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Hawley SA, Russell FM, Hardie DG. AMP-activated protein kinase can be allosterically activated by ADP but AMP remains the key activating ligand. Biochem J 2024; 481:587-599. [PMID: 38592738 PMCID: PMC11088877 DOI: 10.1042/bcj20240082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/10/2024]
Abstract
The AMP-activated protein kinase (AMPK) is a sensor of cellular energy status. When activated by increases in ADP:ATP and/or AMP:ATP ratios (signalling energy deficit), AMPK acts to restore energy balance. Binding of AMP to one or more of three CBS repeats (CBS1, CBS3, CBS4) on the AMPK-γ subunit activates the kinase complex by three complementary mechanisms: (i) promoting α-subunit Thr172 phosphorylation by the upstream kinase LKB1; (ii) protecting against Thr172 dephosphorylation; (iii) allosteric activation. Surprisingly, binding of ADP has been reported to mimic the first two effects, but not the third. We now show that at physiologically relevant concentrations of Mg.ATP2- (above those used in the standard assay) ADP binding does cause allosteric activation. However, ADP causes only a modest activation because (unlike AMP), at concentrations just above those where activation becomes evident, ADP starts to cause competitive inhibition at the catalytic site. Our results cast doubt on the physiological relevance of the effects of ADP and suggest that AMP is the primary activator in vivo. We have also made mutations to hydrophobic residues involved in binding adenine nucleotides at each of the three γ subunit CBS repeats of the human α2β2γ1 complex and examined their effects on regulation by AMP and ADP. Mutation of the CBS3 site has the largest effects on all three mechanisms of AMP activation, especially at lower ATP concentrations, while mutation of CBS4 reduces the sensitivity to AMP. All three sites appear to be required for allosteric activation by ADP.
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Affiliation(s)
- Simon A. Hawley
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Fiona M. Russell
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - D. Grahame Hardie
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
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2
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Payá G, Bautista V, Pastor-Soler S, Camacho M, Esclapez J, Bonete MJ. Analysis of Lsm Protein-Mediated Regulation in the Haloarchaeon Haloferax mediterranei. Int J Mol Sci 2024; 25:580. [PMID: 38203750 PMCID: PMC10779274 DOI: 10.3390/ijms25010580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq found in the Eukarya, Archaea, and Bacteria domains. Archaeal Lsm proteins have been shown to bind sRNAs and are probably involved in various cellular processes, suggesting a similar function in regulating sRNAs by Hfq in bacteria. Moreover, archaeal Lsm proteins probably represent the ancestral Lsm domain from which eukaryotic Sm proteins have evolved. In this work, Haloferax mediterranei was used as a model organism because it has been widely used to investigate the nitrogen cycle and its regulation in Haloarchaea. Predicting this protein's secondary and tertiary structures has resulted in a three-dimensional model like the solved Lsm protein structure of Archaeoglobus fulgidus. To obtain information on the oligomerization state of the protein, homologous overexpression and purification by means of molecular exclusion chromatography have been performed. The results show that this protein can form hexameric complexes, which can aggregate into 6 or 12 hexameric rings depending on the NaCl concentration and without RNA. In addition, the study of transcriptional expression via microarrays has allowed us to obtain the target genes regulated by the Lsm protein under nutritional stress conditions: nitrogen or carbon starvation. Microarray analysis has shown the first universal stress proteins (USP) in this microorganism that mediate survival in situations of nitrogen deficiency.
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Affiliation(s)
| | | | | | | | | | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; (G.P.); (V.B.); (S.P.-S.); (M.C.); (J.E.)
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3
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Liu CY, Al-Ward H, Liu N, Mekontso FN, Chen W, Gao W, Zhang C, Murshed A, Yu ZR, Fan O, Sun YE, Xu H. The Role of Cystathionine-β-Synthase, H 2S, and miRNA-377 in Hypoxic-Ischemic Encephalopathy: Insights from Human and Animal Studies. J Mol Neurosci 2023; 73:921-931. [PMID: 37864623 DOI: 10.1007/s12031-023-02165-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 10/23/2023]
Abstract
We aimed to investigate the mechanism underlying the roles of miRNA-377, Cystathionine-β-synthase (CBS), and hydrogen sulfide (H2S) in the development of hypoxic-ischemic encephalopathy (HIE). We investigated the relationship between CBS, H2S, and miR-377 in both humans with HIE and animals with hypoxic-ischemic insult. An animal model of fetal rats with hypoxic-ischemic brain injury was established, and the fetal rats were randomly assigned to control and hypoxic-ischemic groups for 15 min (mild) and 30 min (moderate) groups. Human samples were collected from children diagnosed with HIE. Healthy or non-neurological disease children were selected as the control group. Hematoxylin-eosin (HE) staining, quantitative real-time polymerase chain reaction (qRT-PCR), enzyme-linked immunosorbent assay (ELISA), and western blot were used to conduct this study. Hypoxia-ischemia induced pathological alterations in brain tissue changes were more severe in groups with severe hypoxic insult. miRNA-377 expression levels were upregulated in brain tissue and serum of fetal rats and human samples with HIE compared to controls. Conversely, CBS and H2S expression levels were significantly decreased in both human and animal samples compared to controls. Our findings suggest that CBS is a target gene of miR-377 which may contribute to the development of HIE by regulating CBS/H2S. H2S has a protective effect against hypoxic damage in brain tissue. The study provides new insights into the potential mechanisms underlying the protective role of H2S in hypoxic brain damage and may contribute to the development of novel therapies for HIE.
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Affiliation(s)
- Chun-Yang Liu
- School of Medicine, AnKang University, Ankang, Shanxi Province, China
| | - Hisham Al-Ward
- School of Medicine, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Ning Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jiamusi University, Jiamusi, China
| | | | - Wei Chen
- School of Medicine, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Wenxia Gao
- School of Medicine, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Chunxue Zhang
- School of Medicine, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Abduh Murshed
- Department of Clinical Laboratory, Shanghai 10Th People's Hospital of Tongji, University, Shanghai, China
| | - Zi-Rui Yu
- Huashan Hospital, Fudan University, Shanghai, China
| | - Orion Fan
- School of Medicine, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Yi Eve Sun
- School of Medicine, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai, China.
| | - Hui Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Jiamusi University, Jiamusi, China.
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Li Y, Zhang L, Shen Y, Peng L, Gao F. CBSX2 is required for the efficient oxidation of chloroplast redox-regulated enzymes in darkness. PLANT DIRECT 2023; 7:e542. [PMID: 38028645 PMCID: PMC10643993 DOI: 10.1002/pld3.542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/10/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
Thiol/disulfide-based redox regulation in plant chloroplasts is essential for controlling the activity of target proteins in response to light signals. One of the examples of such a role in chloroplasts is the activity of the chloroplast ATP synthase (CFoCF1), which is regulated by the redox state of the CF1γ subunit and involves two cysteines in its central domain. To investigate the mechanism underlying the oxidation of CF1γ and other chloroplast redox-regulated enzymes in the dark, we characterized the Arabidopsis cbsx2 mutant, which was isolated based on its altered NPQ (non-photochemical quenching) induction upon illumination. Whereas in dark-adapted WT plants CF1γ was completely oxidized, a small amount of CF1γ remained in the reduced state in cbsx2 under the same conditions. In this mutant, reduction of CF1γ was not affected in the light, but its oxidation was less efficient during a transition from light to darkness. The redox states of the Calvin cycle enzymes FBPase and SBPase in cbsx2 were similar to those of CF1γ during light/dark transitions. Affinity purification and subsequent analysis by mass spectrometry showed that the components of the ferredoxin-thioredoxin reductase/thioredoxin (FTR-Trx) and NADPH-dependent thioredoxin reductase (NTRC) systems as well as several 2-Cys peroxiredoxins (Prxs) can be co-purified with CBSX2. In addition to the thioredoxins, yeast two-hybrid analysis showed that CBSX2 also interacts with NTRC. Taken together, our results suggest that CBSX2 participates in the oxidation of the chloroplast redox-regulated enzymes in darkness, probably through regulation of the activity of chloroplast redox systems in vivo.
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Affiliation(s)
- Yonghong Li
- College of Biology and Brewing EngineeringTaiShan UniversityTaianChina
| | - Lin Zhang
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yurou Shen
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Lianwei Peng
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Fudan Gao
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life SciencesShanghai Normal UniversityShanghaiChina
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life SciencesShanghai Normal UniversityShanghaiChina
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Sakti DH, Cornish EE, Nash BM, Jamieson RV, Grigg JR. IMPDH1-associated autosomal dominant retinitis pigmentosa: natural history of novel variant Lys314Gln and a comprehensive literature search. Ophthalmic Genet 2023; 44:437-455. [PMID: 37259572 DOI: 10.1080/13816810.2023.2215310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Mutations in the inosine monophosphate dehydrogenase 1 gene (IMPDH1) are causative for RP10 autosomal dominant retinitis pigmentosa (adRP). This study reports a novel variant in a family with IMPDH1-associated retinopathy. We also performed a comprehensive review of all reported IMPDH1 disease causing variants with their associated phenotype. MATERIALS AND METHODS Multimodal imaging and functional studies documented the phenotype including best-corrected visual acuity (BCVA), fundus photograph, fundus autofluorescence (FAF), full field electroretinogram (ffERG), optical coherence tomography (OCT) and visual field (VF) data were collected. A literature search was performed in the PubMed and LOVD repositories. RESULTS We report 3 cases from a 2-generation family with a novel heterozygous likely pathogenic variant p. (Lys314Gln) (exon 10). The ophthalmic phenotype showed diffuse outer retinal atrophy with mild pigmentary changes with sparse pigmentary changes. FAF showed early macular involvement with macular hyperautofluorescence (hyperAF) surrounded by hypoAF. Foveal ellipsoid zone island can be found in the youngest patient but not in the older ones. The literature review identified a further 56 heterozygous, 1 compound heterozygous, and 2 homozygous variant. The heterozygous group included 43 missense, 3 in-frame, 1 nonsense, 2 frameshift, 1 synonymous, and 6 intronic variants. Exon 10 was noted as a hotspot harboring 18 variants. CONCLUSIONS We report a novel IMPDH1 variant. IMPDH1-associated retinopathy presents most frequently in the first decade of life with early macular involvement.
