viral kinases to give the triphosphate. The enantioselectivity of NMP kinases has not been thoroughly studied, unlike that of deoxyribonucleoside kinases. We have therefore investigated the capacity of l-enantiomers of some natural (d)NMP to act as substrates for the recombinant forms of human uridylate-cytidylate kinase, thymidylate kinase and adenylate kinases 1 and 2. Both cytosolic and mitochondrial adenylate kinases were strictly enantioselective, as they phosphorylated only d-(d)AMP. l-dTMP was a substrate for thymidylate kinase, but with an efficiency 150-fold less than d-dTMP. Both l-dUMP and l-(d)CMP were phosphorylated by UMP-CMP kinase although much less efficiently than their natural counterparts. The stereopreference was conserved with the 2′-azido derivatives of dUMP and dUMP while, unexpectedly, the 2′-azido-d-dCMP was a 4-fold better substrate for UMP-CMP kinase than was CMP. Docking simulations showed that the small differences in the binding of d-(d)NMP to their respective kinases could account for the differences in interactions of the l-isomers with the enzymes. This in vitro information was then used to develop the in vivo activation pathway for l-dT.
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Affiliation(s)
- Julie A.C. Alexandre
- Laboratoire d’Enzymologie Moléculaire, FRE 2852-CNRS-Université Paris 6, 4, place Jussieu, 75005 Paris Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, case courrier 1705, Bâtiment Chimie 17, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5 and Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex15, France
| | - Béatrice Roy
- Laboratoire d’Enzymologie Moléculaire, FRE 2852-CNRS-Université Paris 6, 4, place Jussieu, 75005 Paris Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, case courrier 1705, Bâtiment Chimie 17, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5 and Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex15, France
| | - Dimitri Topalis
- Laboratoire d’Enzymologie Moléculaire, FRE 2852-CNRS-Université Paris 6, 4, place Jussieu, 75005 Paris Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, case courrier 1705, Bâtiment Chimie 17, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5 and Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex15, France
| | - Sylvie Pochet
- Laboratoire d’Enzymologie Moléculaire, FRE 2852-CNRS-Université Paris 6, 4, place Jussieu, 75005 Paris Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, case courrier 1705, Bâtiment Chimie 17, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5 and Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex15, France
| | - Christian Périgaud
- Laboratoire d’Enzymologie Moléculaire, FRE 2852-CNRS-Université Paris 6, 4, place Jussieu, 75005 Paris Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, case courrier 1705, Bâtiment Chimie 17, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5 and Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex15, France
| | - Dominique Deville-Bonne
- Laboratoire d’Enzymologie Moléculaire, FRE 2852-CNRS-Université Paris 6, 4, place Jussieu, 75005 Paris Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, case courrier 1705, Bâtiment Chimie 17, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5 and Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex15, France
- *To whom correspondence should be addressed.+33 1 44 27 59 93, Fax: +33 1 44 27 59 94
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Topalis D, Kumamoto H, Amaya Velasco MF, Dugué L, Haouz A, Alexandre JAC, Gallois-Montbrun S, Alzari PM, Pochet S, Agrofoglio LA, Deville-Bonne D. Nucleotide binding to human UMP-CMP kinase using fluorescent derivatives -- a screening based on affinity for the UMP-CMP binding site. FEBS J 2007; 274:3704-3714. [PMID: 17608725 DOI: 10.1111/j.1742-4658.2007.05902.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methylanthraniloyl derivatives of ATP and CDP were used in vitro as fluorescent probes for the donor-binding and acceptor-binding sites of human UMP-CMP kinase, a nucleoside salvage pathway kinase. Like all NMP kinases, UMP-CMP kinase binds the phosphodonor, usually ATP, and the NMP at different binding sites. The reaction results from an in-line phosphotransfer from the donor to the acceptor. The probe for the donor site was displaced by the bisubstrate analogs of the Ap5X series (where X = U, dT, A, G), indicating the broad specificity of the acceptor site. Both CMP and dCMP were competitors for the acceptor site probe. To find antimetabolites for antivirus and anticancer therapies, we have developed a method of screening acyclic phosphonate analogs that is based on the affinity of the acceptor-binding site of the human UMP-CMP kinase. Several uracil vinylphosphonate derivatives had affinities for human UMP-CMP kinase similar to those of dUMP and dCMP and better than that of cidofovir, an acyclic nucleoside phosphonate with a broad spectrum of antiviral activities. The uracil derivatives were inhibitors rather than substrates of human UMP-CMP kinase. Also, the 5-halogen-substituted analogs inhibited the human TMP kinase less efficiently. The broad specificity of the enzyme acceptor-binding site is in agreement with a large substrate-binding pocket, as shown by the 2.1 A crystal structure.
