1
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Hossain MA. Targeting the RAS upstream and downstream signaling pathway for cancer treatment. Eur J Pharmacol 2024; 979:176727. [PMID: 38866361 DOI: 10.1016/j.ejphar.2024.176727] [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: 03/08/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Cancer often involves the overactivation of RAS/RAF/MEK/ERK (MAPK) and PI3K-Akt-mTOR pathways due to mutations in genes like RAS, RAF, PTEN, and PIK3CA. Various strategies are employed to address the overactivation of these pathways, among which targeted therapy emerges as a promising approach. Directly targeting specific proteins, leads to encouraging results in cancer treatment. For instance, RTK inhibitors such as imatinib and afatinib selectively target these receptors, hindering ligand binding and reducing signaling initiation. These inhibitors have shown potent efficacy against Non-Small Cell Lung Cancer. Other inhibitors, like lonafarnib targeting Farnesyltransferase and GGTI 2418 targeting geranylgeranyl Transferase, disrupt post-translational modifications of proteins. Additionally, inhibition of proteins like SOS, SH2 domain, and Ras demonstrate promising anti-tumor activity both in vivo and in vitro. Targeting downstream components with RAF inhibitors such as vemurafenib, dabrafenib, and sorafenib, along with MEK inhibitors like trametinib and binimetinib, has shown promising outcomes in treating cancers with BRAF-V600E mutations, including myeloma, colorectal, and thyroid cancers. Furthermore, inhibitors of PI3K (e.g., apitolisib, copanlisib), AKT (e.g., ipatasertib, perifosine), and mTOR (e.g., sirolimus, temsirolimus) exhibit promising efficacy against various cancers such as Invasive Breast Cancer, Lymphoma, Neoplasms, and Hematological malignancies. This review offers an overview of small molecule inhibitors targeting specific proteins within the RAS upstream and downstream signaling pathways in cancer.
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Affiliation(s)
- Md Arafat Hossain
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
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2
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Yin Y, Zeng Z, Wei S, Shen Z, Cong Z, Zhu X. Using the sympathetic system, beta blockers and alpha-2 agonists, to address acute respiratory distress syndrome. Int Immunopharmacol 2024; 139:112670. [PMID: 39018694 DOI: 10.1016/j.intimp.2024.112670] [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: 05/31/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024]
Abstract
Acute Respiratory Distress Syndrome (ARDS) manifests as an acute inflammatory lung injury characterized by persistent hypoxemia, featuring a swift onset, high mortality, and predominantly supportive care as the current therapeutic approach, while effective treatments remain an area of active investigation. Adrenergic receptors (AR) play a pivotal role as stress hormone receptors, extensively participating in various inflammatory processes by initiating downstream signaling pathways. Advancements in molecular biology and pharmacology continually unveil the physiological significance of distinct AR subtypes. Interventions targeting these subtypes have the potential to induce specific alterations in cellular and organismal functions, presenting a promising avenue as a therapeutic target for managing ARDS. This article elucidates the pathogenesis of ARDS and the basic structure and function of AR. It also explores the relationship between AR and ARDS from the perspective of different AR subtypes, aiming to provide new insights for the improvement of ARDS.
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Affiliation(s)
- Yiyuan Yin
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Zhaojin Zeng
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Senhao Wei
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Ziyuan Shen
- Department of Anaesthesiology, Peking University Third Hospital, Beijing, China
| | - Zhukai Cong
- Department of Anaesthesiology, Peking University Third Hospital, Beijing, China.
| | - Xi Zhu
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China.
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3
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Engelhardt D, Marean A, McKean D, Petersen J, Niswander L. RSG1 is required for cilia-dependent neural tube closure. Genesis 2024; 62:e23602. [PMID: 38721990 PMCID: PMC11141724 DOI: 10.1002/dvg.23602] [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: 03/18/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/02/2024]
Abstract
Cilia play a key role in the regulation of signaling pathways required for embryonic development, including the proper formation of the neural tube, the precursor to the brain and spinal cord. Forward genetic screens were used to generate mouse lines that display neural tube defects (NTD) and secondary phenotypes useful in interrogating function. We describe here the L3P mutant line that displays phenotypes of disrupted Sonic hedgehog signaling and affects the initiation of cilia formation. A point mutation was mapped in the L3P line to the gene Rsg1, which encodes a GTPase-like protein. The mutation lies within the GTP-binding pocket and disrupts the highly conserved G1 domain. The mutant protein and other centrosomal and IFT proteins still localize appropriately to the basal body of cilia, suggesting that RSG1 GTPase activity is not required for basal body maturation but is needed for a downstream step in axonemal elongation.
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Affiliation(s)
- David Engelhardt
- Department of Molecular, Cellular and Development Biology, University of Colorado, Boulder, CO 80309
| | - Amber Marean
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus
| | - David McKean
- Cells, Stem Cells and Developmental Biology Graduate Program, University of Colorado Anschutz Medical Campus
| | - Juliette Petersen
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus
| | - Lee Niswander
- Department of Molecular, Cellular and Development Biology, University of Colorado, Boulder, CO 80309
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus
- Cells, Stem Cells and Developmental Biology Graduate Program, University of Colorado Anschutz Medical Campus
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4
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Zhu X, Luo M, An K, Shi D, Hou T, Warshel A, Bai C. Exploring the activation mechanism of metabotropic glutamate receptor 2. Proc Natl Acad Sci U S A 2024; 121:e2401079121. [PMID: 38739800 PMCID: PMC11126994 DOI: 10.1073/pnas.2401079121] [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: 01/17/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Homomeric dimerization of metabotropic glutamate receptors (mGlus) is essential for the modulation of their functions and represents a promising avenue for the development of novel therapeutic approaches to address central nervous system diseases. Yet, the scarcity of detailed molecular and energetic data on mGlu2 impedes our in-depth comprehension of their activation process. Here, we employ computational simulation methods to elucidate the activation process and key events associated with the mGlu2, including a detailed analysis of its conformational transitions, the binding of agonists, Gi protein coupling, and the guanosine diphosphate (GDP) release. Our results demonstrate that the activation of mGlu2 is a stepwise process and several energy barriers need to be overcome. Moreover, we also identify the rate-determining step of the mGlu2's transition from the agonist-bound state to its active state. From the perspective of free-energy analysis, we find that the conformational dynamics of mGlu2's subunit follow coupled rather than discrete, independent actions. Asymmetric dimerization is critical for receptor activation. Our calculation results are consistent with the observation of cross-linking and fluorescent-labeled blot experiments, thus illustrating the reliability of our calculations. Besides, we also identify potential key residues in the Gi protein binding position on mGlu2, mGlu2 dimer's TM6-TM6 interface, and Gi α5 helix by the change of energy barriers after mutation. The implications of our findings could lead to a more comprehensive grasp of class C G protein-coupled receptor activation.
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Affiliation(s)
- Xiaohong Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, People’s Republic of China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei230026, People's Republic of China
| | - Mengqi Luo
- College of Management, Shenzhen University, Shenzhen518060, People's Republic of China
| | - Ke An
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang310005, People's Republic of China
| | - Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, People’s Republic of China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei230026, People's Republic of China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, People's Republic of China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, CA90089-1062
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, People’s Republic of China
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang310005, People's Republic of China
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5
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Torres-Rodriguez MD, Lee SG, Roy Choudhury S, Paul R, Selvam B, Shukla D, Jez JM, Pandey S. Structure-function analysis of plant G-protein regulatory mechanisms identifies key Gα-RGS protein interactions. J Biol Chem 2024; 300:107252. [PMID: 38569936 PMCID: PMC11061236 DOI: 10.1016/j.jbc.2024.107252] [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: 02/09/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Heterotrimeric GTP-binding protein alpha subunit (Gα) and its cognate regulator of G-protein signaling (RGS) protein transduce signals in eukaryotes spanning protists, amoeba, animals, fungi, and plants. The core catalytic mechanisms of the GTPase activity of Gα and the interaction interface with RGS for the acceleration of GTP hydrolysis seem to be conserved across these groups; however, the RGS gene is under low selective pressure in plants, resulting in its frequent loss. Our current understanding of the structural basis of Gα:RGS regulation in plants has been shaped by Arabidopsis Gα, (AtGPA1), which has a cognate RGS protein. To gain a comprehensive understanding of this regulation beyond Arabidopsis, we obtained the x-ray crystal structures of Oryza sativa Gα, which has no RGS, and Selaginella moellendorffi (a lycophyte) Gα that has low sequence similarity with AtGPA1 but has an RGS. We show that the three-dimensional structure, protein-protein interaction with RGS, and the dynamic features of these Gα are similar to AtGPA1 and metazoan Gα. Molecular dynamic simulation of the Gα-RGS interaction identifies the contacts established by specific residues of the switch regions of GTP-bound Gα, crucial for this interaction, but finds no significant difference due to specific amino acid substitutions. Together, our data provide valuable insights into the regulatory mechanisms of plant G-proteins but do not support the hypothesis of adaptive co-evolution of Gα:RGS proteins in plants.