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Affiliation(s)
- Dhimas H Sakti
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elisa E Cornish
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - John R Grigg
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
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Gedeon A, Ayoub N, Brûlé S, Raynal B, Karimova G, Gelin M, Mechaly A, Haouz A, Labesse G, Munier‐Lehmann H. Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases. Protein Sci 2023; 32:e4703. [PMID: 37338125 PMCID: PMC10357500 DOI: 10.1002/pro.4703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/15/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Inosine 5'-monophosphate (IMP) dehydrogenase (IMPDH) is an ubiquitous enzyme that catalyzes the NAD+ -dependent oxidation of inosine 5'-monophosphate into xanthosine 5'-monophosphate. This enzyme is formed of two distinct domains, a core domain where the catalytic reaction occurs, and a less-conserved Bateman domain. Our previous studies gave rise to the classification of bacterial IMPDHs into two classes, according to their oligomeric and kinetic properties. MgATP is a common effector but cause to different effects when it binds within the Bateman domain: it is either an allosteric activator for Class I IMPDHs or a modulator of the oligomeric state for Class II IMPDHs. To get insight into the role of the Bateman domain in the dissimilar properties of the two classes, deleted variants of the Bateman domain and chimeras issued from the interchange of the Bateman domain between the three selected IMPDHs have been generated and characterized using an integrative structural biology approach. Biochemical, biophysical, structural, and physiological studies of these variants unveil the Bateman domain as being the carrier of the molecular behaviors of both classes.
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Affiliation(s)
- Antoine Gedeon
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Unité de Microbiologie Structurale, CNRS UMR3525ParisFrance
| | - Nour Ayoub
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
| | - Sébastien Brûlé
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Bertrand Raynal
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Gouzel Karimova
- Institut Pasteur, Université Paris Cité, Unité de Biochimie des Interactions Macromoléculaires, CNRS UMR3528ParisFrance
| | - Muriel Gelin
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Gilles Labesse
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Hélène Munier‐Lehmann
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
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7
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Alkaissi H, McFarlane SI. Hyperhomocysteinemia and Accelerated Aging: The Pathogenic Role of Increased Homocysteine in Atherosclerosis, Osteoporosis, and Neurodegeneration. Cureus 2023; 15:e42259. [PMID: 37605676 PMCID: PMC10440097 DOI: 10.7759/cureus.42259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2023] [Indexed: 08/23/2023] Open
Abstract
Cardiovascular diseases and osteoporosis, seemingly unrelated disorders that occur with advanced age, share major pathogenetic mechanisms contributing to accelerated atherosclerosis and bone loss. Hyperhomocysteinemia (hHcy) is among these mechanisms that can cause both vascular and bone disease. In its more severe form, hHcy can present early in life as homocystinuria, an inborn error of metabolic pathways of the sulfur-containing amino acid methionine. In its milder forms, hHcy may go undiagnosed and untreated into adulthood. As such, hHcy may serve as a potential therapeutic target for cardiovascular disease, osteoporosis, thrombophilia, and neurodegeneration, collectively representing accelerated aging. Multiple trials to lower cardiovascular risk and improve bone density with homocysteine-lowering agents, yet none has proven to be clinically meaningful. To understand this unmet clinical need, this review will provide mechanistic insight into the pathogenesis of vascular and bone disease in hHcy, using homocystinuria as a model for accelerated atherosclerosis and bone density loss, a model for accelerated aging.
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Affiliation(s)
- Hussam Alkaissi
- Internal Medicine, Kings County Hospital Center, Brooklyn, USA
- Internal Medicine, Veterans Affairs Medical Center, Brooklyn, USA
- Internal Medicine, State University of New York Downstate Medical Center, Brooklyn, USA
| | - Samy I McFarlane
- Endocrinology, State University of New York Downstate Medical Center, Brooklyn, USA
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8
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Tran CM, Mihara S, Yoshida K, Hisabori T. Cystathionine-β-synthase X proteins negatively regulate NADPH-thioredoxin reductase C activity. Biochem Biophys Res Commun 2023; 653:47-52. [PMID: 36857899 DOI: 10.1016/j.bbrc.2023.02.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Redox regulation is a posttranslational modification based on the redox reaction of protein thiols. A small ubiquitous protein thioredoxin (Trx) plays a central role in redox regulation, but a unique redox-regulatory factor called NADPH-Trx reductase C (NTRC) is also found in plant chloroplasts and some cyanobacteria. Several important functions of NTRC have been suggested, but the mechanism for controlling NTRC activity remains undetermined. Cystathionine-β-synthase X (CBSX) proteins have been previously shown to interact with NTRC physically. Based on these observations, this study biochemically investigated the functional interaction between CBSX proteins and NTRC from Arabidopsis thaliana in vitro. Consequently, we concluded that CBSX proteins act as negative regulators of NTRC in the presence of AMP.
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Affiliation(s)
- Chau M Tran
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259-R1, Midori-Ku, Yokohama, 226-8503, Japan
| | - Shoko Mihara
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259-R1, Midori-Ku, Yokohama, 226-8503, Japan
| | - Keisuke Yoshida
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259-R1, Midori-Ku, Yokohama, 226-8503, Japan.
| | - Toru Hisabori
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259-R1, Midori-Ku, Yokohama, 226-8503, Japan.
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9
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Steinberg GR, Hardie DG. New insights into activation and function of the AMPK. Nat Rev Mol Cell Biol 2023; 24:255-272. [PMID: 36316383 DOI: 10.1038/s41580-022-00547-x] [Citation(s) in RCA: 167] [Impact Index Per Article: 167.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
The classical role of AMP-activated protein kinase (AMPK) is as a cellular energy sensor activated by falling energy status, signalled by increases in AMP to ATP and ADP to ATP ratios. Once activated, AMPK acts to restore energy homeostasis by promoting ATP-producing catabolic pathways while inhibiting energy-consuming processes. In this Review, we provide an update on this canonical (AMP/ADP-dependent) activation mechanism, but focus mainly on recently described non-canonical pathways, including those by which AMPK senses the availability of glucose, glycogen or fatty acids and by which it senses damage to lysosomes and nuclear DNA. We also discuss new findings on the regulation of carbohydrate and lipid metabolism, mitochondrial and lysosomal homeostasis, and DNA repair. Finally, we discuss the role of AMPK in cancer, obesity, diabetes, nonalcoholic steatohepatitis (NASH) and other disorders where therapeutic targeting may exert beneficial effects.
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Affiliation(s)
- Gregory R Steinberg
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada.
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
| | - D Grahame Hardie
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.
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10
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Arjun OK, Prakash T. Identification of conserved genomic signatures specific to Bifidobacterium species colonising the human gut. 3 Biotech 2023; 13:97. [PMID: 36852175 PMCID: PMC9958220 DOI: 10.1007/s13205-023-03492-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/25/2023] [Indexed: 02/26/2023] Open
Abstract
Bifidobacterium species are known for their ability to inhabit various habitats and are often regarded as the first colonisers of the human gut. In the present work, we have used comparative genomics to identify conserved genomic signatures specific to Bifidobacterium species associated with the human gut. Our approach discovered five genomic signatures with varying lengths and confidence. Among the predicted five signatures, a 1790 bp multi-drug resistance (MDR) signature was found to be remarkably specific to only those species that can colonise the human gut. The signature codes for a membrane transport protein belonging to the major facilitator superfamily (MFS) generally involved in MDR. Phylogenetic analyses of the MDR signature suggest a lineage-specific evolution of the MDR signature in bifidobacteria colonising the human gut. Functional annotation led to the discovery of two conserved domains in the protein; a catalytic MFS domain involved in the efflux of drugs and toxins, and a regulatory cystathionine-β-synthase (CBS) domain that can interact with adenosyl-carriers. Molecular docking simulation performed with the modelled tertiary structure of the MDR signature revealed the putative functional role of the covalently linked domains. The MFS domain displayed a high affinity towards various protein synthesis inhibitor antibiotics and human bile acids, whereas the C-terminally linked CBS domain exhibited favourable binding with molecular structures of ATP and AMP. Therefore, we believe that the predicted signature represents a niche-specific survival trait involved in bile and antibiotic resistance, imparting an adaptive advantage to the Bifidobacterium species colonising the human gut. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03492-4.
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Affiliation(s)
- O. K. Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175005 India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175005 India
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11
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Vedarethinam V, Jeevanandam J, Acquah C, Danquah MK. Magnetic Nanoparticles for Protein Separation and Purification. Methods Mol Biol 2023; 2699:125-159. [PMID: 37646997 DOI: 10.1007/978-1-0716-3362-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Proteins are essential for various functions such as brain activity and muscle contraction in humans. Even though food is a source of proteins, the bioavailability of proteins in most foods is usually limited due to matrix interaction with other biomolecules. Thus, it is essential to extract these proteins and provide them as a nutraceutical supplement to maintain protein levels and avoid protein deficiency. Hence, protein purification and extraction from natural sources are highly significant in biomedical applications. Chromatography, crude mechanical disruption, use of extractive chemicals, and electrophoresis are some of the methods applied to isolate specific proteins. Even though these methods possess several advantages, they are unable to extract specific proteins with high purity. A suitable alternative is the use of nanoparticles, which can be beneficial in protein purification and extraction. Notably, magnetic iron and iron-based nanoparticles have been employed in protein extraction processes and can be reused via demagnetization due to their magnetic property, smaller size, morphology, high surface-to-volume ratio, and surface charge-mediated property. This chapter is a summary of various magnetic nanoparticles (MNPs) that can be used for the biomolecular separation of proteins.
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Affiliation(s)
- Vadanasundari Vedarethinam
- Med-X Research Institute, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jaison Jeevanandam
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, Funchal, Portugal
| | - Caleb Acquah
- Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Michael K Danquah
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN, USA.
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12
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Liu H, Wang Q, Xie L, Xu K, Zhang F, Ruan X, Li L, Tan G. Genome-wide identification of cystathionine beta synthase genes in wheat and its relationship with anther male sterility under heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1061472. [PMID: 36589045 PMCID: PMC9795209 DOI: 10.3389/fpls.2022.1061472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Cystathionine beta synthase (CBS) domains containing proteins (CDCPs) plays an important role in plant development through regulation of the thioredoxin system, as well as its ability to respond to biotic and abiotic stress conditions. Despite this, no systematic study has examined the wheat CBS gene family and its relation to high temperature-induced male sterility. In this study, 66 CBS family members were identified in the wheat genome, and their gene or protein sequences were used for subsequent analysis. The TaCBS gene family was found to be unevenly distributed on 21 chromosomes, and they were classified into four subgroups according to their gene structure and phylogeny. The results of collinearity analysis showed that there were 25 shared orthologous genes between wheat, rice and Brachypodium distachyon, and one shared orthologous gene between wheat, millet and barley. The cis-regulatory elements of the TaCBS were related to JA, IAA, MYB, etc. GO and KEGG pathway analysis identified these TaCBS genes to be associated with pollination, reproduction, and signaling and cellular processes, respectively. A heatmap of wheat plants based on transcriptome data showed that TaCBS genes were expressed to a higher extent in spikelets relative to other tissues. In addition, 29 putative tae-miRNAs were identified, targeting 41 TaCBS genes. Moreover, qRT-PCR validation of six TaCBS genes indicated their critical role in anther development, as five of them were expressed at lower levels in heat-stressed male sterile anthers than in Normal anthers. Together with anther phenotypes, paraffin sections, starch potassium iodide staining, and qRT-PCR data, we hypothesized that the TaCBS gene has a very important connection with the heat-stressed sterility process in wheat, and these data provide a basis for further insight into their relationship.