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Affiliation(s)
- Dimitri Topalis
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Hiroki Kumamoto
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Maria-Fernanda Amaya Velasco
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Laurence Dugué
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Ahmed Haouz
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Julie Anne C Alexandre
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Sarah Gallois-Montbrun
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Pedro Maria Alzari
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Sylvie Pochet
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Luigi André Agrofoglio
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
| | - Dominique Deville-Bonne
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, FRE 2852 CNRS-Paris 6, Institut Jacques Monod, Paris, France Institut de Chimie Organique et Analytique, UMR CNRS 6005, FR 2708, Université d'Orléans, UFR Sciences, Orléans, France Unité de Biochimie Structurale, URA CNRS 2185, Institut Pasteur, Paris, France Unité de Chimie Organique, URA CNRS 2128, Institut Pasteur, Paris, France Plate-Forme 6- Cristallogénèse et Diffraction des Rayons X, Institut Pasteur, Paris, France Unité de Régulation Enzymatique des Activités Cellulaires, CNRS URA 2185, Institut Pasteur, Paris, France
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Berger S, Bulgakova NA, Grawe F, Johnson K, Knust E. Unraveling the genetic complexity of Drosophila stardust during photoreceptor morphogenesis and prevention of light-induced degeneration. Genetics 2007; 176:2189-200. [PMID: 17603117 PMCID: PMC1950624 DOI: 10.1534/genetics.107.071449] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Drosophila Stardust, a membrane-associated guanylate kinase (MAGUK), recruits the transmembrane protein Crumbs and the cytoplasmic proteins DPATJ and DLin-7 into an apically localized protein scaffold. This evolutionarily conserved complex is required for epithelial cell polarity in Drosophila embryos and mammalian cells in culture. In addition, mutations in Drosophila crumbs and DPATJ impair morphogenesis of photoreceptor cells (PRCs) and result in light-dependent retinal degeneration. Here we show that stardust is a genetically complex locus. While all alleles tested perturb epithelial cell polarity in the embryo, only a subset of them affects morphogenesis of PRCs or induces light-dependent retinal degeneration. Alleles retaining particular postembryonic functions still express some Stardust protein in pupal and/or adult eyes. The phenotypic complexity is reflected by the expression of distinct splice variants at different developmental stages. All proteins expressed in the retina contain the PSD95, Discs Large, ZO-1 (PDZ), Src homology 3 (SH3), and guanylate kinase (GUK) domain, but lack a large region in the N terminus encoded by one exon. These results suggest that Stardust-based protein scaffolds are dynamic, which is not only mediated by multiple interaction partners, but in addition by various forms of the Stardust protein itself.
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Affiliation(s)
- Sandra Berger
- Max-Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-10307 Dresden, Germany
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31
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Gosens I, van Wijk E, Kersten FFJ, Krieger E, van der Zwaag B, Märker T, Letteboer SJF, Dusseljee S, Peters T, Spierenburg HA, Punte IM, Wolfrum U, Cremers FPM, Kremer H, Roepman R. MPP1 links the Usher protein network and the Crumbs protein complex in the retina. Hum Mol Genet 2007; 16:1993-2003. [PMID: 17584769 DOI: 10.1093/hmg/ddm147] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The highly ordered distribution of neurons is an essential feature of a functional mammalian retina. Disruptions in the apico-basal polarity complexes at the outer limiting membrane (OLM) of the retina are associated with retinal patterning defects in vertebrates. We have analyzed the binding repertoire of MPP5/Pals1, a key member of the apico-basal Crumbs polarity complex, that has functionally conserved counterparts in zebrafish (nagie oko) and Drosophila (Stardust). We show that MPP5 interacts with its MAGUK family member MPP1/p55 at the OLM. Mechanistically, this interaction involves heterodimerization of both MAGUK modules in a directional fashion. MPP1 expression in the retina throughout development resembles the expression of whirlin, a multi-PDZ scaffold protein and an important organizer in the Usher protein network. We demonstrate that both proteins interact strongly by both a classical PDZ domain-to-PDZ binding motif (PBM) mechanism, and a mechanism involving internal epitopes. MPP1 and whirlin colocalize in the retina at the OLM, at the outer synaptic layer and at the basal bodies and the ciliary axoneme. In view of the known roles of the Crumbs and Usher protein networks, our findings suggest a novel link of the core developmental processes of actin polymerization and establishment/maintenance of apico-basal cell polarity through MPP1. These processes, essential in neural development and patterning of the retina, may be disrupted in eye disorders that are associated with defects in these protein networks.
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Affiliation(s)
- Ilse Gosens
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E. BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families. Int J Biol Macromol 2007; 41:114-9. [PMID: 17320167 DOI: 10.1016/j.ijbiomac.2007.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 01/10/2007] [Accepted: 01/10/2007] [Indexed: 11/16/2022]
Abstract
The nucleoside monophosphate kinases (NMPK) are important enzymes that control the ratio of mono- and di-phosphate nucleosides and participate in gene regulation and signal transduction in the cell. However, despite their importance only several 3D structures were experimentally determined in contrast to the wealth of sequences available for each of the NMPK families. To fill this gap we present a Web-based database containing structural models for all proteins of the five bacterial nucleoside monophosphate kinase (bNMPK) families. The models were computed by means of homology-based approach using a few experimentally determined bNMPK structures. The database also contains pK(a) values and their components calculated for the homology-based 3D models, which is a unique feature of the database. The BActerial Nucleoside MOnophosphate KInases (BANMOKI) database is freely accessible (http://www.ces.clemson.edu/compbio/banmoki) and offers an easy user-friendly interface for browsing, searching and downloading content of the database. The users can investigate, using the searching tools of the database, the properties of the bNMP kinases in respect to sequence composition, electrostatic interactions and structural differences.