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Affiliation(s)
| | - Soon Goo Lee
- Department of Molecular & Cellular Biology, Kennesaw State University, Kennesaw, Georgia, USA
| | - Swarup Roy Choudhury
- Donald Danforth Plant Science Center, St Louis, Missouri, USA; Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Rabindranath Paul
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Sona Pandey
- Donald Danforth Plant Science Center, St Louis, Missouri, USA.
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6
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Shi L, Yang C, Zhang M, Li K, Wang K, Jiao L, Liu R, Wang Y, Li M, Wang Y, Ma L, Hu S, Bian X. Dissecting the mechanism of atlastin-mediated homotypic membrane fusion at the single-molecule level. Nat Commun 2024; 15:2488. [PMID: 38509071 PMCID: PMC10954664 DOI: 10.1038/s41467-024-46919-z] [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: 07/27/2023] [Accepted: 03/13/2024] [Indexed: 03/22/2024] Open
Abstract
Homotypic membrane fusion of the endoplasmic reticulum (ER) is mediated by dynamin-like GTPase atlastin (ATL). This fundamental process relies on GTP-dependent domain rearrangements in the N-terminal region of ATL (ATLcyto), including the GTPase domain and three-helix bundle (3HB). However, its conformational dynamics during the GTPase cycle remain elusive. Here, we combine single-molecule FRET imaging and molecular dynamics simulations to address this conundrum. Different from the prevailing model, ATLcyto can form a loose crossover dimer upon GTP binding, which is tightened by GTP hydrolysis for membrane fusion. Furthermore, the α-helical motif between the 3HB and transmembrane domain, which is embedded in the surface of the lipid bilayer and self-associates in the crossover dimer, is required for ATL function. To recycle the proteins, Pi release, which disassembles the dimer, activates frequent relative movements between the GTPase domain and 3HB, and subsequent GDP dissociation alters the conformational preference of the ATLcyto monomer for entering the next reaction cycle. Finally, we found that two disease-causing mutations affect human ATL1 activity by destabilizing GTP binding-induced loose crossover dimer formation and the membrane-embedded helix, respectively. These results provide insights into ATL-mediated homotypic membrane fusion and the pathological mechanisms of related disease.
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Affiliation(s)
- Lijun Shi
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Chenguang Yang
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingyuan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Kangning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Keying Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Li Jiao
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruming Liu
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Ming Li
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310027, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Lu Ma
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Shuxin Hu
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, 300071, China.
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7
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Solis GP, Larasati YA, Thiel M, Koval A, Koy A, Katanaev VL. GNAO1 Mutations Affecting the N-Terminal α-Helix of Gαo Lead to Parkinsonism. Mov Disord 2024; 39:601-606. [PMID: 38358016 DOI: 10.1002/mds.29720] [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: 09/25/2023] [Revised: 12/07/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Patients carrying pathogenic variants in GNAO1 present a phenotypic spectrum ranging from severe early-onset epileptic encephalopathy and developmental delay to mild adolescent/adult-onset dystonia. Genotype-phenotype correlation and molecular mechanisms underlying the disease remain understudied. METHODS We analyzed the clinical course of a child carrying the novel GNAO1 mutation c.38T>C;p.Leu13Pro, and structural, biochemical, and cellular properties of the corresponding mutant Gαo-GNAO1-encoded protein-alongside the related mutation c.68T>C;p.Leu23Pro. RESULTS The main clinical feature was parkinsonism with bradykinesia and rigidity, unlike the hyperkinetic movement disorder commonly associated with GNAO1 mutations. The Leu ➔ Pro substitutions have no impact on enzymatic activity or overall folding of Gαo but uniquely destabilize the N-terminal α-helix, blocking formation of the heterotrimeric G-protein and disabling activation by G-protein-coupled receptors. CONCLUSIONS Our study defines a parkinsonism phenotype within the spectrum of GNAO1 disorders and suggests a genotype-phenotype correlation by GNAO1 mutations targeting the N-terminal α-helix of Gαo. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Gonzalo P Solis
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Yonika A Larasati
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Moritz Thiel
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Alexey Koval
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anne Koy
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases, Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Vladimir L Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- School of Medicine and Life Sciences, Department of Pharmacy and Pharmacology, Far Eastern Federal University, Vladivostok, Russia
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8
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Agarwal P, Kumar A, Meena LS. Decoding the structural integrity and multifunctional role of Era protein in the survival of Mycobacterium tuberculosis H 37Rv. J Biomol Struct Dyn 2024:1-16. [PMID: 38319024 DOI: 10.1080/07391102.2024.2309332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/15/2024] [Indexed: 02/07/2024]
Abstract
Era, a widely known GTP binding protein found in many organisms including prokaryotes and eukaryotes and plays a significant role in many fundamental cellular processes like cell growth, differentiation and signaling. In Mycobacterium tuberculosis (Mtb) H37Rv, Era protein had been proved as a GTPase protein but its structural and functional insights are still lacking. Through comparative analysis, structural modeling, docking and using various bioinformatic tools, a detailed investigation of Era was carried out to deduce the structure, function and residues involved in the activity of the protein. Intriguingly, docking results revealed high binding affinity of Era not only with GTP but also with ATP. Myristoylation modifications and phosphorylations on Era were predicted to possibly aid in regulating Era activity and localization; and also the role of Era in translation regulation was foreseen by showing its association with 16s rRNA. Moreover, point mutation of Era residues revealed the effect of W288G and K19G in highly destabilizing the protein structure and activity. Additionally, Era protein was docked with 25 GTPase/ATPase inhibitors, where, Dynasore inhibitor showed the highest affinity for the protein's GTP binding sites and can be used for further drug trials to inhibit growth of mycobacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Preeti Agarwal
- AID, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG, Ghaziabad, India
| | - Ajit Kumar
- AID, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG, Ghaziabad, India
| | - Laxman S Meena
- AID, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG, Ghaziabad, India
- CSIR-Central Drug Research Institute, Lucknow, India
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9
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Luebbers A, Gonzalez-Hernandez AJ, Zhou M, Eyles SJ, Levitz J, Garcia-Marcos M. Dissecting the molecular basis for the modulation of neurotransmitter GPCR signaling by GINIP. Structure 2024; 32:47-59.e7. [PMID: 37989308 PMCID: PMC10872408 DOI: 10.1016/j.str.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/23/2023] [Accepted: 10/25/2023] [Indexed: 11/23/2023]
Abstract
It is well established that G-protein-coupled receptors (GPCRs) stimulated by neurotransmitters are critical for neuromodulation. Much less is known about how heterotrimeric G-protein (Gαβγ) regulation after receptor-mediated activation contributes to neuromodulation. Recent evidence indicates that the neuronal protein GINIP shapes GPCR inhibitory neuromodulation via a unique mechanism of G-protein regulation that controls pain and seizure susceptibility. However, the molecular basis of this mechanism remains ill-defined because the structural determinants of GINIP responsible for binding and regulating G proteins are not known. Here, we combined hydrogen-deuterium exchange mass spectrometry, computational structure predictions, biochemistry, and cell-based biophysical assays to demonstrate an effector-like binding mode of GINIP to Gαi. Specific amino acids of GINIP's PHD domain first loop are essential for G-protein binding and subsequent regulation of Gαi-GTP and Gβγ signaling upon neurotransmitter GPCR stimulation. In summary, these findings shed light onto the molecular basis for a post-receptor mechanism of G-protein regulation that fine-tunes inhibitory neuromodulation.
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Affiliation(s)
- Alex Luebbers
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | | | - Myles Zhou
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10064, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mikel Garcia-Marcos
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; Department of Biology, College of Arts & Sciences, Boston University, Boston, MA 02115, USA.
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10
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Henning RW, Kosheleva I, Šrajer V, Kim IS, Zoellner E, Ranganathan R. BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014301. [PMID: 38304444 PMCID: PMC10834067 DOI: 10.1063/4.0000238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods-UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
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Affiliation(s)
- Robert W. Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Vukica Šrajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - In-Sik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eric Zoellner
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rama Ranganathan
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
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11
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Mahbub L, Kozlov G, Zong P, Lee EL, Tetteh S, Nethramangalath T, Knorn C, Jiang J, Shahsavan A, Yue L, Runnels L, Gehring K. Structural insights into regulation of CNNM-TRPM7 divalent cation uptake by the small GTPase ARL15. eLife 2023; 12:e86129. [PMID: 37449820 PMCID: PMC10348743 DOI: 10.7554/elife.86129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg2+ ions on their own and influx of divalent cations when expressed with the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM-binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg2+ efflux. The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding. A binding deficient ARL15 mutant, R95A, failed to inhibit CNNM and TRPM7 transport of Mg2+ and Zn2+ ions. Structural analysis and binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) showed that ARL15 and PRLs compete for binding CNNM to coordinate regulation of ion transport by CNNM and TRPM7.