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Affiliation(s)
- Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Qi Wang
- School of Network Engineering, Zhoukou Normal University, Zhoukou, Henan, China
| | - Liuyong Xie
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Institute of Plant Protection and Edible Mushrooms, Zhoukou Academy of Agricultural Sciences, Zhoukou, Henan, China
| | - Xianle Ruan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Lili Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
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13
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Nojehdeh ST, Mojbafan M, Hooman N, Hoseini R, Otukesh H. Genetic diagnosis of Bartter syndrome in Iranian patients and detection of a novel homozygous CLCNKB mutation. Clin Case Rep 2022; 10:e6698. [PMID: 36514463 PMCID: PMC9734084 DOI: 10.1002/ccr3.6698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/28/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
An Iranian girl with clinical symptoms of Bartter syndrome like hypokalemia, polyuria, polydipsia, hyponatremia, and hypochloremic alkalosis was referred to us in whom the CLCNKB gene was genetically evaluated using Sanger sequencing. A homozygous pathogenic variant of c.1332_1335delCTCT was detected in this patient.
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Affiliation(s)
| | - Marzieh Mojbafan
- Department of Medical Genetics, School of MedicineIran University of Medical Sciences (IUMS)TehranIran,Department of Medical GeneticsAli‐Asghar Children's HospitalTehranIran
| | - Nakysa Hooman
- Clinical research Development CenterIran University of Medical SciencesTehranIran,Department of Pediatric NephrologyAli‐Asghar Children's HospitalTehranIran
| | - Rozita Hoseini
- Department of Pediatric NephrologyAli‐Asghar Children's HospitalTehranIran
| | - Hasan Otukesh
- Department of Pediatric NephrologyAli‐Asghar Children's HospitalTehranIran
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14
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Role of AMPK in Myocardial Ischemia-Reperfusion Injury-Induced Cell Death in the Presence and Absence of Diabetes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7346699. [PMID: 36267813 PMCID: PMC9578802 DOI: 10.1155/2022/7346699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/29/2022] [Indexed: 11/26/2022]
Abstract
Recent studies indicate cell death is the hallmark of cardiac pathology in myocardial infarction and diabetes. The AMP-activated protein kinase (AMPK) signalling pathway is considered a putative salvaging phenomenon, plays a decisive role in almost all cellular, metabolic, and survival functions, and therefore entails precise regulation of its activity. AMPK regulates various programmed cell death depending on the stimuli and context, including autophagy, apoptosis, necroptosis, and ferroptosis. There is substantial evidence suggesting that AMPK is down-regulated in cardiac tissues of animals and humans with type 2 diabetes or metabolic syndrome compared to non-diabetic control and that stimulation of AMPK (physiological or pharmacological) can ameliorate diabetes-associated cardiovascular complications, such as myocardial ischemia-reperfusion injury. Furthermore, AMPK is an exciting therapeutic target for developing novel drug candidates to treat cell death in diabetes-associated myocardial ischemia-reperfusion injury. Therefore, in this review, we summarized how AMPK regulates autophagic, apoptotic, necroptotic, and ferroptosis pathways in the context of myocardial ischemia-reperfusion injury in the presence and absence of diabetes.
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15
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Baudry K, Barbut F, Domenichini S, Guillaumot D, Thy MP, Vanacker H, Majeran W, Krieger-Liszkay A, Issakidis-Bourguet E, Lurin C. Adenylates regulate Arabidopsis plastidial thioredoxin activities through the binding of a CBS domain protein. PLANT PHYSIOLOGY 2022; 189:2298-2314. [PMID: 35736508 PMCID: PMC9342986 DOI: 10.1093/plphys/kiac199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Cystathionine-β-synthase (CBS) domains are found in proteins of all living organisms and have been proposed to play a role as energy sensors regulating protein activities through their adenosyl ligand binding capacity. In plants, members of the CBSX protein family carry a stand-alone pair of CBS domains. In Arabidopsis (Arabidopsis thaliana), CBSX1 and CBSX2 are targeted to plastids where they have been proposed to regulate thioredoxins (TRXs). TRXs are ubiquitous cysteine thiol oxido-reductases involved in the redox-based regulation of numerous enzymatic activities as well as in the regeneration of thiol-dependent peroxidases. In Arabidopsis, 10 TRX isoforms have been identified in plastids and divided into five sub-types. Here, we show that CBSX2 specifically inhibits the activities of m-type TRXs toward two chloroplast TRX-related targets. By testing activation of NADP-malate dehydrogenase and reduction of 2-Cys peroxiredoxin, we found that TRXm1/2 inhibition by CBSX2 was alleviated in the presence of AMP or ATP. We also determined, by pull-down assays, a direct interaction of CBSX2 with reduced TRXm1 and m2 that was abolished in the presence of adenosyl ligands. In addition, we report that, compared with wild-type plants, the Arabidopsis T-DNA double mutant cbsx1 cbsx2 exhibits growth and chlorophyll accumulation defects in cold conditions, suggesting a function of plastidial CBSX proteins in plant stress adaptation. Together, our results show an energy-sensing regulation of plastid TRX m activities by CBSX, possibly allowing a feedback regulation of ATP homeostasis via activation of cyclic electron flow in the chloroplast, to maintain a high energy level for optimal growth.
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Affiliation(s)
- Kevin Baudry
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Félix Barbut
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | | | - Damien Guillaumot
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Mai Pham Thy
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Hélène Vanacker
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Wojciech Majeran
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
| | - Anja Krieger-Liszkay
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | | | - Claire Lurin
- CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Gif sur Yvette 91190, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, Gif sur Yvette 91190, France
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16
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Jin F, Huang Y, Hattori M. Recent Advances in the Structural Biology of Mg 2+ Channels and Transporters. J Mol Biol 2022; 434:167729. [PMID: 35841930 DOI: 10.1016/j.jmb.2022.167729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 10/17/2022]
Abstract
Magnesium ions (Mg2+) are the most abundant divalent cations in living organisms and are essential for various physiological processes, including ATP utilization and the catalytic activity of numerous enzymes. Therefore, the homeostatic mechanisms associated with cellular Mg2+ are crucial for both eukaryotic and prokaryotic organisms and are thus strictly controlled by Mg2+ channels and transporters. Technological advances in structural biology, such as the expression screening of membrane proteins, in meso phase crystallization, and recent cryo-EM techniques, have enabled the structure determination of numerous Mg2+ channels and transporters. In this review article, we provide an overview of the families of Mg2+ channels and transporters (MgtE/SLC41, TRPM6/7, CorA/Mrs2, CorC/CNNM), and discuss the structural biology prospects based on the known structures of MgtE, TRPM7, CorA and CorC.
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Affiliation(s)
- Fei Jin
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yichen Huang
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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17
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Franken GAC, Huynen MA, Martínez-Cruz LA, Bindels RJM, de Baaij JHF. Structural and functional comparison of magnesium transporters throughout evolution. Cell Mol Life Sci 2022; 79:418. [PMID: 35819535 PMCID: PMC9276622 DOI: 10.1007/s00018-022-04442-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/22/2022] [Accepted: 06/21/2022] [Indexed: 12/16/2022]
Abstract
Magnesium (Mg2+) is the most prevalent divalent intracellular cation. As co-factor in many enzymatic reactions, Mg2+ is essential for protein synthesis, energy production, and DNA stability. Disturbances in intracellular Mg2+ concentrations, therefore, unequivocally result in delayed cell growth and metabolic defects. To maintain physiological Mg2+ levels, all organisms rely on balanced Mg2+ influx and efflux via Mg2+ channels and transporters. This review compares the structure and the function of prokaryotic Mg2+ transporters and their eukaryotic counterparts. In prokaryotes, cellular Mg2+ homeostasis is orchestrated via the CorA, MgtA/B, MgtE, and CorB/C Mg2+ transporters. For CorA, MgtE, and CorB/C, the motifs that form the selectivity pore are conserved during evolution. These findings suggest that CNNM proteins, the vertebrate orthologues of CorB/C, also have Mg2+ transport capacity. Whereas CorA and CorB/C proteins share the gross quaternary structure and functional properties with their respective orthologues, the MgtE channel only shares the selectivity pore with SLC41 Na+/Mg2+ transporters. In eukaryotes, TRPM6 and TRPM7 Mg2+ channels provide an additional Mg2+ transport mechanism, consisting of a fusion of channel with a kinase. The unique features these TRP channels allow the integration of hormonal, cellular, and transcriptional regulatory pathways that determine their Mg2+ transport capacity. Our review demonstrates that understanding the structure and function of prokaryotic magnesiotropic proteins aids in our basic understanding of Mg2+ transport.
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Affiliation(s)
- G A C Franken
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - M A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L A Martínez-Cruz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park, Derio, 48160, Bizkaia, Spain
| | - R J M Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - J H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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18
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Tseng H, Zeng Y, Lin YJ, Huang J, Lin C, Lee M, Yang F, Fang T, Mar A, Su J. A novel AMPK activator shows therapeutic potential in hepatocellular carcinoma by suppressing HIF1α-mediated aerobic glycolysis. Mol Oncol 2022; 16:2274-2294. [PMID: 35298869 PMCID: PMC9168760 DOI: 10.1002/1878-0261.13211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/15/2022] [Accepted: 03/15/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is characterized by rapid growth, early vascular invasion, and high metastasis. Currently available US Food and Drug Administration (FDA)-approved drugs show low therapeutic efficacy, limiting HCC treatment to chemotherapy. We designed and synthesized a novel small molecule, SCT-1015, that allosterically activated adenosine monophosphate-activated protein kinase (AMPK) to suppress the aerobic glycolysis in HCC. SCT-1015 was shown to bind the AMPK α and β-subunit interface, thereby exposing the kinase α domain to the upstream kinases, resulting in the increased AMPK activity. SCT-1015 dramatically reduced HCC cell growth in vitro and tumor growth in vivo. We further found that AMPK formed protein complexes with hypoxia-inducible factor 1-alpha (HIF1α) and that SCT-1015-activated AMPK promoted hydroxylation of HIF1α (402P and 564P), resulting in HIF1α degradation by the ubiquitin-proteasome system. With declined HIF1α abundance, many glycolysis-related enzymes were downregulated, suppressing aerobic glycolysis, and promoting oxidative phosphorylation. These results indicated that SCT-1015 channeled HCC cells into an unfavorable metabolic status. Overall, we reported SCT-1015 as a direct activator of AMPK signaling that held therapeutic potential in HCC.