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Affiliation(s)
- Petras Kundrotas
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29642, USA
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33
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Aigner K, Dampier B, Descovich L, Mikula M, Sultan A, Schreiber M, Mikulits W, Brabletz T, Strand D, Obrist P, Sommergruber W, Schweifer N, Wernitznig A, Beug H, Foisner R, Eger A. The transcription factor ZEB1 (deltaEF1) promotes tumour cell dedifferentiation by repressing master regulators of epithelial polarity. Oncogene 2007; 26:6979-88. [PMID: 17486063 PMCID: PMC2899859 DOI: 10.1038/sj.onc.1210508] [Citation(s) in RCA: 484] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epithelial to mesenchymal transition (EMT) is implicated in the progression of primary tumours towards metastasis and is likely caused by a pathological activation of transcription factors regulating EMT in embryonic development. To analyse EMT-causing pathways in tumourigenesis, we identified transcriptional targets of the E-cadherin repressor ZEB1 in invasive human cancer cells. We show that ZEB1 repressed multiple key determinants of epithelial differentiation and cell-cell adhesion, including the cell polarity genes Crumbs3, HUGL2 and Pals1-associated tight junction protein. ZEB1 associated with their endogenous promoters in vivo, and strongly repressed promotor activities in reporter assays. ZEB1 downregulation in undifferentiated cancer cells by RNA interference was sufficient to upregulate expression of these cell polarity genes on the RNA and protein level, to re-establish epithelial features and to impair cell motility in vitro. In human colorectal cancer, ZEB1 expression was limited to the tumour-host interface and was accompanied by loss of intercellular adhesion and tumour cell invasion. In invasive ductal and lobular breast cancer, upregulation of ZEB1 was stringently coupled to cancer cell dedifferentiation. Our data show that ZEB1 represents a key player in pathologic EMTs associated with tumour progression.
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Affiliation(s)
- K Aigner
- Max F Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
| | - B Dampier
- Department of Obstetrics and Gynecology, Medical University Vienna, Vienna, Austria
| | - L Descovich
- Research Institute of Molecular Pathology, Vienna, Austria
| | - M Mikula
- Research Institute of Molecular Pathology, Vienna, Austria
| | - A Sultan
- Max F Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
| | - M Schreiber
- Department of Obstetrics and Gynecology, Medical University Vienna, Vienna, Austria
| | - W Mikulits
- Department of Medicine I, Institute of Cancer Research, Medical University Vienna, Vienna, Austria
| | - T Brabletz
- Department of Visceral and General Surgery, Albert-Ludwigs-University, Freiburg, Germany
| | - D Strand
- First Department of Internal Medicine, Johannes Gutenberg University, Mainz, Germany
| | - P Obrist
- Pathology Laboratories Obrist and Brunhuber OEG, Zams, Austria
| | | | - N Schweifer
- Boehringer-Ingelheim Austria, Vienna, Austria
| | | | - H Beug
- Research Institute of Molecular Pathology, Vienna, Austria
| | - R Foisner
- Max F Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
| | - A Eger
- Max F Perutz Laboratories, Department of Medical Biochemistry, Medical University Vienna, Vienna, Austria
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Tu JL, Chin KH, Wang AHJ, Chou SH. The crystallization of apo-form UMP kinase from Xanthomonas campestris is significantly improved in a strong magnetic field. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:438-42. [PMID: 17565191 PMCID: PMC2335002 DOI: 10.1107/s1744309107018787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 04/16/2007] [Indexed: 05/15/2023]
Abstract
Bacterial UMP kinases (UMPKs) are crucial enzymes that are responsible for microbial UTP biosynthesis. Interestingly, eukaryotic and prokaryotic cells use different enzymes for UMP-phosphorylation reactions. Prokaryotic UMPKs are thus believed to be potential targets for antimicrobial drug development. Here, the cloning, expression and crystallization of SeMet-substituted XC1936, a bacterial UMPK from Xanthomonas campestris pathovar campestris, are reported. The crystallization of the apo-form UMPK was found to be significantly improved in a strong magnetic field; the crystals diffracted to a resolution of 2.35 A, a dramatic improvement over the original value of 3.6 A. Preliminary structural analyses of apo-form XC1936 using crystals grown in a strong magnetic field clearly reveal well defined loop regions involved in substrate-analogue binding that were previously not visible. Crystallization in a strong magnetic field thus was found to be indispensable in determining the flexible region of the XC1936 UMPK structure.