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Affiliation(s)
- Luba Mahbub
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Guennadi Kozlov
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Pengyu Zong
- Department of Cell Biology, UCONN Health CenterFarmingtonUnited States
| | - Emma L Lee
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Sandra Tetteh
- Rutgers-Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | | | - Caroline Knorn
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Jianning Jiang
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Ashkan Shahsavan
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
| | - Lixia Yue
- Department of Cell Biology, UCONN Health CenterFarmingtonUnited States
| | - Loren Runnels
- Rutgers-Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Kalle Gehring
- Department of Biochemistry, McGill UniversityMontrealCanada
- Centre de recherche en biologie structurale, McGill UniversityMontréalCanada
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12
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Ganotra J, Sharma B, Biswal B, Bhardwaj D, Tuteja N. Emerging role of small GTPases and their interactome in plants to combat abiotic and biotic stress. PROTOPLASMA 2023; 260:1007-1029. [PMID: 36525153 DOI: 10.1007/s00709-022-01830-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/05/2022] [Indexed: 06/07/2023]
Abstract
Plants are frequently subjected to abiotic and biotic stress which causes major impediments in their growth and development. It is emerging that small guanosine triphosphatases (small GTPases), also known as monomeric GTP-binding proteins, assist plants in managing environmental stress. Small GTPases function as tightly regulated molecular switches that get activated with the aid of guanosine triphosphate (GTP) and deactivated by the subsequent hydrolysis of GTP to guanosine diphosphate (GDP). All small GTPases except Rat sarcoma (Ras) are found in plants, including Ras-like in brain (Rab), Rho of plant (Rop), ADP-ribosylation factor (Arf) and Ras-like nuclear (Ran). The members of small GTPases in plants interact with several downstream effectors to counteract the negative effects of environmental stress and disease-causing pathogens. In this review, we describe processes of stress alleviation by developing pathways involving several small GTPases and their associated proteins which are important for neutralizing fungal infections, stomatal regulation, and activation of abiotic stress-tolerant genes in plants. Previous reviews on small GTPases in plants were primarily focused on Rab GTPases, abiotic stress, and membrane trafficking, whereas this review seeks to improve our understanding of the role of all small GTPases in plants as well as their interactome in regulating mechanisms to combat abiotic and biotic stress. This review brings to the attention of scientists recent research on small GTPases so that they can employ genome editing tools to precisely engineer economically important plants through the overexpression/knock-out/knock-in of stress-related small GTPase genes.
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Affiliation(s)
- Jahanvi Ganotra
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India
| | - Bhawana Sharma
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India
| | - Brijesh Biswal
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India
| | - Deepak Bhardwaj
- Department of Botany, Central University of Jammu, Jammu and Kashmir, Jammu, 181143, India.
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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13
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Dandekar B, Ahalawat N, Sinha S, Mondal J. Markov State Models Reconcile Conformational Plasticity of GTPase with Its Substrate Binding Event. JACS AU 2023; 3:1728-1741. [PMID: 37388689 PMCID: PMC10302740 DOI: 10.1021/jacsau.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023]
Abstract
Ras GTPase is an enzyme that catalyzes the hydrolysis of guanosine triphosphate (GTP) and plays an important role in controlling crucial cellular signaling pathways. However, this enzyme has always been believed to be undruggable due to its strong binding affinity with its native substrate GTP. To understand the potential origin of high GTPase/GTP recognition, here we reconstruct the complete process of GTP binding to Ras GTPase via building Markov state models (MSMs) using a 0.1 ms long all-atom molecular dynamics (MD) simulation. The kinetic network model, derived from the MSM, identifies multiple pathways of GTP en route to its binding pocket. While the substrate stalls onto a set of non-native metastable GTPase/GTP encounter complexes, the MSM accurately discovers the native pose of GTP at its designated catalytic site in crystallographic precision. However, the series of events exhibit signatures of conformational plasticity in which the protein remains trapped in multiple non-native conformations even when GTP has already located itself in its native binding site. The investigation demonstrates mechanistic relays pertaining to simultaneous fluctuations of switch 1 and switch 2 residues which remain most instrumental in maneuvering the GTP-binding process. Scanning of the crystallographic database reveals close resemblance between observed non-native GTP binding poses and precedent crystal structures of substrate-bound GTPase, suggesting potential roles of these binding-competent intermediates in allosteric regulation of the recognition process.
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Affiliation(s)
| | - Navjeet Ahalawat
- Department
of Bioinformatics and Computational Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004 Haryana, India
| | - Suman Sinha
- Institute
of Pharmaceutical Research, GLA University, Mathura, 281406 Uttar Pradesh, India
| | - Jagannath Mondal
- Tata
Institute of Fundamental Research, Hyderabad, Telangana 500046, India
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14
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Mafi A, Kim SK, Goddard WA. The dynamics of agonist-β 2-adrenergic receptor activation induced by binding of GDP-bound Gs protein. Nat Chem 2023:10.1038/s41557-023-01238-6. [PMID: 37349378 DOI: 10.1038/s41557-023-01238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 05/12/2023] [Indexed: 06/24/2023]
Abstract
There is considerable uncertainty about the mechanism by which the β2-adrenergic receptor (β2AR) is activated. Here we use molecular metadynamics computations to predict the mechanism by which an agonist induces the activation of the β2AR and its cognate Gs protein. We found that binding agonist alone to the inactive β2AR does not break the ionic lock and hence does not drive the β2AR towards the activated conformation. However, we found that attaching the inactive Gs protein to the agonist-bound inactive β2AR (containing the ionic lock) leads to partial insertion of Gαs-α5 into the core of β2AR, which breaks the ionic lock, leading to activation of the Gs protein coupled to β2AR. Upon activation, the Gαs protein undergoes a remarkable opening of the GDP binding pocket, making the GDP available for exchange or release. Concomitantly, Gαs-α5 undergoes a remarkable expansion in the β2AR cytoplasmic region after the ionic lock is broken, inducing TM6 to displace outward by ~5 Å from TM3.
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Affiliation(s)
- Amirhossein Mafi
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - William A Goddard
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA.
- California Institute of Technology, Pasadena, CA, USA.
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15
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Lin Z, Li R, Han Z, Liu Y, Gao L, Huang S, Miao Y, Miao R. The Universally Conserved Unconventional G Protein YchF Is Critical for Growth and Stress Response. Life (Basel) 2023; 13:life13041058. [PMID: 37109587 PMCID: PMC10144078 DOI: 10.3390/life13041058] [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: 02/15/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The ancient guanine nucleotide-binding (G) proteins are a group of critical regulatory and signal transduction proteins, widely involved in diverse cellular processes of all kingdoms of life. YchF is a kind of universally conserved novel unconventional G protein that appears to be crucial for growth and stress response in eukaryotes and bacteria. YchF is able to bind and hydrolyze both adenine nucleoside triphosphate (ATP) and guanosine nucleoside triphosphate (GTP), unlike other members of the P-loop GTPases. Hence, it can transduce signals and mediate multiple biological functions by using either ATP or GTP. YchF is not only a nucleotide-dependent translational factor associated with the ribosomal particles and proteasomal subunits, potentially bridging protein biosynthesis and degradation, but also sensitive to reactive oxygen species (ROS), probably recruiting many partner proteins in response to environmental stress. In this review, we summarize the latest insights into how YchF is associated with protein translation and ubiquitin-dependent protein degradation to regulate growth and maintain proteostasis under stress conditions.
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Affiliation(s)
- Zhaoheng Lin
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rongfang Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhiwei Han
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Liu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liyang Gao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Suchang Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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16
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Xiong XX, Liu Y, Zhang LL, Li XJ, Zhao Y, Zheng Y, Yang QH, Yang Y, Min DH, Zhang XH. G-Protein β-Subunit Gene TaGB1-B Enhances Drought and Salt Resistance in Wheat. Int J Mol Sci 2023; 24:ijms24087337. [PMID: 37108500 PMCID: PMC10138664 DOI: 10.3390/ijms24087337] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
In the hexaploid wheat genome, there are three Gα genes, three Gβ and twelve Gγ genes, but the function of Gβ in wheat has not been explored. In this study, we obtained the overexpression of TaGB1 Arabidopsis plants through inflorescence infection, and the overexpression of wheat lines was obtained by gene bombardment. The results showed that under drought and NaCl treatment, the survival rate of Arabidopsis seedlings' overexpression of TaGB1-B was higher than that of the wild type, while the survival rate of the related mutant agb1-2 was lower than that of the wild type. The survival rate of wheat seedlings with TaGB1-B overexpression was higher than that of the control. In addition, under drought and salt stress, the levels of superoxide dismutase (SOD) and proline (Pro) in the wheat overexpression of TaGB1-B were higher than that of the control, and the concentration of malondialdehyde (MDA) was lower than that of the control. This indicates that TaGB1-B could improve the drought resistance and salt tolerance of Arabidopsis and wheat by scavenging active oxygen. Overall, this work provides a theoretical basis for wheat G-protein β-subunits in a further study, and new genetic resources for the cultivation of drought-tolerant and salt-tolerant wheat varieties.