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Affiliation(s)
- Hsing‐I Tseng
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Institute of Biopharmaceutical SciencesNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yi‐Siang Zeng
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Department & Institute of PhysiologyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Ying‐Chung Jimmy Lin
- Department of Life Science and Institute of Plant BiologyNational Taiwan UniversityTaipeiTaiwan
- Genome and Systems Biology Degree ProgramNational Taiwan University and Academia SinicaTaipeiTaiwan
| | - Jui‐Wen Huang
- Biomedical Technology and Device Research LabsIndustrial Technology Research InstituteHsinchuTaiwan
| | - Chih‐Lung Lin
- Biomedical Technology and Device Research LabsIndustrial Technology Research InstituteHsinchuTaiwan
| | - Meng‐Hsuan Lee
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Fan‐Wei Yang
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Te‐Ping Fang
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Ai‐Chung Mar
- Taiwan International Graduate Program in Molecular MedicineNational Yang Ming Chiao Tung University and Academia SinicaTaipeiTaiwan
| | - Jung‐Chen Su
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
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19
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Tran JU, Brown BL. Structural Basis for Allostery in PLP-dependent Enzymes. Front Mol Biosci 2022; 9:884281. [PMID: 35547395 PMCID: PMC9081730 DOI: 10.3389/fmolb.2022.884281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes are found ubiquitously in nature and are involved in a variety of biological pathways, from natural product synthesis to amino acid and glucose metabolism. The first structure of a PLP-dependent enzyme was reported over 40 years ago, and since that time, there is a steady wealth of structural and functional information revealed for a wide array of these enzymes. A functional mechanism that is gaining more appreciation due to its relevance in drug design is that of protein allostery, where binding of a protein or ligand at a distal site influences the structure, organization, and function at the active site. Here, we present a review of current structure-based mechanisms of allostery for select members of each PLP-dependent enzyme family. Knowledge of these mechanisms may have a larger potential for identifying key similarities and differences among enzyme families that can eventually be exploited for therapeutic development.
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Affiliation(s)
- Jenny U. Tran
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Breann L. Brown
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
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20
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Tomar S, Subba A, Bala M, Singh AK, Pareek A, Singla-Pareek SL. Genetic Conservation of CBS Domain Containing Protein Family in Oryza Species and Their Association with Abiotic Stress Responses. Int J Mol Sci 2022; 23:ijms23031687. [PMID: 35163610 PMCID: PMC8836131 DOI: 10.3390/ijms23031687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance.
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Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Ashish Subba
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
- National Agri-Food Biotechnology Institute, Mohali 140306, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
- Correspondence:
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21
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Olave-Rodriguez JA, Bonilla-Escobar FJ, Candelo E, Rodriguez-Rojas LX. First Two Case Reports of Becker's Type Myotonia Congenita in Colombia: Clinical and Genetic Features. Appl Clin Genet 2021; 14:473-479. [PMID: 34938096 PMCID: PMC8687676 DOI: 10.2147/tacg.s323559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
Background Becker's type myotonia congenita is an autosomal recessive nondystrophic skeletal muscle disorder characterized by muscle stiffness and the inability of muscle relaxation after voluntary contraction. It is caused by mutations in the CLCN1 gene, which encodes for a chloride channel mainly expressed in the striated muscle. Most cases have been reported in the European population, and only mexiletine has demonstrated a randomized placebo-controlled, double-blinded effectiveness. Case Presentation We present two male siblings from Colombia with Latino ancestry, without parental consanguinity, with myotonia during voluntary movements, muscle hypertrophy of lower extremities, transient weakness, and severe muscle fatigue after exercise from three years of age. A genetic panel for dystrophic muscle disorders and a muscle biopsy were both negative. Genetic testing was performed in their second decade of life. Both patients' exomic sequencing test reported the mutation c.1129C >T (p.Arg377*) affecting exon 10 of the CLCN1, generating a premature stop codon. This mutation was described as pathogenic and observed in only one other patient in the United Kingdom. Conclusion To our knowledge, these are the first cases of Becker's type myotonia congenita reported in Colombia. Increasing awareness of healthcare providers for this type of disease in the region could lead to the identification of undiagnosed patients. Limited availability of medical geneticists as well as genetic testing may be the cause of the lack of previous description of cases, in addition to the delay in the diagnosis of the patients. Further epidemiological studies can reveal underdiagnosed myotonias in the country and in the Latin-American region.
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Affiliation(s)
| | - Francisco Javier Bonilla-Escobar
- Somos Ciencia al Servicio de la Comunidad, Fundación SCISCO/Science to Serve the Community, SCISCO Foundation, Cali, Colombia.,Universidad del Valle, Cali, Colombia.,Institute for Clinical Research Education, University of Pittsburgh, Pittsburgh, PA, USA
| | - Estephania Candelo
- Centro de Investigaciones Clínicas, Fundación Valle del Lili, Cali, Colombia.,Centro enfermedades raras y malformaciones congenitas (CIACER), Universidad Icesi, Cali, Colombia
| | - Lisa Ximena Rodriguez-Rojas
- Universidad Icesi, Faculty of Health Sciences, Cali, Colombia.,Human Genetics Department, Fundación Valle del Lili, Cali, Colombia
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22
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Ali F, Li Y, Li F, Wang Z. Genome-wide characterization and expression analysis of cystathionine β-synthase genes in plant development and abiotic stresses of cotton (Gossypium spp.). Int J Biol Macromol 2021; 193:823-837. [PMID: 34687765 DOI: 10.1016/j.ijbiomac.2021.10.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022]
Abstract
Cystathionine β-synthase (CBS) domains containing proteins (CDCPs) form a large family and play roles in development via regulation of the thioredoxin system as well as abiotic and biotic stress responses of plant. However, the comprehensive study of CBS genes remained elusive in cotton. Here, we identified 237 CBS genes in 11 plant species and the phylogenetic analysis categorized CBS genes into four groups. Whole-genome or segmental with dispersed duplication events contributed to GhCBS gene family expansion. Moreover, orthologous/paralogous genes among three cotton species (G. hirsutum, G. arboreum, and G. raimondii) were detected from the syntenic map among eight plant species. Strong purifying selection for dicotyledonous and monocotyledonous CBS genes, and cis-elements related to plant growth and development, abiotic and hormonal response were observed. Transcriptomic data and qRT-PCR validation of 12 GhCBS genes indicated their critical role in ovule development as most of the genes showed high enrichment. Further, some of GhCBS (GhCBS5, GhCBS16, GhCBS17, GhCBS24, GhCBS25, GhCBS26, and GhCBS52) genes were regulated under various abiotic and hormonal treatments for different time points and involve in ovule and fiber development which provided key genes for future cotton breeding programs. In addition, transgenic tobacco plants overexpressing GhCBS4 transiently exhibited higher water and chlorophyll content indicating improved tolerance toward drought stress. Overall, this study provides the characterization of GhCBS genes for plant growth, abiotic and hormonal stresses, thereby, intimating their significance in cotton molecular breeding for resistant cultivars.
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Affiliation(s)
- Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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23
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Kruger WD. How to fix a broken protein: restoring function to mutant human cystathionine β-synthase. Hum Genet 2021; 141:1299-1308. [PMID: 34636997 DOI: 10.1007/s00439-021-02386-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022]
Abstract
Inborn errors of metabolism (IEM) comprise a large class of recessive genetic diseases involving disorders of cellular metabolism that tend to be caused by missense mutations in which a single incorrect amino acid is substituted in the polypeptide chain. Cystathionine beta-synthase (CBS) deficiency is an example of an IEM that causes large elevations of blood total homocysteine levels, resulting in phenotypes in several tissues. Current treatment strategies involve dietary restriction and vitamin therapy, but these are only partially effective and do not work in all patients. Over 85% of the described mutations in CBS-deficient patients are missense mutations in which the mutant protein fails to fold into an active conformation. The ability of CBS to achieve an active conformation is affected by a variety of intracellular protein networks including the chaperone system and the ubiquitin/proteasome system, collectively referred to as the proteostasis network. Proteostasis modulators are drugs that perturb various aspects of these networks. In this article, we will review the evidence that modulation of the intracellular protein folding environment can be used as a potential therapeutic strategy to treat CBS deficiency and discuss the pros and cons of such a strategy.
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Affiliation(s)
- Warren D Kruger
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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24
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Russell FM, Hardie DG. AMP-Activated Protein Kinase: Do We Need Activators or Inhibitors to Treat or Prevent Cancer? Int J Mol Sci 2020; 22:E186. [PMID: 33375416 PMCID: PMC7795930 DOI: 10.3390/ijms22010186] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
AMP-activated protein kinase (AMPK) is a key regulator of cellular energy balance. In response to metabolic stress, it acts to redress energy imbalance through promotion of ATP-generating catabolic processes and inhibition of ATP-consuming processes, including cell growth and proliferation. While findings that AMPK was a downstream effector of the tumour suppressor LKB1 indicated that it might act to repress tumourigenesis, more recent evidence suggests that AMPK can either suppress or promote cancer, depending on the context. Prior to tumourigenesis AMPK may indeed restrain aberrant growth, but once a cancer has arisen, AMPK may instead support survival of the cancer cells by adjusting their rate of growth to match their energy supply, as well as promoting genome stability. The two isoforms of the AMPK catalytic subunit may have distinct functions in human cancers, with the AMPK-α1 gene often being amplified, while the AMPK-α2 gene is more often mutated. The prevalence of metabolic disorders, such as obesity and Type 2 diabetes, has led to the development of a wide range of AMPK-activating drugs. While these might be useful as preventative therapeutics in individuals predisposed to cancer, it seems more likely that AMPK inhibitors, whose development has lagged behind that of activators, would be efficacious for the treatment of pre-existing cancers.
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Affiliation(s)
| | - David Grahame Hardie
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dow Street, Dundee, Scotland DD1 5EH, UK;
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25
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Dadinova LA, Anashkin VA, Shtykova EV. Small-Angle X-ray Scattering Study of Changes in the Quaternary Structure of Nucleotide-Regulated Pyrophosphatase from Desulfitobacterium hafniense upon Ligand Binding in Solution. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520050053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Liang J, Hu X, Lü A, Sun J. First report on the characterization of pathogenic Rahnella aquatilis KCL-5 from crucian carp: Revealed by genomic and proteomic analyses. JOURNAL OF FISH DISEASES 2020; 43:889-914. [PMID: 32608057 DOI: 10.1111/jfd.13200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Rahnella aquatilis is an important pathogen of several aquatic organisms and is found widely distributed in the freshwater, soil, fish and human clinical samples. Our previously published study reported a novel pathogenic R. aquatilis strain KCL-5 to crucian carp (Carassius auratus). To further investigate the characteristics and pathogenesis caused by R. aquatilis, we here report on the pathological changes, bacterial genomic and proteomic analyses of strain KCL-5. Significantly pathological changes in liver, intestine, spleen and gills were observed in infected fish. The genome consists of one circular chromosome 5,062,299 bp with 52.02% GC content and two plasmids (506,827 bp, 52.16%; 173,433 bp, 50.00%) and predicted 5,653 genes, 77 tRNAs and 22 rRNAs. Some virulence factors were characterized, including outer membrane protein, haemolysin, RTX toxin, chemotaxis and T3SS secretion system. Antimicrobial resistance genes such as EmrAB-TolC, MexABC-OpmB and RosAB efflux pump were found in strain KCL-5. KEGG analysis showed that mainly functional modules were ABC transporters, biosynthesis of amino acids, two-component system, quorum sensing, flagellum assembly and chemotaxis, in which most of them were identified by using 2-DE/MS analyses. To our knowledge, this was first report on the molecular characteristics of R. aquatilis by multi-omics approaches, which will provide insights into the pathogenic mechanism of R. aquatilis infection in fish.