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Affiliation(s)
- Jhe-Le Tu
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Ko-Hsin Chin
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
- National Chung-Hsing University Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
- Core Facility for Protein Crystallography, Academia Sinica, Nankang, Taipei, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
- National Chung-Hsing University Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
- Correspondence e-mail:
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35
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Affiliation(s)
- Christopher Baum
- Department of Experimental Hematology, Hannover Medical School, Hannover, Germany. baum.christopher@mh-hannover
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Sato T, Neschadim A, Konrad M, Fowler DH, Lavie A, Medin JA. Engineered human tmpk/AZT as a novel enzyme/prodrug axis for suicide gene therapy. Mol Ther 2007; 15:962-70. [PMID: 17375075 DOI: 10.1038/mt.sj.6300122] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Gene therapy and stem cell transplantation safety could be enhanced by control over the fate of therapeutic cells. Suicide gene therapy uses enzymes that convert prodrugs to cytotoxic entities; however, heterologous moieties with poor kinetics are employed. We describe a novel enzyme/prodrug combination for selectively inducing apoptosis in lentiviral vector-transduced cells. Rationally designed variants of human thymidylate kinase (tmpk) that effectively phosphorylate 3'-azido-3'-deoxythymidine (AZT) were efficiently delivered. Transduced Jurkat cell lines were eliminated by AZT. We demonstrate that this schema targeted both dividing and non-dividing cells, with a novel killing mechanism involving apoptosis induction via disruption of the mitochondrial inner membrane potential and activation of caspase-3. Primary murine and human T cells were also transduced and responded to AZT. Furthermore, low-dose AZT administration to non-obese diabetic/severe combined immunodeficiency (NOD/SCID) mice injected with transduced K562 cells suppressed tumor growth. This novel suicide gene therapy approach can thus be integrated as a safety switch into therapeutic vectors.
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Affiliation(s)
- Takeya Sato
- Division of Stem Cell and Developmental Biology, Ontario Cancer Institute, Toronto, Ontario, Canada
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37
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Vernejoul F, Ghénassia L, Souque A, Lulka H, Drocourt D, Cordelier P, Pradayrol L, Pyronnet S, Buscail L, Tiraby G. Gene therapy based on gemcitabine chemosensitization suppresses pancreatic tumor growth. Mol Ther 2006; 14:758-67. [PMID: 17000136 DOI: 10.1016/j.ymthe.2006.07.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 07/07/2006] [Accepted: 07/17/2006] [Indexed: 11/16/2022] Open
Abstract
Excepting surgical resection, there is no efficient treatment against pancreatic cancer. The chemotherapeutic agent gemcitabine improves the patient's clinical status but survival is not prolonged. The aim of this study was to design a new strategy to render gemcitabine more efficient in the treatment of pancreatic cancer using gene therapy. We have generated a fusion gene (DCK::UMK) combining deoxycytidine kinase (DCK) and uridine monophosphate kinase (UMK), which converts gemcitabine into its toxic phosphorylated metabolite. Antitumor effects of DCK::UMK gene expression were tested in vitro and in vivo in an orthotopic transplantable model of pancreatic cancer established in hamsters. DCK::UMK sensitizes pancreatic cancer cells to gemcitabine by reducing dramatically both in vitro cell viability and in vivo tumor volume. We found that in vivo expression of DCK::UMK resulted in an antitumor bystander effect due to apoptosis of untransduced cells. In vivo intratumoral gene transfer of DCK::UMK using the synthetic carrier PEI induced a potent tumor regression. Taken together, the results show that the fusion gene DCK::UMK sensitizes pancreatic cancer cells to gemcitabine treatment to induce cell death by apoptosis and tumor regression. Intratumoral delivery of the DCK::UMK gene in combination with gemcitabine might be of high interest for pancreatic cancer management.
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Affiliation(s)
- Fabienne Vernejoul
- INSERM U531, Institut Louis Bugnard IFR31, Centre Hospitalier Universitaire Rangueil, 31403 Toulouse Cedex 4, France
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van Rossum AGSH, Aartsen WM, Meuleman J, Klooster J, Malysheva A, Versteeg I, Arsanto JP, Le Bivic A, Wijnholds J. Pals1/Mpp5 is required for correct localization of Crb1 at the subapical region in polarized Muller glia cells. Hum Mol Genet 2006; 15:2659-72. [PMID: 16885194 DOI: 10.1093/hmg/ddl194] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mutations in the human Crumbs homologue-1 (CRB1) gene cause retinal diseases including Leber's congenital amaurosis (LCA) and retinitis pigmentosa type 12. The CRB1 transmembrane protein localizes at a subapical region (SAR) above intercellular adherens junctions between photoreceptor and Müller glia (MG) cells. We demonstrate that the Crb1-/- phenotype, as shown in Crb1-/- mice, is accelerated and intensified in primary retina cultures. Immuno-electron microscopy showed strong Crb1 immunoreactivity at the SAR in MG cells but barely in photoreceptor cells, whereas Crb2, Crb3, Patj, Pals1 and Mupp1 were present in both cell types. Human CRB1, introduced in MG cells in Crb1-/- primary retinas, was targeted to the SAR. RNA interference-induced silencing of the Crb1-interacting-protein Pals1 (protein associated with Lin7; Mpp5) in MG cells resulted in loss of Crb1, Crb2, Mupp1 and Veli3 protein localization and partial loss of Crb3. We conclude that Pals1 is required for correct localization of Crb family members and its interactors at the SAR of polarized MG cells.