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Affiliation(s)
- Xin-Xin Xiong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Li-Li Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiao-Jian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yue Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yan Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qian-Hui Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yan Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Dong-Hong Min
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiao-Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
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17
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Hewitt N, Ma N, Arang N, Martin SA, Prakash A, DiBerto JF, Knight KM, Ghosh S, Olsen RHJ, Roth BL, Gutkind JS, Vaidehi N, Campbell SL, Dohlman HG. Catalytic site mutations confer multiple states of G protein activation. Sci Signal 2023; 16:eabq7842. [PMID: 36787384 PMCID: PMC10021883 DOI: 10.1126/scisignal.abq7842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) that function as molecular switches for cellular growth and metabolism are activated by GTP and inactivated by GTP hydrolysis. In uveal melanoma, a conserved glutamine residue critical for GTP hydrolysis in the G protein α subunit is often mutated in Gαq or Gα11 to either leucine or proline. In contrast, other glutamine mutations or mutations in other Gα subtypes are rare. To uncover the mechanism of the genetic selection and the functional role of this glutamine residue, we analyzed all possible substitutions of this residue in multiple Gα isoforms. Through cell-based measurements of activity, we showed that some mutants were further activated and inactivated by G protein-coupled receptors. Through biochemical, molecular dynamics, and nuclear magnetic resonance-based structural studies, we showed that the Gα mutants were functionally distinct and conformationally diverse, despite their shared inability to hydrolyze GTP. Thus, the catalytic glutamine residue contributes to functions beyond GTP hydrolysis, and these functions include subtype-specific, allosteric modulation of receptor-mediated subunit dissociation. We conclude that G proteins do not function as simple on-off switches. Rather, signaling emerges from an ensemble of active states, a subset of which are favored in disease and may be uniquely responsive to receptor-directed ligands.
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Affiliation(s)
- Natalie Hewitt
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Nadia Arang
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Sarah A. Martin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey F. DiBerto
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Knight
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Soumadwip Ghosh
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Current address: Illumina Inc, 5200 Illumina Way, San Diego, CA 92037, USA
| | - Reid H. J. Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Current address: GPCR Pharmacology, Discovery Biology, Exscientia Ai, Oxford, UK OX4 4GE
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Silvio Gutkind
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G. Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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18
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Mahbub L, Kozlov G, Zong P, Tetteh S, Nethramangalath T, Knorn C, Jiang J, Shahsavan A, Lee E, Yue L, Runnels LW, Gehring K. Structural insights into regulation of TRPM7 divalent cation uptake by the small GTPase ARL15. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524765. [PMID: 36711628 PMCID: PMC9882303 DOI: 10.1101/2023.01.19.524765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg 2+ ions on their own or uptake of divalent cations when coupled to the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP-binding protein and demonstrate that it binds the CNNM CBS-pair domain with low micromolar affinity. The crystal structure of the complex between ARL15 GTPase domain and CNNM2 CBS-pair domain reveals the molecular determinants of the interaction and allowed the identification of mutations in ARL15 and CNNM2 mutations that abrogate binding. Loss of CNNM binding prevented ARL15 suppression of TRPM7 channel activity in support of previous reports that the proteins function as a ternary complex. Binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) revealed that ARL15 and PRLs compete for binding CNNM, suggesting antagonistic regulation of divalent cation transport by the two proteins.
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Affiliation(s)
- Luba Mahbub
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Guennadi Kozlov
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Pengyu Zong
- Dept. of Cell Biology. UCONN Health Center, Farmington, Connecticut, United States
| | - Sandra Tetteh
- Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States
| | | | - Caroline Knorn
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Jianning Jiang
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Ashkan Shahsavan
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Emma Lee
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Lixia Yue
- Dept. of Cell Biology. UCONN Health Center, Farmington, Connecticut, United States
| | - Loren W. Runnels
- Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montréal, Canada,Centre de recherche en biologie structurale, McGill University, Montréal, Canada,Corresponding author:
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19
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Cheung MY, Li X, Ku YS, Chen Z, Lam HM. Co-crystalization reveals the interaction between AtYchF1 and ppGpp. Front Mol Biosci 2022; 9:1061350. [PMID: 36533075 PMCID: PMC9748339 DOI: 10.3389/fmolb.2022.1061350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/07/2022] [Indexed: 08/18/2023] Open
Abstract
AtYchF1 is an unconventional G-protein in Arabidopsis thaliana that exhibits relaxed nucleotide-binding specificity. The bindings between AtYchF1 and biomolecules including GTP, ATP, and 26S rRNA have been reported. In this study, we demonstrated the binding of AtYchF1 to ppGpp in addition to the above molecules. AtYchF1 is a cytosolic protein previously reported as a negative regulator of both biotic and abiotic stresses while the accumulation of ppGpp in the cytoplasm induces retarded plant growth and development. By co-crystallization, in vitro pull-down experiments, and hydrolytic biochemical assays, we demonstrated the binding and hydrolysis of ppGpp by AtYchF1. ppGpp inhibits the binding of AtYchF1 to ATP, GTP, and 26S rRNA. The ppGpp hydrolyzing activity of AtYchF1 failed to be activated by AtGAP1. The AtYchF1-ppGpp co-crystal structure suggests that ppGpp might prevent His136 from executing nucleotide hydrolysis. In addition, upon the binding of ppGpp, the conformation between the TGS and helical domains of AtYchF1 changes. Such structural changes probably influence the binding between AtYchF1 and other molecules such as 26S rRNA. Since YchF proteins are conserved among different kingdoms of life, the findings advance the knowledge on the role of AtYchF1 in regulating nucleotide signaling as well as hint at the possible involvement of YchF proteins in regulating ppGpp level in other species.
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Affiliation(s)
- Ming-Yan Cheung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xiaorong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yee-Shan Ku
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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20
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Van Trigt WK, Kelly KM, Hughes CCW. GNAQ mutations drive port wine birthmark-associated Sturge-Weber syndrome: A review of pathobiology, therapies, and current models. Front Hum Neurosci 2022; 16:1006027. [PMID: 36405075 PMCID: PMC9670321 DOI: 10.3389/fnhum.2022.1006027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Port-wine birthmarks (PWBs) are caused by somatic, mosaic mutations in the G protein guanine nucleotide binding protein alpha subunit q (GNAQ) and are characterized by the formation of dilated, dysfunctional blood vessels in the dermis, eyes, and/or brain. Cutaneous PWBs can be treated by current dermatologic therapy, like laser intervention, to lighten the lesions and diminish nodules that occur in the lesion. Involvement of the eyes and/or brain can result in serious complications and this variation is termed Sturge-Weber syndrome (SWS). Some of the biggest hurdles preventing development of new therapeutics are unanswered questions regarding disease biology and lack of models for drug screening. In this review, we discuss the current understanding of GNAQ signaling, the standard of care for patients, overlap with other GNAQ-associated or phenotypically similar diseases, as well as deficiencies in current in vivo and in vitro vascular malformation models.
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Affiliation(s)
- William K. Van Trigt
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States,*Correspondence: William K. Van Trigt,
| | - Kristen M. Kelly
- Department of Dermatology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Christopher C. W. Hughes
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States,Christopher C. W. Hughes,
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21
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Pálfy G, Menyhárd DK, Ákontz‐Kiss H, Vida I, Batta G, Tőke O, Perczel A. The Importance of Mg 2+ -Free State in Nucleotide Exchange of Oncogenic K-Ras Mutants. Chemistry 2022; 28:e202201449. [PMID: 35781716 PMCID: PMC9804424 DOI: 10.1002/chem.202201449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Indexed: 01/05/2023]
Abstract
For efficient targeting of oncogenic K-Ras interaction sites, a mechanistic picture of the Ras-cycle is necessary. Herein, we used NMR relaxation techniques and molecular dynamics simulations to decipher the role of slow dynamics in wild-type and three oncogenic P-loop mutants of K-Ras. Our measurements reveal a dominant two-state conformational exchange on the ms timescale in both GDP- and GTP-bound K-Ras. The identified low-populated higher energy state in GDP-loaded K-Ras has a conformation reminiscent of a nucleotide-bound/Mg2+ -free state characterized by shortened β2/β3-strands and a partially released switch-I region preparing K-Ras for the interaction with the incoming nucleotide exchange factor and subsequent reactivation. By providing insight into mutation-specific differences in K-Ras structural dynamics, our systematic analysis improves our understanding of prolonged K-Ras signaling and may aid the development of allosteric inhibitors targeting nucleotide exchange in K-Ras.