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Affiliation(s)
- Jing Liang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Aijun Lü
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
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27
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Kurdrid P, Phuengcharoen P, Senachak J, Saree S, Hongsthong A. Revealing the key point of the temperature stress response of Arthrospira platensis C1 at the interconnection of C- and N- metabolism by proteome analyses and PPI networking. BMC Mol Cell Biol 2020; 21:43. [PMID: 32532219 PMCID: PMC7291507 DOI: 10.1186/s12860-020-00285-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/28/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Growth-temperature stress causes biochemical changes in the cells and reduction of biomass yield. Quantitative proteome of Arthrospira platensis C1 in response to low- and high temperature stresses was previously analysed to elucidate the stress response mechanism. The data highlighted the linkage of signaling proteins and proteins involved in nitrogen and ammonia assimilation, photosynthesis and oxidative stress. RESULTS After phosphoproteome analysis was carried out in this study, the tentative temperature response cascade of A. platensis C1 was drawn based on data integration of quantitative proteome and phosphoproteome analysis and protein-protein interaction (PPI) networks. The integration revealed 31 proteins regulated at the protein-expression and post-translational levels; thus, this group of proteins was designated bi-level regulated proteins. PPI networks were then constructed based on A. platensis C1 gene inference from publicly available interaction data. The key two-component system (TCS) proteins, SPLC1_S082010 and SPLC1_S230960, were identified as bi-level regulated proteins and were linked to SPLC1_S270380 or glutamate synthase, an important enzyme in nitrogen assimilation that synthesizes glutamate from 2-oxoglutarate, which is known as the signal compound that regulates the carbon/nitrogen (C/N) balance of cells. Moreover, the role of the p-site in the PPIs of some phosphoproteins of interest was determined using site-directed mutagenesis and a yeast two-hybrid system. Evidence showing the critical role of the p-site in the PPI was observed for the multi-sensor histidine kinase SPLC1_S041070 (Hik28) and glutamate synthase. PPI subnetwork also showed that the Hik28 involved with the enzymes in fatty acid desaturation and nitrogen metabolism. The effect of Hik28-deletion was validated by fatty acid analysis and measurement of photosynthetic activity under nitrogen depletion. CONCLUSIONS Taken together, the data clearly represents (i) the multi-level regulation of proteins involved in the stress response mechanism and (ii) the key point of the temperature stress response at the interconnection of C- and N- metabolism.
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Affiliation(s)
- Pavinee Kurdrid
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Mailing Address: IBEG/BIOTEC@KMUTT, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Phutnichar Phuengcharoen
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Jittisak Senachak
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Mailing Address: IBEG/BIOTEC@KMUTT, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Sirilak Saree
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Apiradee Hongsthong
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Mailing Address: IBEG/BIOTEC@KMUTT, 49 Soi Thian Thale 25, Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand.
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28
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Grieschat M, Guzman RE, Langschwager K, Fahlke C, Alekov AK. Metabolic energy sensing by mammalian CLC anion/proton exchangers. EMBO Rep 2020; 21:e47872. [PMID: 32390228 PMCID: PMC7271328 DOI: 10.15252/embr.201947872] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
CLC anion/proton exchangers control the pH and [Cl- ] of the endolysosomal system that is essential for cellular nutrient uptake. Here, we use heterologous expression and whole-cell electrophysiology to investigate the regulation of the CLC isoforms ClC-3, ClC-4, and ClC-5 by the adenylic system components ATP, ADP, and AMP. Our results show that cytosolic ATP and ADP but not AMP and Mg2+ -free ADP enhance CLC ion transport. Biophysical analysis reveals that adenine nucleotides alter the ratio between CLC ion transport and CLC gating charge and shift the CLC voltage-dependent activation. The latter effect is suppressed by blocking the intracellular entrance of the proton transport pathway. We suggest, therefore, that adenine nucleotides regulate the internal proton delivery into the CLC transporter machinery and alter the probability of CLC transporters to undergo silent non-transporting cycles. Our findings suggest that the CBS domains in mammalian CLC transporters serve as energy sensors that regulate vesicular Cl- /H+ exchange by detecting changes in the cytosolic ATP/ADP/AMP equilibrium. Such sensing mechanism links the endolysosomal activity to the cellular metabolic state.
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Affiliation(s)
| | - Raul E Guzman
- Institute of Complex SystemsZelluläre Biophysik (ICS‐4), Forschungszentrum JülichJülichGermany
| | | | - Christoph Fahlke
- Institute of Complex SystemsZelluläre Biophysik (ICS‐4), Forschungszentrum JülichJülichGermany
| | - Alexi K Alekov
- Institute of NeurophysiologyHannover Medical SchoolHannoverGermany
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29
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Portillo F, Vázquez J, Pajares MA. Protein-protein interactions involving enzymes of the mammalian methionine and homocysteine metabolism. Biochimie 2020; 173:33-47. [DOI: 10.1016/j.biochi.2020.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
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30
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Al-Sadeq DW, Nasrallah GK. The Spectrum of Mutations of Homocystinuria in the MENA Region. Genes (Basel) 2020; 11:genes11030330. [PMID: 32245022 PMCID: PMC7140887 DOI: 10.3390/genes11030330] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
Homocystinuria is an inborn error of metabolism due to the deficiency in cystathionine beta-synthase (CBS) enzyme activity. It leads to the elevation of both homocysteine and methionine levels in the blood and urine. Consequently, this build-up could lead to several complications such as nearsightedness, dislocated eye lenses, a variety of psychiatric and behavioral disorders, as well as vascular system complications. The prevalence of homocystinuria is around 1/200,000 births worldwide. However, its prevalence in the Gulf region, notably Qatar, is exceptionally high and reached 1:1800. To date, more than 191 pathogenic CBS mutations have been documented. The majority of these mutations were identified in Caucasians of European ancestry, whereas only a few mutations from African-Americans or Asians were reported. Approximately 87% of all CBS mutations are missense and do not target the CBS catalytic site, but rather result in unstable misfolded proteins lacking the normal biological function, designating them for degradation. The early detection of homocystinuria along with low protein and methionine-restricted diet is the best treatment approach for all types of homocystinuria patients. Yet, less than 50% of affected individuals show a significant reduction in plasma homocysteine levels after treatment. Patients who fail to lower the elevated homocysteine levels, through high protein-restricted diet or by B6 and folic acid supplements, are at higher risk for cardiovascular diseases, neurodegenerative diseases, neural tube defects, and other severe clinical complications. This review aims to examine the mutations spectrum of the CBS gene, the disease management, as well as the current and potential treatment approaches with a greater emphasis on studies reported in the Middle East and North Africa (MENA) region.
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Affiliation(s)
- Duaa W. Al-Sadeq
- Biomedical Research Center, Qatar University, P.O. Box 2713 Doha, Qatar
- College of Medicine, Member of QU Health, Qatar University, P.O. Box 2713 Doha, Qatar
- Correspondence: (G.K.N.); (D.W.A-S.); Tel.: +974-4403-6623 (D.W.A-S.); +974-4403-4817 (G.K.N.); Fax: +974-4403-1351 (G.K.N.)
| | - Gheyath K. Nasrallah
- Biomedical Research Center, Qatar University, P.O. Box 2713 Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Qatar University, P.O. Box 2713 Doha, Qatar
- Correspondence: (G.K.N.); (D.W.A-S.); Tel.: +974-4403-6623 (D.W.A-S.); +974-4403-4817 (G.K.N.); Fax: +974-4403-1351 (G.K.N.)
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31
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Hoang HH, Wang PC, Chen SC. The protective efficacy of recombinant hypoxic response protein 1 of Nocardia seriolae in largemouth bass (Micropterus salmoides). Vaccine 2020; 38:2925-2936. [PMID: 32115295 DOI: 10.1016/j.vaccine.2020.02.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/18/2022]
Abstract
Nocardia seriolae has become one of the major pathogens affecting the aquaculture industry and causes Nocardiosis, a highly devastating disease of marine and freshwater fish that leads to severe economic losses. Therefore, research efforts towards developing efficacious vaccines to control this disease are of high importance. In this study, the hypoxic response protein 1 (HRP1) cloned into pET32a vector was expressed, and produced in Escherichia coli strain BL21 (DE3). The antigenicity of purified recombinant TRX-tagged HRP (rHRP1) was analysed by western blotting using largemouth bass anti-N. seriolae sera. The results showed that largemouth bass anti-N. seriolae sera could specifically detect a 33 kDa rHRP1 protein. Further, the vaccine efficacy of rHRP1 was evaluated in a largemouth bass fish model by calculating the relative percent survival (RPS). rHRP1 incurred an RPS of 73.33% as compared to the control group. Immunological analysis showed that rHRP1 could produce significantly higher serum concentrations of anti-N. seriolae antibodies and serum lysozyme activity as compared to the control groups. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that rHRP1 significantly enhanced the expression of immune-related genes, such as IL-12p40, IL-8, IL-1β, TNFα, IFNγ, NKEF, MHCIα, MHCIIα, CD4-1, CD8α, IgM, NF-κβ, STAT3, IRF4, RORα, and CCL20. These results indicate that rHRP1 may be a promising vaccine candidate against nocardiosis.
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Affiliation(s)
- Huy Hoa Hoang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan.
| | - Pei-Chi Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan; Southern Taiwan Fish Disease Centre, National Pingtung University of Science and Technology, No. 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan.
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan; Southern Taiwan Fish Disease Centre, National Pingtung University of Science and Technology, No. 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan; International Degree Program of Ornamental Fish Science and Technology, International College, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan; Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan.
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32
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Johnson MC, Kollman JM. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. eLife 2020; 9:e53243. [PMID: 31999252 PMCID: PMC7018514 DOI: 10.7554/elife.53243] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.