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Affiliation(s)
- Agnes G S H van Rossum
- Department of Neuromedical Genetics, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
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Kempkens O, Médina E, Fernandez-Ballester G, Ozüyaman S, Le Bivic A, Serrano L, Knust E. Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6. Eur J Cell Biol 2006; 85:753-67. [PMID: 16697075 DOI: 10.1016/j.ejcb.2006.03.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 03/06/2006] [Accepted: 03/07/2006] [Indexed: 12/28/2022] Open
Abstract
Formation of multiprotein complexes is a common theme to pattern a cell, thereby generating spatially and functionally distinct entities at specialised regions. Central components of these complexes are scaffold proteins, which contain several protein-protein interaction domains and provide a platform to recruit a variety of additional components. There is increasing evidence that protein complexes are dynamic structures and that their components can undergo various interactions depending on the cellular context. However, little is known so far about the factors regulating this behaviour. One evolutionarily conserved protein complex, which can be found both in Drosophila and mammalian epithelial cells, is composed of the transmembrane protein Crumbs/Crb3 and the scaffolding proteins Stardust/Pals1 and DPATJ/PATJ, respectively, and localises apically to the zonula adherens. Here we show by in vitro analysis that, similar as in vertebrates, the single PDZ domain of Drosophila DmPar-6 can bind to the four C-terminal amino acids (ERLI) of the transmembrane protein Crumbs. To further evaluate the binding capability of Crumbs to DmPar-6 and the MAGUK protein Stardust, analysis of the PDZ structural database and modelling of the interactions between the C-terminus of Crumbs and the PDZ domains of these two proteins were performed. The results suggest that both PDZ domains bind Crumbs with similar affinities. These data are supported by quantitative yeast two-hybrid interactions. In vivo analysis performed in cell cultures and in the Drosophila embryo show that the cytoplasmic domain of Crumbs can recruit DmPar-6 and DaPKC to the plasma membrane. The data presented here are discussed with respect to possible dynamic interactions between these proteins.
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Affiliation(s)
- Ozlem Kempkens
- Institut für Genetik, Heinrich-Heine Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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Abstract
This work reports the construction of Escherichia coli in-frame deletion strains of tmk, which encodes thymidylate kinase, Tmk. The tmk gene is located at the third position of a putative five-gene operon at 24.9 min on the E. coli chromosome, which comprises the genes pabC, yceG, tmk, holB, and ycfH. To avoid potential polar effects on downstream genes of the operon, as well as recombination with plasmid-encoded tmk, the tmk gene was replaced by the kanamycin resistance gene kka1, encoding amino glycoside 3'-phosphotransferase kanamycin kinase. The kanamycin resistance gene is expressed under the control of the natural promoter(s) of the putative operon. The E. coli tmk gene is essential under any conditions tested. To show functional complementation in bacteria, the E. coli tmk gene was replaced by thymidylate kinases of bacteriophage T4 gp1, E. coli tmk, Saccharomyces cerevisiae cdc8, or the Homo sapiens homologue, dTYMK. Growth of these transgenic E. coli strains is completely dependent on thymidylate kinase activities of various origin expressed from plasmids. The substitution constructs show no polar effects on the downstream genes holB and ycfH with respect to cell viability. The presented transgenic bacteria could be of interest for testing of thymidylate kinase-specific phosphorylation of nucleoside analogues that are used in therapies against cancer and infectious diseases.
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Affiliation(s)
- David-Nicolas Chaperon
- Département de Biochimie Médicale, Centre Médical Universitaire, Université de Genève, CH-1211 Geneva, Switzerland.
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Kotaka M, Dhaliwal B, Ren J, Nichols CE, Angell R, Lockyer M, Hawkins AR, Stammers DK. Structures of S. aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding. Protein Sci 2006; 15:774-84. [PMID: 16522804 PMCID: PMC2242479 DOI: 10.1110/ps.052002406] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to human health, particularly through hospital acquired infection. The spread of MRSA means that novel targets are required to develop potential inhibitors to combat infections caused by such drug-resistant bacteria. Thymidylate kinase (TMK) is attractive as an antibacterial target as it is essential for providing components for DNA synthesis. Here, we report crystal structures of unliganded and thymidylate-bound forms of S. aureus thymidylate kinase (SaTMK). His-tagged and untagged SaTMK crystallize with differing lattice packing and show variations in conformational states for unliganded and thymidylate (TMP) bound forms. In addition to open and closed forms of SaTMK, an intermediate conformation in TMP binding is observed, in which the site is partially closed. Analysis of these structures indicates a sequence of events upon TMP binding, with helix alpha3 shifting position initially, followed by movement of alpha2 to close the substrate site. In addition, we observe significant conformational differences in the TMP-binding site in SaTMK as compared to available TMK structures from other bacterial species, Escherichia coli and Mycobacterium tuberculosis as well as human TMK. In SaTMK, Arg 48 is situated at the base of the TMP-binding site, close to the thymine ring, whereas a cis-proline occupies the equivalent position in other TMKs. The observed TMK structural differences mean that design of compounds highly specific for the S. aureus enzyme looks possible; such inhibitors could minimize the transfer of drug resistance between different bacterial species.