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Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,MTA-ELTE Protein Modeling Research GroupEötvös Loránd Research Network (ELKH)1/a Pázmány Péter stny.Budapest1117Hungary
| | - Dóra K. Menyhárd
- MTA-ELTE Protein Modeling Research GroupEötvös Loránd Research Network (ELKH)1/a Pázmány Péter stny.Budapest1117Hungary
| | - Hanna Ákontz‐Kiss
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,Hevesy György PhD School of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary
| | - István Vida
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,Hevesy György PhD School of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary
| | - Gyula Batta
- Structural Biology Research GroupDepartment of Organic ChemistryUniversity of Debrecen1 Egyetem térDebrecen4032Hungary
| | - Orsolya Tőke
- Laboratory for NMR SpectroscopyResearch Centre for Natural Sciences (RCNS)2 Magyar tudósok körútjaBudapest1117Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,MTA-ELTE Protein Modeling Research GroupEötvös Loránd Research Network (ELKH)1/a Pázmány Péter stny.Budapest1117Hungary
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22
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Shi M, Tie HC, Divyanshu M, Sun X, Zhou Y, Boh BK, Vardy LA, Lu L. Arl15 upregulates the TGFβ family signaling by promoting the assembly of the Smad-complex. eLife 2022; 11:76146. [PMID: 35834310 PMCID: PMC9352346 DOI: 10.7554/elife.76146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
The hallmark event of the canonical transforming growth factor β (TGFβ) family signaling is the assembly of the Smad-complex, consisting of the common Smad, Smad4, and phosphorylated receptor-regulated Smads. How the Smad-complex is assembled and regulated is still unclear. Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome. The binding relieves the autoinhibition of Smad4, which is imposed by the intramolecular interaction between its MH1 and MH2 domains. Activated Smad4 subsequently interacts with phosphorylated receptor-regulated Smads, forming the Smad-complex. Our observations suggest that Smad4 functions as an effector and a GTPase activating protein (GAP) of Arl15. Assembly of the Smad-complex enhances the GAP activity of Smad4 toward Arl15, therefore dissociating Arl15 before the nuclear translocation of the Smad-complex. Our data further demonstrate that Arl15 positively regulates the TGFβ family signaling.
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Affiliation(s)
- Meng Shi
- Skin Research Laboratory, A*STAR, Singapore, singapore, Singapore
| | - Hieng Chiong Tie
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Mahajan Divyanshu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiuping Sun
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yan Zhou
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Boon Kim Boh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Leah A Vardy
- Skin Research Laboratory, A*STAR, Singapore, singapore, Singapore
| | - Lei Lu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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23
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Interacting partners of Brassica juncea Regulator of G-protein Signaling protein suggest its role in cell wall metabolism and cellular signaling. Biosci Rep 2022; 42:231472. [PMID: 35737296 PMCID: PMC9284343 DOI: 10.1042/bsr20220302] [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: 02/19/2022] [Revised: 06/08/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Heterotrimeric G-proteins interact with various upstream and downstream effectors to regulate various aspects of plant growth and development. G-protein effectors have been recently reported in Arabidopsis thaliana; however, less information is available from polyploid crop species having complex networks of G-protein components. Regulator of G-protein signaling (RGS) is a well-characterized GTPase accelerating protein, which plays an important role in the regulation of the G-protein cycle in plants. In the present study, four homologs encoding RGS proteins were isolated from the allotetraploid Brassica juncea, a globally important oilseed, vegetable, and condiment crop. The B. juncea RGS proteins were grouped into distinct BjuRGS1 and BjuRGS2 orthologous clades, and the expression of BjuRGS1 homologs was predominantly higher than BjuRGS2 homologs across the tested tissue types of B. juncea. Utilizing B. juncea Y2H library screening, a total of 30 nonredundant interacting proteins with the RGS-domain of the highly expressed BjuA.RGS1 was identified. Gene ontology analysis indicated that these effectors exerted various molecular, cellular, and physiological functions. Many of them were known to regulate cell wall metabolism (BjuEXP6, Bju-α-MAN, BjuPGU4, BjuRMS3) and phosphorylation-mediated cell signaling (BjuMEK4, BjuDGK3, and BjuKinase). Furthermore, transcript analysis indicated that the identified interacting proteins have a coexpression pattern with the BjuRGS homologs. These findings increase our knowledge about the novel targets of G-protein components from a globally cultivated Brassica crop and provide an important resource for developing a plant G-protein interactome network.
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24
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G-Protein Phosphorylation: Aspects of Binding Specificity and Function in the Plant Kingdom. Int J Mol Sci 2022; 23:ijms23126544. [PMID: 35742988 PMCID: PMC9224535 DOI: 10.3390/ijms23126544] [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: 05/24/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Plant survival depends on adaptive mechanisms that constantly rely on signal recognition and transduction. The predominant class of signal discriminators is receptor kinases, with a vast member composition in plants. The transduction of signals occurs in part by a simple repertoire of heterotrimeric G proteins, with a core composed of α-, β-, and γ-subunits, together with a 7-transmembrane Regulator G Signaling (RGS) protein. With a small repertoire of G proteins in plants, phosphorylation by receptor kinases is critical in regulating the active state of the G-protein complex. This review describes the in vivo detected phosphosites in plant G proteins and conservation scores, and their in vitro corresponding kinases. Furthermore, recently described outcomes, including novel arrestin-like internalization of RGS and a non-canonical phosphorylation switching mechanism that drives G-protein plasticity, are discussed.
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25
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Mafi A, Kim SK, Goddard WA. The mechanism for ligand activation of the GPCR-G protein complex. Proc Natl Acad Sci U S A 2022; 119:e2110085119. [PMID: 35452328 PMCID: PMC9170043 DOI: 10.1073/pnas.2110085119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 03/24/2022] [Indexed: 12/28/2022] Open
Abstract
G protein–coupled receptors (GPCRs) activate cellular responses ranging from odorants to neurotransmitters. Binding an agonist leads to activation of a heterotrimeric G protein (GP) that stimulates external signaling. Unfortunately, the mechanism remains unknown. We show for 15 class A GPCRs, including opioids, adrenergics, adenosines, chemokines, muscarinics, cannabinoids, serotonins, and dopamines, that interaction of an inactive GP, including Gs, Gi, Go, G11, and Gq, to the inactive GPCR, containing the intracellular ionic lock between transmembrane (TM) helices 3 and 6, evolves exothermically to form a precoupled GPCR-GP complex with an opened TM3-TM6 and the GP-α5 helix partially inserted into the GPCR but not activated. We show that binding of agonist to this precoupled GPCR-GP complex causes the Gα protein to open into its active form, with the guanosine diphosphate exposed for signaling. This GP-first paradigm provides a strategy for developing selective agonists for GPCRs since it is the pharmacophore for the precoupled GPCR-GP complex that should be used to design drugs.
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Affiliation(s)
- Amirhossein Mafi
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125
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26
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Vaccaro FA, Drennan CL. The role of nucleoside triphosphate hydrolase metallochaperones in making metalloenzymes. Metallomics 2022; 14:6575898. [PMID: 35485745 PMCID: PMC9164220 DOI: 10.1093/mtomcs/mfac030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022]
Abstract
Metalloenzymes catalyze a diverse set of challenging chemical reactions that are essential for life. These metalloenzymes rely on a wide range of metallocofactors, from single metal ions to complicated metallic clusters. Incorporation of metal ions and metallocofactors into apo-proteins often requires the assistance of proteins known as metallochaperones. Nucleoside triphosphate hydrolases (NTPases) are one important class of metallochaperones and are found widely distributed throughout the domains of life. These proteins use the binding and hydrolysis of nucleoside triphosphates, either adenosine triphosphate (ATP) or guanosine triphosphate (GTP), to carry out highly specific and regulated roles in the process of metalloenzyme maturation. Here, we review recent literature on NTPase metallochaperones and describe the current mechanistic proposals and available structural data. By using representative examples from each type of NTPase, we also illustrate the challenges in studying these complicated systems. We highlight open questions in the field and suggest future directions. This minireview is part of a special collection of articles in memory of Professor Deborah Zamble, a leader in the field of nickel biochemistry.
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Affiliation(s)
- Francesca A Vaccaro
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
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27
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Quantitative live-cell imaging of GPCR downstream signaling dynamics. Biochem J 2022; 479:883-900. [PMID: 35383830 DOI: 10.1042/bcj20220021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022]
Abstract
G-protein-coupled receptors (GPCRs) play an important role in sensing various extracellular stimuli, such as neurotransmitters, hormones, and tastants, and transducing the input information into the cell. While the human genome encodes more than 800 GPCR genes, only four Gα-proteins (Gαs, Gαi/o, Gαq/11, and Gα12/13) are known to couple with GPCRs. It remains unclear how such divergent GPCR information is translated into the downstream G-protein signaling dynamics. To answer this question, we report a live-cell fluorescence imaging system for monitoring GPCR downstream signaling dynamics. Genetically encoded biosensors for cAMP, Ca2+, RhoA, and ERK were selected as markers for GPCR downstream signaling, and were stably expressed in HeLa cells. GPCR was further transiently overexpressed in the cells. As a proof-of-concept, we visualized GPCR signaling dynamics of 5 dopamine receptors and 12 serotonin receptors, and found heterogeneity between GPCRs and between cells. Even when the same Gα proteins were known to be coupled, the patterns of dynamics in GPCR downstream signaling, including the signal strength and duration, were substantially distinct among GPCRs. These results suggest the importance of dynamical encoding in GPCR signaling.