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Affiliation(s)
- Matthew C Johnson
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
| | - Justin M Kollman
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
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33
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Anashkin V, Salminen A, Osipova E, Kurilova SA, Deltsov ID, Lahti R, Baykov AA. Residue Network Involved in the Allosteric Regulation of Cystathionine β-Synthase Domain-Containing Pyrophosphatase by Adenine Nucleotides. ACS OMEGA 2019; 4:15549-15559. [PMID: 31572856 PMCID: PMC6761619 DOI: 10.1021/acsomega.9b01879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Inorganic pyrophosphatase containing regulatory cystathionine β-synthase (CBS) domains (CBS-PPase) is inhibited by adenosine monophosphate (AMP) and adenosine diphosphate and activated by adenosine triphosphate (ATP) and diadenosine polyphosphates; mononucleotide binding to CBS domains and substrate binding to catalytic domains are characterized by positive cooperativity. This behavior implies three pathways for regulatory signal transduction - between regulatory and active sites, between two active sites, and between two regulatory sites. Bioinformatics analysis pinpointed six charged or polar amino acid residues of Desulfitobacterium hafniense CBS-PPase as potentially important for enzyme regulation. Twelve mutant enzyme forms were produced, and their kinetics of pyrophosphate hydrolysis was measured in wide concentration ranges of the substrate and various adenine nucleotides. The parameters derived from this analysis included catalytic activity, Michaelis constants for two active sites, AMP-, ATP-, and diadenosine tetraphosphate-binding constants for two regulatory sites, and the degree of activation/inhibition for each nucleotide. Replacements of arginine 295 and asparagine 312 by alanine converted ATP from an activator to an inhibitor and markedly affected practically all the above parameters, indicating involvement of these residues in all the three regulatory signaling pathways. Replacements of asparagine 312 and arginine 334 abolished or reversed kinetic cooperativity in the absence of nucleotides but conferred it in the presence of diadenosine tetraphosphate, without effects on nucleotide-binding parameters. Modeling and molecular dynamics simulations revealed destabilization of the subunit interface as a result of asparagine 312 and arginine 334 replacements by alanine, explaining abolishment of kinetic cooperativity. These findings identify residues 295, 312, and 334 as crucial for CBS-PPase regulation via CBS domains.
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Affiliation(s)
- Viktor
A. Anashkin
- Belozersky
Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Anu Salminen
- Department
of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Ekaterina Osipova
- Belozersky
Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Svetlana A. Kurilova
- Belozersky
Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Ilia D. Deltsov
- Belozersky
Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Reijo Lahti
- Department
of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Alexander A. Baykov
- Belozersky
Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
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Anti-Tumor Potential of IMP Dehydrogenase Inhibitors: A Century-Long Story. Cancers (Basel) 2019; 11:cancers11091346. [PMID: 31514446 PMCID: PMC6770829 DOI: 10.3390/cancers11091346] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 01/15/2023] Open
Abstract
The purine nucleotides ATP and GTP are essential precursors to DNA and RNA synthesis and fundamental for energy metabolism. Although de novo purine nucleotide biosynthesis is increased in highly proliferating cells, such as malignant tumors, it is not clear if this is merely a secondary manifestation of increased cell proliferation. Suggestive of a direct causative effect includes evidence that, in some cancer types, the rate-limiting enzyme in de novo GTP biosynthesis, inosine monophosphate dehydrogenase (IMPDH), is upregulated and that the IMPDH inhibitor, mycophenolic acid (MPA), possesses anti-tumor activity. However, historically, enthusiasm for employing IMPDH inhibitors in cancer treatment has been mitigated by their adverse effects at high treatment doses and variable response. Recent advances in our understanding of the mechanistic role of IMPDH in tumorigenesis and cancer progression, as well as the development of IMPDH inhibitors with selective actions on GTP synthesis, have prompted a reappraisal of targeting this enzyme for anti-cancer treatment. In this review, we summarize the history of IMPDH inhibitors, the development of new inhibitors as anti-cancer drugs, and future directions and strategies to overcome existing challenges.
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Anashkin VA, Aksenova VA, Salminen A, Lahti R, Baykov AA. Cooperativity in catalysis by canonical family II pyrophosphatases. Biochem Biophys Res Commun 2019; 517:266-271. [DOI: 10.1016/j.bbrc.2019.07.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
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Parveen A, Mirza MU, Vanmeert M, Akhtar J, Bashir H, Khan S, Shehzad S, Froeyen M, Ahmed W, Ansar M, Wasif N. A novel pathogenic missense variant in CNNM4 underlying Jalili syndrome: Insights from molecular dynamics simulations. Mol Genet Genomic Med 2019; 7:e902. [PMID: 31347285 PMCID: PMC6732295 DOI: 10.1002/mgg3.902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/04/2019] [Accepted: 07/08/2019] [Indexed: 12/24/2022] Open
Abstract
Background Jalili syndrome (JS) is a rare cone‐rod dystrophy (CRD) associated with amelogenesis imperfecta (AI). The first clinical presentation of JS patients was published in 1988 by Jalili and Smith. Pathogenic mutations in the Cyclin and CBS Domain Divalent Metal Cation Transport Mediator 4 (CNNM4) magnesium transporter protein have been reported as the leading cause of this anomaly. Methods In the present study, a clinical and genetic investigation was performed in a consanguineous family of Pakistani origin, showing characteristic features of JS. Sanger sequencing was successfully used to identify the causative variant in CNNM4. Molecular dynamics (MD) simulations were performed to study the effect of amino acid change over CNNM4 protein. Results Sequence analysis of CNNM4 revealed a novel missense variant (c.1220G>T, p.Arg407Leu) in exon‐1 encoding cystathionine‐β‐synthase (CBS) domain. To comprehend the mutational consequences in the structure, the mutant p.Arg407Leu was modeled together with a previously reported variant (c.1484C>T, p.Thr495Ile) in the same domain. Additionally, docking analysis deciphered the binding mode of the adenosine triphosphate (ATP) cofactor. Furthermore, 60ns MD simulations were carried out on wild type (p.Arg407/p.Thr495) and mutants (p.Arg407Leu/p.Thr495Ile) to understand the structural and energetic changes in protein structure and its dynamic behavior. An evident conformational shift of ATP in the binding site was observed in simulated mutants disrupting the native ATP‐binding mode. Conclusion The novel identified variant in CNNM4 is the first report from the Pakistani population. Overall, the study is valuable and may give a novel insight into metal transport in visual function and biomineralization.
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Affiliation(s)
- Asia Parveen
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan.,Faculty of Life Sciences, University of Central Punjab (UCP), Lahore, Pakistan
| | - Muhammad U Mirza
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Michiel Vanmeert
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Javed Akhtar
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan
| | - Hina Bashir
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan.,Department of Biochemistry, Sharif Medical and Dental College, Lahore, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Saqib Shehzad
- Faculty of Life Sciences, University of Central Punjab (UCP), Lahore, Pakistan
| | - Matheus Froeyen
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Wasim Ahmed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Naveed Wasif
- Institute of Molecular Biology and Biotechnology (IMBB), Centre for Research in Molecular Medicine (CRiMM), The University of Lahore, Lahore, Pakistan.,Institute of Human Genetics, University of Ulm & University Hospital, Ulm, Germany.,Institute of Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
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Yang L, Ru Y, Cai X, Yin Z, Liu X, Xiao Y, Zhang H, Zheng X, Wang P, Zhang Z. MoImd4 mediates crosstalk between MoPdeH-cAMP signalling and purine metabolism to govern growth and pathogenicity in Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2019; 20:500-518. [PMID: 30426699 PMCID: PMC6422694 DOI: 10.1111/mpp.12770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The high-affinity cyclic adenosine monophosphate (cAMP) phosphodiesterase MoPdeH is important not only for cAMP signalling and pathogenicity, but also for cell wall integrity (CWI) maintenance in the rice blast fungus Magnaporthe oryzae. To explore the underlying mechanism, we identified MoImd4 as an inosine-5'-monophosphate dehydrogenase (IMPDH) homologue that interacts with MoPdeH. Targeted deletion of MoIMD4 resulted in reduced de novo purine biosynthesis and growth, as well as attenuated pathogenicity, which were suppressed by exogenous xanthosine monophosphate (XMP). Treatment with mycophenolic acid (MPA), which specifically inhibits MoImd4 activity, resulted in reduced growth and virulence attenuation. Intriguingly, further analysis showed that MoImd4 promotes the phosphodiesterase activity of MoPdeH, thereby decreasing intracellular cAMP levels, and MoPdeH also promotes the IMPDH activity of MoImd4. Our studies revealed the presence of a novel crosstalk between cAMP regulation and purine biosynthesis in M. oryzae, and indicated that such a link is also important in the pathogenesis of M. oryzae.
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Affiliation(s)
- Lina Yang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Yanyan Ru
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Xingjia Cai
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Ziyi Yin
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Yuhan Xiao
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
| | - Ping Wang
- Departments of Pediatrics, and Microbiology, Immunology, and ParasitologyLouisiana State University Health Sciences CenterNew OrleansLA70112USA
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing210095China
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First-in-class allosteric inhibitors of bacterial IMPDHs. Eur J Med Chem 2019; 167:124-132. [PMID: 30769241 DOI: 10.1016/j.ejmech.2019.01.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/10/2018] [Accepted: 01/27/2019] [Indexed: 01/18/2023]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH) is an essential enzyme in many bacterial pathogens and is considered as a potential drug target for the development of new antibacterial agents. Our recent work has revealed the crucial role of one of the two structural domains (i.e. Bateman domain) in the regulation of the quaternary structure and enzymatic activity of bacterial IMPDHs. Thus, we have screened chemical libraries to search for compounds targeting the Bateman domain and identified first in-class allosteric inhibitors of a bacterial IMPDH. These inhibitors were shown to counteract the activation by the natural positive effector, MgATP, and to block the enzyme in its apo conformation (low affinity for IMP). Our structural studies demonstrate the versatility of the Bateman domain to accommodate totally unrelated chemical scaffolds and pave the way for the development of allosteric inhibitors, an avenue little explored until now.
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Matsumoto A, Matsui I, Mori T, Sakaguchi Y, Mizui M, Ueda Y, Takahashi A, Doi Y, Shimada K, Yamaguchi S, Kubota K, Hashimoto N, Oka T, Takabatake Y, Sohara E, Hamano T, Uchida S, Isaka Y. Severe Osteomalacia with Dent Disease Caused by a Novel Intronic Mutation of the CLCN5 gene. Intern Med 2018; 57:3603-3610. [PMID: 30101934 PMCID: PMC6355425 DOI: 10.2169/internalmedicine.1272-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We present a case of Dent disease caused by a novel intronic mutation, 1348-1G>A, of the chloride voltage-gated channel 5 (CLCN5) gene. Cultured proximal tubule cells obtained from the patient showed impaired acidification of the endosome and/or lysosome, indicating that the 1348-1G>A mutation was indeed the cause of Dent disease. Although the prevalence of osteomalacia in Dent disease is low in Japan, several factors-including poor medication adherence-caused severe osteomalacia in the current case. Oral supplementation with calcium and native/active vitamin D therapy, with careful attention to medication adherence, led to the improvement of the patient's bone status.