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Affiliation(s)
- Masayo Kotaka
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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Johansson M, Amiri M, Karlsson A. Phosphorylation of 9-beta-D-arabinofuranosylguanine monophosphate by Drosophila melanogaster guanylate kinase. Biochem Pharmacol 2005; 70:987-92. [PMID: 16084842 DOI: 10.1016/j.bcp.2005.06.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 06/14/2005] [Accepted: 06/15/2005] [Indexed: 11/18/2022]
Abstract
Nucleoside monophosphate kinases have an important role in the synthesis of nucleotides that are required for cellular metabolism. These enzymes are also important for the phosphorylation of nucleoside- and nucleotide analogs used in cancer and anti-viral therapy. We report the cDNA cloning and characterization of a 23 kDa guanylate kinase from Drosophila melanogaster (Dm-GUK). The predicted amino acid sequence was 58% identical to the human guanylate kinase and the enzyme was shown to phosphorylate GMP and dGMP with ATP as phosphate donor. The monophosphates of the deoxyguanosine analogs 2',2'-difluorodeoxyguanosine (dFdG) and 9-beta-D-arabinofuranosylguanine (araG) were also shown to be phosphorylated by the enzyme. We used the enzyme to reconstitute the complete in vitro three-step phosphorylation pathway for the conversion of dGuo and araG to the corresponding triphosphates.
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Affiliation(s)
- Magnus Johansson
- Karolinska Institute, Department of Laboratory Medicine, Novum, S-141 57 Stockholm, Sweden
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43
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Hible G, Renault L, Schaeffer F, Christova P, Zoe Radulescu A, Evrin C, Gilles AM, Cherfils J. Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. J Mol Biol 2005; 352:1044-59. [PMID: 16140325 DOI: 10.1016/j.jmb.2005.07.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 07/11/2005] [Accepted: 07/14/2005] [Indexed: 10/25/2022]
Abstract
Guanosine monophosphate kinases (GMPKs), which catalyze the phosphorylation of GMP and dGMP to their diphosphate form, have been characterized as monomeric enzymes in eukaryotes and prokaryotes. Here, we report that GMPK from Escherichia coli (ecGMPK) assembles in solution and in the crystal as several different oligomers. Thermodynamic analysis of ecGMPK using differential scanning calorimetry shows that the enzyme is in equilibrium between a dimer and higher order oligomers, whose relative amounts depend on protein concentration, ionic strength, and the presence of ATP. Crystallographic structures of ecGMPK in the apo, GMP and GDP-bound forms were solved at 3.2A, 2.9A and 2.4A resolution, respectively. ecGMPK forms a hexamer with D3 symmetry in all crystal forms, in which the two nucleotide-binding domains are able to undergo closure comparable to that of monomeric GMPKs. The 2-fold and 3-fold interfaces involve a 20-residue C-terminal extension and a sequence signature, respectively, that are missing from monomeric eukaryotic GMPKs, explaining why ecGMPK forms oligomers. These signatures are found in GMPKs from proteobacteria, some of which are human pathogens. GMPKs from these bacteria are thus likely to form the same quaternary structures. The shift of the thermodynamic equilibrium towards the dimer at low ecGMPK concentration together with the observation that inter-subunit interactions partially occlude the ATP-binding site in the hexameric structure suggest that the dimer may be the active species at physiological enzyme concentration.
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Affiliation(s)
- Guillaume Hible
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette 91198, France
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Marco-Marín C, Gil-Ortiz F, Rubio V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J Mol Biol 2005; 352:438-54. [PMID: 16095620 DOI: 10.1016/j.jmb.2005.07.045] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2005] [Revised: 07/12/2005] [Accepted: 07/14/2005] [Indexed: 11/21/2022]
Abstract
UMP kinase (UMPK), the enzyme responsible for microbial UMP phosphorylation, plays a key role in pyrimidine nucleotide biosynthesis, regulating this process via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). We present crystal structures of Pyrococcus furiosus UMPK, free or complexed with AMPPNP or AMPPNP and UMP, at 2.4 A, 3 A and 2.55 A resolution, respectively, providing a true snapshot of the catalytically competent bisubstrate complex. The structure proves that UMPK does not resemble other nucleoside monophosphate kinases, including the UMP/CMP kinase found in animals, and thus UMPK may be a potential antimicrobial target. This enzyme has a homohexameric architecture centred around a hollow nucleus, and is organized as a trimer of dimers. The UMPK polypeptide exhibits the amino acid kinase family (AAKF) fold that has been reported in carbamate kinase and acetylglutamate kinase. Comparison with acetylglutamate kinase reveals that the substrates bind within each subunit at equivalent, adequately adapted sites. The UMPK structure contains two bound Mg ions, of which one helps stabilize the transition state, thus having the same catalytic role as one lysine residue found in acetylglutamate kinase, which is missing from P.furiosus UMPK. Relative to carbamate kinase and acetylglutamate kinase, UMPK presents a radically different dimer architecture, lacking the characteristic 16-stranded beta-sheet backbone that was considered a signature of AAKF enzymes. Its hexameric architecture, also a novel trait, results from equatorial contacts between the A and B subunits of adjacent dimers combined with polar contacts between A or B subunits, and may be required for the UMPK regulatory functions, such as gene regulation, proposed here to be mediated by hexamer-hexamer interactions with the DNA-binding protein PepA.