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28
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the 'old' field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
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29
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Allosteric modulation of dopamine D 2L receptor in complex with G i1 and G i2 proteins: the effect of subtle structural and stereochemical ligand modifications. Pharmacol Rep 2022; 74:406-424. [PMID: 35064921 PMCID: PMC8964653 DOI: 10.1007/s43440-021-00352-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 12/28/2022]
Abstract
Background Allosteric modulation of G protein-coupled receptors (GPCRs) is nowadays one of the hot topics in drug discovery. In particular, allosteric modulators of D2 receptor have been proposed as potential modern therapeutics to treat schizophrenia and Parkinson’s disease. Methods To address some subtle structural and stereochemical aspects of allosteric modulation of D2 receptor, we performed extensive in silico studies of both enantiomers of two compounds (compound 1 and compound 2), and one of them (compound 2) was synthesized as a racemate in-house and studied in vitro. Results Our molecular dynamics simulations confirmed literature reports that the R enantiomer of compound 1 is a positive allosteric modulator of the D2L receptor, while its S enantiomer is a negative allosteric modulator. Moreover, based on the principal component analysis (PCA), we hypothesized that both enantiomers of compound 2 behave as silent allosteric modulators, in line with our in vitro studies. PCA calculations suggest that the most pronounced modulator-induced receptor rearrangements occur at the transmembrane helix 7 (TM7). In particular, TM7 bending at the conserved P7.50 and G7.42 was observed. The latter resides next to the Y7.43, which is a significant part of the orthosteric binding site. Moreover, the W7.40 conformation seems to be affected by the presence of the positive allosteric modulator. Conclusions Our work reveals that allosteric modulation of the D2L receptor can be affected by subtle ligand modifications. A change in configuration of a chiral carbon and/or minor structural modulator modifications are solely responsible for the functional outcome of the allosteric modulator. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s43440-021-00352-x.
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30
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Alegre KO, Paknejad N, Su M, Lou JS, Huang J, Jordan KD, Eng ET, Meyerson JR, Hite RK, Huang XY. Structural basis and mechanism of activation of two different families of G proteins by the same GPCR. Nat Struct Mol Biol 2021; 28:936-944. [PMID: 34759376 DOI: 10.1038/s41594-021-00679-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 09/30/2021] [Indexed: 01/14/2023]
Abstract
The β1-adrenergic receptor (β1-AR) can activate two families of G proteins. When coupled to Gs, β1-AR increases cardiac output, and coupling to Gi leads to decreased responsiveness in myocardial infarction. By comparative structural analysis of turkey β1-AR complexed with either Gi or Gs, we investigate how a single G-protein-coupled receptor simultaneously signals through two G proteins. We find that, although the critical receptor-interacting C-terminal α5-helices on Gαi and Gαs interact similarly with β1-AR, the overall interacting modes between β1-AR and G proteins vary substantially. Functional studies reveal the importance of the differing interactions and provide evidence that the activation efficacy of G proteins by β1-AR is determined by the entire three-dimensional interaction surface, including intracellular loops 2 and 4 (ICL2 and ICL4).
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Affiliation(s)
- Kamela O Alegre
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Navid Paknejad
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minfei Su
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Jian-Shu Lou
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Jianyun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Kelsey D Jordan
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Edward T Eng
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Joel R Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Xin-Yun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA.
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31
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Verma Y, Mehra U, Pandey DK, Kar J, Pérez-Martinez X, Jana SS, Datta K. MRX8, the conserved mitochondrial YihA GTPase family member, is required for de novo Cox1 synthesis at suboptimal temperatures in Saccharomyces cerevisiae. Mol Biol Cell 2021; 32:ar16. [PMID: 34432493 PMCID: PMC8693954 DOI: 10.1091/mbc.e20-07-0457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The synthesis of Cox1, the conserved catalytic-core subunit of Complex IV, a multisubunit machinery of the mitochondrial oxidative phosphorylation (OXPHOS) system under environmental stress, has not been sufficiently addressed. In this study, we show that the putative YihA superfamily GTPase, Mrx8, is a bona fide mitochondrial protein required for Cox1 translation initiation and elongation during suboptimal growth condition at 16°C. Mrx8 was found in a complex with mitochondrial ribosomes, consistent with a role in protein synthesis. Cells expressing mutant Mrx8 predicted to be defective in guanine nucleotide binding and hydrolysis were compromised for robust cellular respiration. We show that the requirement of Pet309 and Mss51 for cellular respiration is not bypassed by overexpression of Mrx8 and vice versa. Consistently the ribosomal association of Mss51 is independent of Mrx8. Significantly, we find that GTPBP8, the human orthologue, complements the loss of cellular respiration in Δmrx8 cells and GTPBP8 localizes to the mitochondria in mammalian cells. This strongly suggests a universal role of the MRX8 family of proteins in regulating mitochondrial function.
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Affiliation(s)
- Yash Verma
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | - Upasana Mehra
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
| | | | - Joy Kar
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Xochitl Pérez-Martinez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Siddhartha S Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kaustuv Datta
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, India
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32
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Maruta N, Trusov Y, Jones AM, Botella JR. Heterotrimeric G Proteins in Plants: Canonical and Atypical Gα Subunits. Int J Mol Sci 2021; 22:11841. [PMID: 34769272 PMCID: PMC8584482 DOI: 10.3390/ijms222111841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Heterotrimeric GTP-binding proteins (G proteins), consisting of Gα, Gβ and Gγ subunits, transduce signals from a diverse range of extracellular stimuli, resulting in the regulation of numerous cellular and physiological functions in Eukaryotes. According to the classic G protein paradigm established in animal models, the bound guanine nucleotide on a Gα subunit, either guanosine diphosphate (GDP) or guanosine triphosphate (GTP) determines the inactive or active mode, respectively. In plants, there are two types of Gα subunits: canonical Gα subunits structurally similar to their animal counterparts and unconventional extra-large Gα subunits (XLGs) containing a C-terminal domain homologous to the canonical Gα along with an extended N-terminal domain. Both Gα and XLG subunits interact with Gβγ dimers and regulator of G protein signalling (RGS) protein. Plant G proteins are implicated directly or indirectly in developmental processes, stress responses, and innate immunity. It is established that despite the substantial overall similarity between plant and animal Gα subunits, they convey signalling differently including the mechanism by which they are activated. This review emphasizes the unique characteristics of plant Gα subunits and speculates on their unique signalling mechanisms.
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Affiliation(s)
- Natsumi Maruta
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia; (N.M.); (Y.T.)
| | - Yuri Trusov
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia; (N.M.); (Y.T.)
| | - Alan M. Jones
- Departments of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Departments of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jose R. Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia; (N.M.); (Y.T.)
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33
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Mafi A, Kim SK, Chou KC, Güthrie B, Goddard WA. Predicted Structure of Fully Activated Tas1R3/1R3' Homodimer Bound to G Protein and Natural Sugars: Structural Insights into G Protein Activation by a Class C Sweet Taste Homodimer with Natural Sugars. J Am Chem Soc 2021; 143:16824-16838. [PMID: 34585929 DOI: 10.1021/jacs.1c08839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Tas1R3 G protein-coupled receptor constitutes the main component of sweet taste sensory response in humans via forming a heterodimer with Tas1R2 or a homodimer with Tas1R3. The Tas1R3/1R3' homodimer serves as a low-affinity sweet taste receptor, stimulating gustducin G protein (GGust) signaling in the presence of a high concentration of natural sugars. This provides an additional means to detect the taste of natural sugars, thereby differentiating the flavors between natural sugars and artificial sweeteners. We report here the predicted 3D structure of active state Tas1R3/1R3' homodimer complexed with heterotrimeric GGust and sucrose. We discovered that the GGust makes ionic anchors to intracellular loops 1 and 2 of Tas1R3 while the Gα-α5 helix engages the cytoplasmic region extensively through salt bridge and hydrophobic interactions. We show that in the activation of this complex the Venus flytrap domains of the homodimer undergo a remarkable twist up to ∼100° rotation around the vertical axis to adopt a closed-closed conformation while the intracellular region relaxes to an open-open conformation. We find that binding of sucrose to the homodimer stabilizes a preactivated conformation with a largely open intracellular region that recruits and activates the GGust. Upon activation, the Gα subunit spontaneously opens up the nucleotide-binding site, making nucleotide exchange facile for signaling. This activation of GGust promotes the interdomain twist of the Venus flytrap domains. These structures and transformations could potentially be a basis for the design of new sweeteners with higher activity and less unpleasant flavors.