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Affiliation(s)
- Ayumi Matsumoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Isao Matsui
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Yusuke Sakaguchi
- Department of Comprehensive Kidney Disease Research, Osaka University Graduate School of Medicine, Japan
| | - Masayuki Mizui
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Yoshiyasu Ueda
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Atsushi Takahashi
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Yohei Doi
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Karin Shimada
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Satoshi Yamaguchi
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Keiichi Kubota
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Nobuhiro Hashimoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | - Tatsufumi Oka
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
| | | | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Takayuki Hamano
- Department of Comprehensive Kidney Disease Research, Osaka University Graduate School of Medicine, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Japan
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40
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Anashkin VA, Orlov VN, Lahti R, Baykov AA. An arginine residue involved in allosteric regulation of cystathionine β-synthase (CBS) domain-containing pyrophosphatase. Arch Biochem Biophys 2018; 662:40-48. [PMID: 30502330 DOI: 10.1016/j.abb.2018.11.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/11/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
Inorganic pyrophosphatase containing a pair of regulatory CBS domains (CBS-PPase1) is allosterically inhibited by AMP and ADP and activated by ATP and diadenosine polyphosphates. Mononucleotide binding to CBS domains and substrate binding to catalytic domains are characterized by positive co-operativity. Bioinformatics analysis pinpointed a conserved arginine residue at the interface of the regulatory and catalytic domains in bacterial CBS-PPases as potentially involved in enzyme regulation. The importance of this residue was assessed by site-directed mutagenesis using the CBS-PPase from Desulfitobacterium hafniense (dhPPase) as a model. The mutants R276A, R276K and R276E were constructed and purified, and the impact of the respective mutation on catalysis, nucleotide binding and regulation was analysed. Overall, the effects decreased in the following order R276A > R276E > R276K. The variants retained ≥50% catalytic efficiency but exhibited reduced kinetic co-operativity or even its inversion (R276A). Negative co-operativity was retained in the R276A variant in the presence of mononucleotides but was reversed by diadenosine tetraphosphate. Positive nucleotide-binding co-operativity was retained in all variants but the R276A and R276E variants exhibited a markedly reduced affinity to AMP and ADP and greater residual activity at their saturating concentrations. The R276A substitution abolished activation by ATP and diadenosine tetraphosphate, while preserving the ability to bind them. The results suggest that the H-bond formed by the Arg276 sidechain is essential for signal transduction between the regulatory and catalytic domains within one subunit and between the catalytic but not regulatory domains of different subunits.
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Affiliation(s)
- Viktor A Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119899, Russia
| | - Victor N Orlov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119899, Russia
| | - Reijo Lahti
- Department of Biochemistry, University of Turku, FIN-20014, Turku, Finland.
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119899, Russia.
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Wang C, Chen Y, Zheng B, Zhu M, Fan J, Wang J, Jia Z, Huang S, Zhang A. Novel compound heterozygous CLCNKB gene mutations (c.1755A>G/c.848_850delTCT) cause classic Bartter syndrome. Am J Physiol Renal Physiol 2018; 315:F844-F851. [PMID: 29442545 DOI: 10.1152/ajprenal.00077.2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Inactivated variants in CLCNKB gene encoding the basolateral chloride channel ClC-Kb cause classic Bartter syndrome characterized by hypokalemic metabolic alkalosis and hyperreninemic hyperaldosteronism. Here, we identified two cBS siblings presenting hypokalemia in a Chinese family due to novel compound heterozygous CLCNKB mutations (c.848_850delTCT/c.1755A>G). Compound heterozygosity was confirmed by amplifying and sequencing the patient's genomic DNA. The synonymous mutation c.1755A>G (Thr585Thr) was located at +2 bp from the 5' splice donor site in exon 15. Further transcript analysis demonstrated that this single nucleotide mutation causes exclusion of exon 15 in the cDNA from the proband and his mother. Furthermore, we investigated the expression and protein trafficking change of c.848_850delTCT (ΔTCT) and exon 15 deletion (ΔE15) mutation in vitro. The ΔE15 mutation markedly decreased the expression of ClC-Kb and resulted in a low-molecular-weight band (~55 kDa) trapping in the endoplasmic reticulum, while the ΔTCT mutant only decreased the total and plasma membrane ClC-Kb protein expression but did not affect the subcellular localization. Finally, we studied the physiological functions of mutations by using whole cell patch-clamp and found that the ΔE15 or ΔTCT mutation decreased the current of the ClC-Kb/barttin channel. These results suggested that the compound defective mutations of the CLCNKB gene are the molecular mechanism of the two cBS siblings.
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Affiliation(s)
- Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University , Nanjing , China
| | - Ying Chen
- Department of Nephrology, Children's Hospital of Nanjing Medical University , Nanjing , China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University , Nanjing , China
| | - Mengshu Zhu
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University , Nanjing , China
| | - Jia Fan
- Department of Physiology, Nanjing Medical University , Nanjing , China
| | - Juejin Wang
- Department of Physiology, Nanjing Medical University , Nanjing , China
| | - Zhanjun Jia
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University , Nanjing , China
| | - Songming Huang
- Department of Nephrology, Children's Hospital of Nanjing Medical University , Nanjing , China.,Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University , Nanjing , China
| | - Aihua Zhang
- Department of Nephrology, Children's Hospital of Nanjing Medical University , Nanjing , China.,Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University , Nanjing , China
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He Q, Tang QY, Sun YF, Zhou M, Gärtner W, Zhao KH. Chromophorylation of cyanobacteriochrome Slr1393 from Synechocystis sp. PCC 6803 is regulated by protein Slr2111 through allosteric interaction. J Biol Chem 2018; 293:17705-17715. [PMID: 30242127 DOI: 10.1074/jbc.ra118.003830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/13/2018] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are photochromic proteins in cyanobacteria that act as photosensors. CBCRs bind bilins as chromophores and sense nearly the entire visible spectrum of light, but the regulation of the chromophorylation of CBCRs is unknown. Slr1393 from Synechocystis sp. PCC 6803 is a CBCR containing three consecutive GAF (cGMP phosphodiesterase, adenylyl cyclase, and FhlA protein) domains, of which only the third one (Slr1393g3) can be phycocyanobilin-chromophorylated. The protein Slr2111 from Synechocystis sp. PCC 6803 includes a cystathionine β-synthase (CBS) domain pair of an as yet unknown function at its N terminus. CBS domains are often characterized as sensors of cellular energy status by binding nucleotides. In this work, we demonstrate that Slr2111 strongly interacts with Slr1393 in vivo and in vitro, which generates a complex in a 1:1 molar ratio. This tight interaction inhibits the chromophorylation of Slr1393g3, even if the chromophore is present. Instead, the complex stability and thereby the chromophorylation of Slr1393 are regulated by the binding of nucleotides (ATP, ADP, AMP) to the CBS domains of Slr2111 with varying affinities. It is demonstrated that residues Asp-53 and Arg-97 of Slr2111 are involved in nucleotide binding. While ATP binds to Slr2111, the association between the two proteins gets weaker and chromophorylation of Slr1393 are enabled. In contrast, AMP binding to Slr2111 leads to a stronger association, thereby inhibiting the chromophorylation. It is concluded that Slr2111 acts as a sensor of the cellular energy status that regulates the chromophorylation of Slr1393 and thereby its function as a light-driven histidine kinase.
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Affiliation(s)
- Qi He
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Qi-Ying Tang
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ya-Fang Sun
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ming Zhou
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Kai-Hong Zhao
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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43
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Accogli A, Scala M, Calcagno A, Napoli F, Di Iorgi N, Arrigo S, Mancardi MM, Prato G, Pisciotta L, Nagel M, Severino M, Capra V. CNNM2 homozygous mutations cause severe refractory hypomagnesemia, epileptic encephalopathy and brain malformations. Eur J Med Genet 2018; 62:198-203. [PMID: 30026055 DOI: 10.1016/j.ejmg.2018.07.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/01/2018] [Accepted: 07/14/2018] [Indexed: 12/19/2022]
Abstract
Magnesium (Mg2+) plays a crucial role in many biological processes especially in the brain, heart and skeletal muscle. Mg2+ homeostasis is regulated by intestinal absorption and renal reabsorption, involving a combination of different epithelial transport pathways. Mutations in any of these transporters result in hypomagnesemia with variable clinical presentations. Among these, CNNM2 is found along the basolateral membrane of distal tubular segments where it is involved in Mg2+ reabsorption. To date, heterozygous mutations in CNNM2 have been associated with a variable phenotype, ranging from isolated hypomagnesemia to intellectual disability and epilepsy. The only homozygous mutation reported so far, is responsible for hypomagnesemia associated with a severe neurological phenotype characterized by refractory epilepsy, microcephaly, severe global developmental delay and intellectual disability. Here, we report the second homozygous CNNM2 mutation (c.1642G > A,p.Val548Met) in a Moroccan patient, presenting with hypomagnesemia and severe epileptic encephalopathy. Thus, we review and discuss the phenotypic spectrum associated with CNNM2 mutations.
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Affiliation(s)
- Andrea Accogli
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genova, Italy; Università degli studi di Genova, Italy
| | - Marcello Scala
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genova, Italy; Università degli studi di Genova, Italy
| | | | - Flavia Napoli
- UOC Clinica Pediatrica, Istituto Giannina Gaslini, Genova, Italy
| | - Natascia Di Iorgi
- Università degli studi di Genova, Italy; UOC Clinica Pediatrica, Istituto Giannina Gaslini, Genova, Italy
| | - Serena Arrigo
- UOC Gastroenterologia and Endoscopia Pediatrica, Istituto Giannina Gaslini, Genova, Italy
| | | | - Giulia Prato
- UOC Neuropsichiatria Infantile - Centro Epilessia, Istituto Giannina Gaslini, Genova, Italy
| | - Livia Pisciotta
- Università degli studi di Genova, Italy; UOC Neuropsichiatria Infantile - Centro Epilessia, Istituto Giannina Gaslini, Genova, Italy
| | - Mato Nagel
- Center for Nephrology and Metabolic Disorders, Weisswasser, Germany
| | | | - Valeria Capra
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genova, Italy.
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Jentsch TJ, Pusch M. CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease. Physiol Rev 2018; 98:1493-1590. [DOI: 10.1152/physrev.00047.2017] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals, ClC-1, -2, -Ka/-Kb are plasma membrane Cl−channels, whereas ClC-3 through ClC-7 are 2Cl−/H+-exchangers in endolysosomal membranes. Biological roles of CLCs were mostly studied in mammals, but also in plants and model organisms like yeast and Caenorhabditis elegans. CLC Cl−channels have roles in the control of electrical excitability, extra- and intracellular ion homeostasis, and transepithelial transport, whereas anion/proton exchangers influence vesicular ion composition and impinge on endocytosis and lysosomal function. The surprisingly diverse roles of CLCs are highlighted by human and mouse disorders elicited by mutations in their genes. These pathologies include neurodegeneration, leukodystrophy, mental retardation, deafness, blindness, myotonia, hyperaldosteronism, renal salt loss, proteinuria, kidney stones, male infertility, and osteopetrosis. In this review, emphasis is laid on biophysical structure-function analysis and on the cell biological and organismal roles of mammalian CLCs and their role in disease.