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Affiliation(s)
- Clara Marco-Marín
- Instituto de Biomedicina de Valencia (IBV-CSIC), Jaume Roig 11,Valencia 46010, Spain
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45
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Holzer GW, Mayrhofer J, Gritschenberger W, Falkner FG. Dominant negative selection of vaccinia virus using a thymidine kinase/thymidylate kinase fusion gene and the prodrug azidothymidine. Virology 2005; 337:235-41. [PMID: 15882885 DOI: 10.1016/j.virol.2005.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 03/25/2005] [Accepted: 04/07/2005] [Indexed: 10/25/2022]
Abstract
The Escherichia coli thymidine kinase/thymidylate kinase (tk/tmk) fusion gene encodes an enzyme that efficiently converts the prodrug 3'-azido-2',3'-dideoxythymidine (AZT) into its toxic triphosphate derivative, a substance which stops DNA chain elongation. Integration of this marker gene into vaccinia virus that normally is not inhibited by AZT allowed the establishment of a powerful selection procedure for recombinant viruses. In contrast to the conventional vaccinia thymidine kinase (tk) selection that is performed in tk-negative cell lines, AZT selection can be performed in normal (tk-positive) cell lines. The technique is especially useful for the generation of replication-deficient vaccinia viruses and may also be used for gene knock-out studies of essential vaccinia genes.
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Affiliation(s)
- Georg W Holzer
- Baxter BioScience/Vaccines, Biomedical Research Center, Uferstrasse 15, A-2304 Orth/Donau, Austria
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Patrie KM. Identification and characterization of a novel tight junction-associated family of proteins that interacts with a WW domain of MAGI-1. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 2005; 1745:131-44. [PMID: 16019084 DOI: 10.1016/j.bbamcr.2005.05.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2004] [Revised: 05/24/2005] [Accepted: 05/25/2005] [Indexed: 10/25/2022]
Abstract
The membrane-associated guanylate kinase protein, MAGI-1, has been shown to be a component of epithelial tight junctions in both Madin-Darby canine kidney cells and in intestinal epithelium. Because we have previously observed MAGI-1 expression in glomerular visceral epithelial cells (podocytes) of the kidney, we screened a glomerular cDNA library to identify the potential binding partners of MAGI-1 and isolated a partial cDNA encoding a novel protein. The partial cDNA exhibited a high degree of identity to an uncharacterized human cDNA clone, KIAA0989, which encodes a protein of 780 amino acids and contains a predicted coiled-coil domain in the middle of the protein. In vitro binding assays using the partial cDNA as a GST fusion protein confirm the binding to full-length MAGI-1 expressed in HEK293 cells, as well as endogenous MAGI-1, and also identified the first WW domain of MAGI-1 as the domain responsible for binding to this novel protein. Although a conventional PPxY binding motif for WW domains was not present in the partial cDNA clone, a variant WW binding motif was identified, LPxY, and found to be necessary for interacting with MAGI-1. When expressed in Madin-Darby canine kidney cells, the full-length novel protein was found to colocalize with MAGI-1 at the tight junction of these cells and the coiled-coil domain was found to be necessary for this localization. Because of its interaction with MAGI-1 and its localization to cell-cell junctions, this novel protein has been given the name MAGI-1-associated coiled-coil tight junction protein (MASCOT).
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Affiliation(s)
- Kevin M Patrie
- Department of Internal Medicine, University of Michigan, 1580 MSRB II, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0676, USA.
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Kantardzhieva A, Gosens I, Alexeeva S, Punte IM, Versteeg I, Krieger E, Neefjes-Mol CA, den Hollander AI, Letteboer SJF, Klooster J, Cremers FPM, Roepman R, Wijnholds J. MPP5 Recruits MPP4 to the CRB1 Complex in Photoreceptors. ACTA ACUST UNITED AC 2005; 46:2192-201. [PMID: 15914641 DOI: 10.1167/iovs.04-1417] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PURPOSE Mutations in the human Crumbs homologue 1 (CRB1) gene are a frequent cause of Leber congenital amaurosis (LCA) and various forms of retinitis pigmentosa. CRB1 is thought to organize an intracellular protein scaffold in the retina that is involved in photoreceptor polarity. This study was focused on the identification, subcellular localization, and binding characteristics of a novel member of the protein scaffold connected to CRB1. METHODS To dissect the protein scaffold connected to CRB1, the yeast two-hybrid approach was used to screen for interacting proteins. Glutathione S-transferase (GST) pull-down analysis and immunoprecipitation were used to verify protein-protein interactions. The subcellular localization of the proteins was visualized by immunohistochemistry and confocal microscopy on human retinas and immunoelectron microscopy on mouse retinas. RESULTS A novel member of the scaffold connected to CRB1, called membrane palmitoylated protein (MPP) subfamily member 4 (MPP4), a membrane-associated guanylate kinase (MAGUK) protein, was identified. MPP4 was found to exist in a complex with CRB1 through direct interaction with the MPP subfamily member MPP5 (PALS1). 3D homology modeling provided evidence for a mechanism that regulates the recruitment of both homo- and heterodimers of MPP4 and -5 proteins to the complex. Localization studies in the retina showed that CRB1, MPP5, and MPP4 colocalize at the outer limiting membrane (OLM). CONCLUSIONS These data imply that MPP4 and -5 have a role in photoreceptor polarity and, by association with CRB1, pinpoint the cognate genes as functional candidate genes for inherited retinopathies.