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Affiliation(s)
- Amirhossein Mafi
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Keng C Chou
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Brian Güthrie
- Cargill Global Food Research, Wayzata, Minnesota 55391, United States
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
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34
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Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G, Connolley L, Giacomelli G, Feddersen H, Corrales-Guerrero L, Giammarinaro PI, Hanßmann J, Bramkamp M, Viollier PH, Murray S, Schäfer LV, Bange G, Thanbichler M. The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol Cell 2021; 81:3992-4007.e10. [PMID: 34562373 DOI: 10.1016/j.molcel.2021.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/27/2021] [Accepted: 08/31/2021] [Indexed: 01/29/2023]
Abstract
ParB-like CTPases mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromere of target DNA molecules and spread laterally to form large nucleoprotein complexes serving as docking points for the DNA segregation machinery. Here, we solve crystal structures of ParB in the pre- and post-hydrolysis state and illuminate the catalytic mechanism of nucleotide hydrolysis. Moreover, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. The study of CTPase-deficient ParB variants reveals that CTP hydrolysis serves to limit the sliding time of ParB clamps and thus drives the establishment of a well-defined ParB diffusion gradient across the centromere whose dynamics are critical for DNA segregation. These findings clarify the role of the ParB CTPase cycle in partition complex assembly and function and thus advance our understanding of this prototypic CTP-dependent molecular switch.
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Affiliation(s)
- Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Florian Altegoer
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Connolley
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Helge Feddersen
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | | | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Seán Murray
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
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Nagai K, Niihori T, Okamoto N, Kondo A, Suga K, Ohhira T, Hayabuchi Y, Homma Y, Nakagawa R, Ifuku T, Abe T, Mizuguchi T, Matsumoto N, Aoki Y. Duplications in the G3 domain or switch II region in HRAS identified in patients with Costello syndrome. Hum Mutat 2021; 43:3-15. [PMID: 34618388 DOI: 10.1002/humu.24287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022]
Abstract
Costello syndrome (CS) is an autosomal-dominant disorder characterized by distinctive facial features, hypertrophic cardiomyopathy, skeletal abnormalities, intellectual disability, and predisposition to cancers. Germline variants in HRAS have been identified in patients with CS. Intragenic HRAS duplications have been reported in three patients with a milder phenotype of CS. In this study, we identified two known HRAS variants, p.(Glu63_Asp69dup), p.(Glu62_Arg68dup), and one novel HRAS variant, p.(Ile55_Asp57dup), in patients with CS, including a patient with craniosynostosis. These intragenic duplications are located in the G3 domain and the switch II region. Cells expressing cDNA with these three intragenic duplications showed an increase in ELK-1 transactivation. Injection of wild-type or mutant HRAS mRNAs with intragenic duplications in zebrafish embryos showed significant elongation of the yolk at 11 h postfertilization, which was improved by MEK inhibitor treatment, and a variety of developmental abnormalities at 3 days post fertilization was observed. These results indicate that small in-frame duplications affecting the G3 domain and switch II region of HRAS increase the activation of the ERK pathway, resulting in developmental abnormalities in zebrafish or patients with CS.
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Affiliation(s)
- Koki Nagai
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Akane Kondo
- Perinatal Medical Center, Shikoku Medical Center for Children and Adults, National Hospital Organization, Kagawa, Japan
| | - Kenichi Suga
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Tomoko Ohhira
- Department of Pediatrics, Miyazaki Prefectural Miyazaki Hospital, Miyazaki, Japan
| | - Yasunobu Hayabuchi
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yukako Homma
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Ryuji Nakagawa
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Toshinobu Ifuku
- Department of Pediatrics, Miyazaki Prefectural Miyazaki Hospital, Miyazaki, Japan
| | - Taiki Abe
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
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Liu X, Zhang Z, Zhang M, Zhao X, Zhang T, Liu W, Zhang J. A ras-related nuclear protein Ran participates in the 20E signaling pathway and is essential for the growth and development of Locusta migratoria. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 178:104945. [PMID: 34446211 DOI: 10.1016/j.pestbp.2021.104945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
The small GTPase Ran is a member of the Ras superfamily of small GTP-binding proteins, which plays a key role in the translocation of RNA and proteins through the nuclear pore complex. In this study, the full-length cDNA sequence of LmRan gene was obtained, which consists of 648-nucleotides open reading frame (ORF) and encodes 215 amino acids. RT-qPCR results revealed that LmRan was expressed in all developmental days and tissues investigated. Injection of dsLmRan into 4th and 5th instar nymphs, resulted in a significant down-regulation of LmRan transcripts, respectively. All dsLmRan-injected nymphs died before molting. Further hematoxylin and eosin staining of the integument showed that there was no apolysis occurred after silencing LmRan. In addition, the weight of dsLmRan-injected nymphs was significantly lower than that of the control group, and the gastric caecum and midgut was severely smaller. Especiallly, the mRNA level of LmCYP302a1, LmCYP315a1 and LmCYP314a1 responsible for 20E synthesis, LmE75 and LmE74 genes involved in the 20E signaling pathway, LmGfat, LmUAP1 and LmCHT10 genes involved in chitin metabolism pathway were dramatically decreased in the dsLmRan-injected nymphs. Together, the results indicated that LmRan participate in the 20E signaling pathway, which is essential for the growth and development of locusts.
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Affiliation(s)
- Xiaojian Liu
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Zheng Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Min Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Xiaoming Zhao
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingting Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Weimin Liu
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Jianzhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China.
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HflX is a GTPase that controls hypoxia-induced replication arrest in slow-growing mycobacteria. Proc Natl Acad Sci U S A 2021; 118:2006717118. [PMID: 33723035 DOI: 10.1073/pnas.2006717118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
GTPase high frequency of lysogenization X (HflX) is highly conserved in prokaryotes and acts as a ribosome-splitting factor as part of the heat shock response in Escherichia coli. Here we report that HflX produced by slow-growing Mycobacterium bovis bacillus Calmette-Guérin (BCG) is a GTPase that plays a critical role in the pathogen's transition to a nonreplicating, drug-tolerant state in response to hypoxia. Indeed, HflX-deficient M. bovis BCG (KO) replicated markedly faster in the microaerophilic phase of a hypoxia model that resulted in premature entry into dormancy. The KO mutant displayed hallmarks of nonreplicating mycobacteria, including phenotypic drug resistance, altered morphology, low intracellular ATP levels, and overexpression of Dormancy (Dos) regulon proteins. Mice nasally infected with HflX KO mutant displayed increased bacterial burden in the lungs, spleen, and lymph nodes during the chronic phase of infection, consistent with the higher replication rate observed in vitro in microaerophilic conditions. Unlike fast growing mycobacteria, M. bovis BCG HlfX was not involved in antibiotic resistance under aerobic growth. Proteomics, pull-down, and ribo-sequencing approaches supported that mycobacterial HflX is a ribosome-binding protein that controls translational activity of the cell. With HflX fully conserved between M. bovis BCG and M. tuberculosis, our work provides further insights into the molecular mechanisms deployed by pathogenic mycobacteria to adapt to their hypoxic microenvironment.
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Asli A, Higazy-Mreih S, Avital-Shacham M, Kosloff M. Residue-level determinants of RGS R4 subfamily GAP activity and specificity towards the G i subfamily. Cell Mol Life Sci 2021; 78:6305-6318. [PMID: 34292354 PMCID: PMC11072900 DOI: 10.1007/s00018-021-03898-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/18/2021] [Accepted: 07/09/2021] [Indexed: 01/01/2023]
Abstract
The structural basis for the GTPase-accelerating activity of regulators of G protein signaling (RGS) proteins, as well as the mechanistic basis for their specificity in interacting with the heterotrimeric (αβγ) G proteins they inactivate, is not sufficiently understood at the family level. Here, we used biochemical assays to compare RGS domains across the RGS family and map those individual residues that favorably contribute to GTPase-accelerating activity, and those residues responsible for attenuating RGS domain interactions with Gα subunits. We show that conserved interactions of RGS residues with both the Gα switch I and II regions are crucial for RGS activity, while the reciprocal effects of "modulatory" and "disruptor" residues selectively modulate RGS activity. Our results quantify how specific interactions between RGS domains and Gα subunits are set by a balance between favorable RGS residue interactions with particular Gα switch regions, and unfavorable interactions with the Gα helical domain.
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Affiliation(s)
- Ali Asli
- The Department of Human Biology, Faculty of Natural Science, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel
| | - Sabreen Higazy-Mreih
- The Department of Human Biology, Faculty of Natural Science, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel
| | - Meirav Avital-Shacham
- The Department of Human Biology, Faculty of Natural Science, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel
| | - Mickey Kosloff
- The Department of Human Biology, Faculty of Natural Science, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel.