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Affiliation(s)
- Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany; and Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Genova, Italy
| | - Michael Pusch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany; and Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Genova, Italy
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45
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Shen ZJ, Chen J, Ghoto K, Hu WJ, Gao GF, Luo MR, Li Z, Simon M, Zhu XY, Zheng HL. Proteomic analysis on mangrove plant Avicennia marina leaves reveals nitric oxide enhances the salt tolerance by up-regulating photosynthetic and energy metabolic protein expression. TREE PHYSIOLOGY 2018; 38:1605-1622. [PMID: 29917117 DOI: 10.1093/treephys/tpy058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 05/01/2018] [Indexed: 05/25/2023]
Affiliation(s)
- Zhi-jun Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
| | - Juan Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, PR China
| | - Kabir Ghoto
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
| | - Wen-jun Hu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Gui-feng Gao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
| | - Mei-rong Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
| | - Zan Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
| | - Martin Simon
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
| | - Xue-yi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
| | - Hai-lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, PR China
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Chacko S, Boshoff HIM, Singh V, Ferraris DM, Gollapalli DR, Zhang M, Lawson AP, Pepi MJ, Joachimiak A, Rizzi M, Mizrahi V, Cuny GD, Hedstrom L. Expanding Benzoxazole-Based Inosine 5'-Monophosphate Dehydrogenase (IMPDH) Inhibitor Structure-Activity As Potential Antituberculosis Agents. J Med Chem 2018; 61:4739-4756. [PMID: 29746130 DOI: 10.1021/acs.jmedchem.7b01839] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
New drugs and molecular targets are urgently needed to address the emergence and spread of drug-resistant tuberculosis. Mycobacterium tuberculosis ( Mtb) inosine 5'-monophosphate dehydrogenase 2 ( MtbIMPDH2) is a promising yet controversial potential target. The inhibition of MtbIMPDH2 blocks the biosynthesis of guanine nucleotides, but high concentrations of guanine can potentially rescue the bacteria. Herein we describe an expansion of the structure-activity relationship (SAR) for the benzoxazole series of MtbIMPDH2 inhibitors and demonstrate that minimum inhibitory concentrations (MIC) of ≤1 μM can be achieved. The antibacterial activity of the most promising compound, 17b (Q151), is derived from the inhibition of MtbIMPDH2 as demonstrated by conditional knockdown and resistant strains. Importantly, guanine does not change the MIC of 17b, alleviating the concern that guanine salvage can protect Mtb in vivo. These findings suggest that MtbIMPDH2 is a vulnerable target for tuberculosis.
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Affiliation(s)
| | - Helena I M Boshoff
- Tuberculosis Research Section , National Institute of Allergy and Infectious Diseases , Bethesda , Maryland 20892 , United States
| | - Vinayak Singh
- Department of Drug Discovery and Development & Institute of Infectious Disease and Molecular Medicine , H3D Drug Discovery and Development Centre, University of Cape Town , Rondebosch , Cape Town 7701 , South Africa
| | - Davide M Ferraris
- Dipartimento di Scienze del Farmaco , Universitá del Piemonte Orientale , Via Bovio 6 , 28100 Novara , Italy
| | | | | | | | | | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Biology , University of Chicago , Chicago , Illinois 60557 , United States.,Structural Biology Center, Biosciences , Argonne National Laboratory , 9700 S. Cass Avenue, Argonne , Illinois 60439 , United States
| | - Menico Rizzi
- Dipartimento di Scienze del Farmaco , Universitá del Piemonte Orientale , Via Bovio 6 , 28100 Novara , Italy
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology , University of Cape Town , Anzio Road , Observatory 7925 , South Africa
| | - Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy , University of Houston , Health Building 2, 4849 Calhoun Road , Houston , Texas 77204 , United States
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Li DX, Li XY, Dong H, Liu YP, Ding Y, Song JQ, Jin Y, Zhang Y, Wang Q, Yang YL. Eight novel mutations of CBS gene in nine Chinese patients with classical homocystinuria. World J Pediatr 2018; 14:197-203. [PMID: 29508359 DOI: 10.1007/s12519-018-0135-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/05/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND Classical homocystinuria (homocysteinemia type 1, MIM# 236200) is a rare inherited disorder in Mainland China. This study aimed to identify mutations in the cystathionine β-synthase (CBS) gene which are associated with classical homocystinuria in nine Chinese patients. METHODS Nine Chinese patients were diagnosed at the age of 5 years 4 months to 18 years by plasma total homocysteine and blood methionine determination. CBS gene analysis was performed for the patients and their families. RESULTS All nine patients had significantly increased plasma total homocysteine (142-500 μmol/L vs. the normal range of 0-15 μmol/L) and blood methionine (144.3-500 μmol/L vs. the normal range of 0-50 μmol/L). None of the patients was pyridoxine responsive. Eleven mutations in CBS gene were identified in the nine patients. Eight mutations (IVS3+1G>A, p.Thr493fsX46, p.Thr236Asn, p.Leu230Gln, p.Lys72Ile, p.Ser201ProfsX36, p.Met337IlefsX115, and IVS14-1G>C) were novel. Three mutations (p.Arg125Gln, p.Thr257Met and p.Gly116Arg) had been previously reported. CONCLUSIONS In this study, eight novel mutations in CBS were identified in nine Chinese patients with classical homocystinuria. None of the hotspot mutations reported in other regions previously was found. These data indicated that Chinese maybe had different CBS mutation spectrum from other population. The identification of mutations not only confirms the diagnosis but also enables accurate genetic counselling and prenatal diagnosis for the fetuses of the families.
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Affiliation(s)
- Dong-Xiao Li
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Xi-Yuan Li
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Hui Dong
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Yu-Peng Liu
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Yuan Ding
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Jin-Qing Song
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Ying Jin
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Yao Zhang
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Qiao Wang
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China
| | - Yan-Ling Yang
- Department of Pediatrics, Peking University First Hospital, No. 1 Xi'anmen Street, West District, Beijing, 100034, China.
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48
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Ibrahim S, Maqbool S, Azam M, Iqbal MP, Qamar R. CBS mutations and MTFHR SNPs causative of hyperhomocysteinemia in Pakistani children. Mol Biol Rep 2018; 45:353-360. [PMID: 29600437 DOI: 10.1007/s11033-018-4169-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/24/2018] [Indexed: 11/26/2022]
Abstract
Three index patients with hyperhomocysteinemia and ocular anomalies were screened for cystathionine beta synthase (CBS) and methylenetetrahydrofolate reductase (MTHFR) polymorphisms. Genotyping of hyperhomocysteinemia associated MTHFR polymorphisms C677T (rs1801133) and A1298C (rs1801131) was done by PCR-restriction fragment length polymorphism. Sanger sequencing was performed for CBS exonic sequences along with consensus splice sites. In the case of MTHFR polymorphisms, all the patients were heterozygous CT for the single nucleotide polymorphism (SNP) C677T and were therefore carriers of the risk allele (T), while the patients were homozygous CC for the risk genotype of the SNP A1298C. CBS sequencing resulted in the identification of two novel mutations, a missense change (c.467T>C; p.Leu156Pro) in exon 7 and an in-frame deletion (c.808_810del; p.Glu270del) in exon 10. In addition, a recurrent missense mutation (c.770C>T; p.Thr257Met) in exon 10 of the gene was also identified. The mutations were present homozygously in the patients and were inherited from the carrier parents. This is the first report from Pakistan where novel as well as recurrent CBS mutations causing hyperhomocysteinemia and lens dislocation in three patients from different families are being reported with the predicted effect of the risk allele of the MTHFR SNP in causing hyperhomocysteinemia.
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Affiliation(s)
- Shahnaz Ibrahim
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Saadia Maqbool
- COMSATS Institute of Information Technology, Park Road, Tarlai Kalan, Islamabad, 45600, Pakistan
| | - Maleeha Azam
- COMSATS Institute of Information Technology, Park Road, Tarlai Kalan, Islamabad, 45600, Pakistan
| | - Mohammad Perwaiz Iqbal
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Raheel Qamar
- COMSATS Institute of Information Technology, Park Road, Tarlai Kalan, Islamabad, 45600, Pakistan.
- Pakistan Academy of Sciences, Islamabad, Pakistan.
- Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan.
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Abstract
Mammalian AMPK is known to be activated by falling cellular energy status, signaled by rising AMP/ATP and ADP/ATP ratios. We review recent information about how this occurs but also discuss new studies suggesting that AMPK is able to sense glucose availability independently of changes in adenine nucleotides. The glycolytic intermediate fructose-1,6-bisphosphate (FBP) is sensed by aldolase, which binds to the v-ATPase on the lysosomal surface. In the absence of FBP, interactions between aldolase and the v-ATPase are altered, allowing formation of an AXIN-based AMPK-activation complex containing the v-ATPase, Ragulator, AXIN, LKB1, and AMPK, causing increased Thr172 phosphorylation and AMPK activation. This nutrient-sensing mechanism activates AMPK but also primes it for further activation if cellular energy status subsequently falls. Glucose sensing at the lysosome, in which AMPK and other components of the activation complex act antagonistically with another key nutrient sensor, mTORC1, may have been one of the ancestral roles of AMPK.
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Affiliation(s)
- Sheng-Cai Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang'an Campus, Xiamen, Fujian 361102, China.
| | - D Grahame Hardie
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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50
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Maia CMF, Machado RA, Gil-da-Silva-Lopes VL, Lustosa-Mendes E, Rim PHH, Dias VO, Martelli DRB, Nasser LS, Coletta RD, Martelli-Júnior H. Report of two unrelated families with Jalili syndrome and a novel nonsense heterozygous mutation in CNNM4 gene. Eur J Med Genet 2018; 61:384-387. [PMID: 29421602 DOI: 10.1016/j.ejmg.2018.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/10/2018] [Accepted: 02/03/2018] [Indexed: 12/18/2022]
Abstract
Jalili syndrome (JS) is an autosomal recessive disease characterized by a combination of cone-rode retinal dytrophy (CRD) and amelogenesis imperfect (AI). Mutations in cyclin and CBS domain divalent metal cation transport mediator 4 (CNNM4) gene cause JS. Here we described 2 families (3 members) affected by JS. In the first family, JS was caused by the homozygous p.Leu324Pro (c.971T > C) missense mutation and the affected patient developed both CRD and AI. In the second family, a specific combination of a compound heterozygous mutation was found - the p.Leu324Pro (c.971T > C) missense transition and the novel p.Tyr581* (c.1743C > G) nonsense mutation. The proband showed CRD and AI, but her father just developed eye alterations. Together, these findings suggest that the p.Leu324Pro mutation in homozygosis induces a complete phenotype with both CRD and AI, but in heterozygosis and in composition with the novel p.Tyr581* nonsense mutation in CNNM4 promotes variable clinical expressivity, particularly with lack of dental phenotypes. These different phenotypes could be explained by deletions affecting the proband's homologous allele, epistasia or interactions with environmental factors leading to residual activity of protein.
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Affiliation(s)
| | - Renato Assis Machado
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil.
| | | | - Elaine Lustosa-Mendes
- Department of Medical Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Priscila Hae Hyun Rim
- Department of Medical Genetics, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Verônica Oliveira Dias
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | | | - Luciano Sólia Nasser
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Hercílio Martelli-Júnior
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil; Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
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