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Abstract
Tissue development, differentiation, and physiology require specialized cellular adhesion and signal transduction at sites of cell-cell contact. Scaffolding proteins that tether adhesion molecules, receptors, and intracellular signaling enzymes organize macromolecular protein complexes at cellular junctions to integrate these functions. One family of such scaffolding proteins is the large group of membrane-associated guanylate kinases (MAGUKs). Genetic studies have highlighted critical roles for MAGUK proteins in the development and physiology of numerous tissues from a variety of metazoan organisms. Mutation of Drosophila discs large (dlg) disrupts epithelial septate junctions and causes overgrowth of imaginal discs. Similarly, mutation of lin-2, a related MAGUK in Caenorhabditis elegans, blocks vulval development, and mutation of the postsynaptic density protein PSD-95 impairs synaptic plasticity in mammalian brain. These diverse roles are explained by recent biochemical and structural analyses of MAGUKs, which demonstrate their capacity to assemble well--efined--yet adaptable--protein complexes at cellular junctions.
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Affiliation(s)
- Lars Funke
- Department of Physiology, University of California at San Francisco, California 94143, USA.
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49
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Fassy F, Krebs O, Lowinski M, Ferrari P, Winter J, Collard-Dutilleul V, Salahbey Hocini K. UMP kinase from Streptococcus pneumoniae: evidence for co-operative ATP binding and allosteric regulation. Biochem J 2005; 384:619-27. [PMID: 15324307 PMCID: PMC1134148 DOI: 10.1042/bj20040440] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
UMP kinase catalyses the phosphorylation of UMP by ATP to yield UDP and ADP. In prokaryotes, the reaction is carried out by a hexameric enzyme, activated by GTP and inhibited by UTP. In the present study, Streptococcus pneumoniae UMP kinase was studied as a target for antibacterial research and its interest was confirmed by the demonstration of the essentiality of the gene for cell growth. In the presence of MnCl2 or MgCl2, the saturation kinetics of recombinant purified UMP kinase was hyperbolic for UMP (K(m)=0.1 mM) and sigmoidal for ATP (the substrate concentration at half-saturation S0.5=9.4+/-0.7 mM and n=1.9+/-0.1 in the presence of MgCl2). GTP increased the affinity for ATP and decreased the Hill coefficient (n). UTP decreased the affinity for ATP and only slightly increased the Hill coefficient. The kcat (175+/-13 s(-1) in the presence of MgCl2) was not affected by the addition of GTP or UTP, whose binding site was shown to be different from the active site. The hydrodynamic radius of the protein similarly decreased in the presence of ATP or GTP. There was a shift in the pH dependence of the activity when the ATP concentration was switched from low to high. These results support the hypothesis of an allosteric transition from a conformation with low affinity for ATP to a form with high affinity, which would be induced by the presence of ATP or GTP.
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Affiliation(s)
- Florence Fassy
- Aventis Pharma, 13 quai Jules Guesde, 94403 Vitry sur Seine Cedex, France.
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Briozzo P, Evrin C, Meyer P, Assairi L, Joly N, Barzu O, Gilles AM. PTEN, but not SHIP2, suppresses insulin signaling through the phosphatidylinositol 3-kinase/Akt pathway in 3T3-L1 adipocytes. J Biol Chem 2005; 280:25533-40. [PMID: 15857829 DOI: 10.1074/jbc.m501849200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glucose homeostasis is controlled by insulin in part through the stimulation of glucose transport in muscle and fat cells. This insulin signaling pathway requires phosphatidylinositol (PI) 3-kinase-mediated 3'-polyphosphoinositide generation and activation of Akt/protein kinase B. Previous experiments using dominant negative constructs and gene ablation in mice suggested that two phosphoinositide phosphatases, SH2 domain-containing inositol 5'-phosphatase 2 (SHIP2) and phosphatase and tensin homolog deleted on chromosome 10 (PTEN) negatively regulate this insulin signaling pathway. Here we directly tested this hypothesis by selectively inhibiting the expression of SHIP2 or PTEN in intact cultured 3T3-L1 adipocytes through the use of short interfering RNA (siRNA). Attenuation of PTEN expression by RNAi markedly enhanced insulin-stimulated Akt and glycogen synthase kinase 3alpha (GSK-3alpha) phosphorylation, as well as deoxyglucose transport in 3T3-L1 adipocytes. In contrast, depletion of SHIP2 protein by about 90% surprisingly failed to modulate these insulin-regulated events under identical assay conditions. In control studies, no diminution of insulin signaling to the mitogen-activated protein kinases Erk1 and Erk2 was observed when either PTEN or SHIP2 were depleted. Taken together, these results demonstrate that endogenous PTEN functions as a suppressor of insulin signaling to glucose transport through the PI 3-kinase pathway in cultured 3T3-L1 adipocytes.
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Affiliation(s)
- Pierre Briozzo
- Unité de Chimie Biologique, UMR 206 Institut National de la Recherche Agronomique, Institut National Agronomique Paris-Grignon, 78850 Thiverval-Grignon, URA 2171 CNRS, Institut Pasteur, 75724 Paris Cedex 15.
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