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Adhikari N, McGill IN, Hadwiger JA. MAPK docking motif in the Dictyostelium Gα2 subunit is required for aggregation and transcription factor translocation. Cell Signal 2021; 87:110117. [PMID: 34418534 DOI: 10.1016/j.cellsig.2021.110117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 01/05/2023]
Abstract
Some G protein alpha subunits contain a mitogen-activated protein kinase (MAPK) docking motif (D-motif) near the amino terminus that can impact cellular responses to external signals. The Dictyostelium Gα2 G protein subunit is required for chemotaxis to cAMP during the onset of multicellular development and this subunit contains a putative D-motif near the amino terminus. The Gα2 subunit D-motif was altered to examine its potential role in chemotaxis and multicellular development. In gα2- cells the expression of the D-motif mutant (Gα2D-) or wild-type subunit from high copy number vectors rescued cell aggregation but blocked the transition of mounds into slugs. This phenotype was also observed in parental strains with a wild-type gα2 locus indicating that the heterologous Gα2 subunit expression interferes with multicellular morphogenesis. Expression of the Gα2D- subunit from a low copy number vectors in gα2- cells did not rescue aggregation whereas the wild-type Gα2 subunit rescued aggregation efficiently and allowed wild-type morphological development. The Gα2D- and Gα2 subunit were both capable of restoring comparable levels of cAMP stimulated motility and the ability to co-aggregate with wild-type cells implying that the aggregation defect of Gα2D- expressing cells is due to insufficient intercellular signaling. Expression of the Gα2 subunit but not the Gα2D- subunit fully restored the ability of cAMP to stimulate the translocation of the GtaC transcription factor suggesting the D-motif is important for transcription factor regulation. These results suggest that the D-motif of Gα2 plays a role in aggregation and other developmental responses involved with cAMP signaling.
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Affiliation(s)
- Nirakar Adhikari
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Imani N McGill
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America
| | - Jeffrey A Hadwiger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078-3020, United States of America.
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Research Advances in Heterotrimeric G-Protein α Subunits and Uncanonical G-Protein Coupled Receptors in Plants. Int J Mol Sci 2021; 22:ijms22168678. [PMID: 34445383 PMCID: PMC8395518 DOI: 10.3390/ijms22168678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/22/2022] Open
Abstract
As crucial signal transducers, G-proteins and G-protein-coupled receptors (GPCRs) have attracted increasing attention in the field of signal transduction. Research on G-proteins and GPCRs has mainly focused on animals, while research on plants is relatively rare. The mode of action of G-proteins is quite different from that in animals. The G-protein α (Gα) subunit is the most essential member of the G-protein signal cycle in animals and plants. The G-protein is activated when Gα releases GDP and binds to GTP, and the relationships with the GPCR and the downstream signal are also achieved by Gα coupling. It is important to study the role of Gα in the signaling pathway to explore the regulatory mechanism of G-proteins. The existence of a self-activated Gα in plants makes it unnecessary for the canonical GPCR to activate the G-protein by exchanging GDP with GTP. However, putative GPCRs have been found and proven to play important roles in G-protein signal transduction. The unique mode of action of G-proteins and the function of putative GPCRs in plants suggest that the same definition used in animal research cannot be used to study uncanonical GPCRs in plants. This review focuses on the different functions of the Gα and the mode of action between plants and animals as well as the functions of the uncanonical GPCR. This review employs a new perspective to define uncanonical GPCRs in plants and emphasizes the role of uncanonical GPCRs and Gα subunits in plant stress resistance and agricultural production.
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41
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The G protein-first activation mechanism of opioid receptors by Gi protein and agonists. QRB DISCOVERY 2021. [PMID: 37529677 PMCID: PMC10392629 DOI: 10.1017/qrd.2021.7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AbstractWe report the G protein-first mechanism for activation of G protein-coupled receptors (GPCR) for the three closest subtypes of the opioid receptors (OR), μOR, κOR and δOR. We find that they couple to the inactive Gi protein-bound guanosine diphosphate (GDP) prior to agonist binding. The inactive Gi protein forms anchors to the intracellular loops of the inactive apo-μOR, apo-κOR and apo-δOR, inducing opening of the cytoplasmic region to form a pre-activated state that holds Gi protein in place until agonist binds. Then, agonist binds to μOR, κOR and δOR already complexed with Gi protein, to trigger the Gαi to open up the tightly coupled GDP binding site, making GDP accessible for GTP exchange, an essential step for Gi signalling. We show that the agonist alone cannot open the intracellular region of μOR and κOR, requiring Gi protein to open the cytoplasmic region by itself. We consider that this G protein-first mechanism may apply to activation of other Class A GPCRs. However, for δOR, agonist binding can open up the intracellular region to encourage Gi protein recruitment. Thus, activation of Gi protein mediated by δOR favourably may proceed with either ligand-first or G protein-first activation mechanisms.
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42
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Signaling Pathways Regulated by UBR Box-Containing E3 Ligases. Int J Mol Sci 2021; 22:ijms22158323. [PMID: 34361089 PMCID: PMC8346999 DOI: 10.3390/ijms22158323] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/31/2022] Open
Abstract
UBR box E3 ligases, also called N-recognins, are integral components of the N-degron pathway. Representative N-recognins include UBR1, UBR2, UBR4, and UBR5, and they bind destabilizing N-terminal residues, termed N-degrons. Understanding the molecular bases of their substrate recognition and the biological impact of the clearance of their substrates on cellular signaling pathways can provide valuable insights into the regulation of these pathways. This review provides an overview of the current knowledge of the binding mechanism of UBR box N-recognin/N-degron interactions and their roles in signaling pathways linked to G-protein-coupled receptors, apoptosis, mitochondrial quality control, inflammation, and DNA damage. The targeting of these UBR box N-recognins can provide potential therapies to treat diseases such as cancer and neurodegenerative diseases.
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Hwang J, Jang B, Kim A, Lee Y, Lee J, Kim C, Kim J, Moon KM, Kim K, Wagle R, Song YH, Oh ES. Syndecan Transmembrane Domain Specifically Regulates Downstream Signaling Events of the Transmembrane Receptor Cytoplasmic Domain. Int J Mol Sci 2021; 22:ijms22157918. [PMID: 34360683 PMCID: PMC8347082 DOI: 10.3390/ijms22157918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the known importance of the transmembrane domain (TMD) of syndecan receptors in cell adhesion and signaling, the molecular basis for syndecan TMD function remains unknown. Using in vivo invertebrate models, we found that mammalian syndecan-2 rescued both the guidance defects in C. elegans hermaphrodite-specific neurons and the impaired development of the midline axons of Drosophila caused by the loss of endogenous syndecan. These compensatory effects, however, were reduced significantly when syndecan-2 dimerization-defective TMD mutants were introduced. To further investigate the role of the TMD, we generated a chimera, 2eTPC, comprising the TMD of syndecan-2 linked to the cytoplasmic domain of platelet-derived growth factor receptor (PDGFR). This chimera exhibited SDS-resistant dimer formation that was lost in the corresponding dimerization-defective syndecan-2 TMD mutant, 2eT(GL)PC. Moreover, 2eTPC specifically enhanced Tyr 579 and Tyr 857 phosphorylation in the PDGFR cytoplasmic domain, while the TMD mutant failed to support such phosphorylation. Finally, 2eTPC, but not 2eT(GL)PC, induced phosphorylation of Src and PI3 kinase (known downstream effectors of Tyr 579 phosphorylation) and promoted Src-mediated migration of NIH3T3 cells. Taken together, these data suggest that the TMD of a syndecan-2 specifically regulates receptor cytoplasmic domain function and subsequent downstream signaling events controlling cell behavior.
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Affiliation(s)
- Jisun Hwang
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea; (J.H.); (B.J.); (A.K.); (Y.L.)
| | - Bohee Jang
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea; (J.H.); (B.J.); (A.K.); (Y.L.)
| | - Ayoung Kim
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea; (J.H.); (B.J.); (A.K.); (Y.L.)
| | - Yejin Lee
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea; (J.H.); (B.J.); (A.K.); (Y.L.)
| | - Joonha Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (J.L.); (C.K.)
| | - Chungho Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (J.L.); (C.K.)
| | - Jinmahn Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.K.); (K.M.M.); (K.K.)
| | - Kyeong Min Moon
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.K.); (K.M.M.); (K.K.)
| | - Kyuhyung Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.K.); (K.M.M.); (K.K.)
| | - Ram Wagle
- Department of Biomedical Gerontology, Ilsong Institute of Life Science, Hallym University, Anyang-si 14066, Korea; (R.W.); (Y.-H.S.)
| | - Young-Han Song
- Department of Biomedical Gerontology, Ilsong Institute of Life Science, Hallym University, Anyang-si 14066, Korea; (R.W.); (Y.-H.S.)
| | - Eok-Soo Oh
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Korea; (J.H.); (B.J.); (A.K.); (Y.L.)
- Correspondence: ; Tel./Fax: +82-2-3277-3761
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44
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Palanisamy S, Xue C, Ishiyama S, Naga Prasad SV, Gabrielson K. GPCR-ErbB transactivation pathways and clinical implications. Cell Signal 2021; 86:110092. [PMID: 34303814 DOI: 10.1016/j.cellsig.2021.110092] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022]
Abstract
Cell surface receptors including the epidermal growth factor receptor (EGFR) family and G-protein coupled receptors (GPCRs) play quintessential roles in physiology, and in diseases, including cardiovascular diseases. While downstream signaling from these individual receptor families has been well studied, the cross-talk between EGF and GPCR receptor families is still incompletely understood. Including members of both receptor families, the number of receptor and ligand combinations for unique interactions is vast, offering a frontier of pharmacologic targets to explore for preventing and treating disease. This molecular cross-talk, called receptor transactivation, is reviewed here with a focus on the cardiovascular system featuring the well-studied GPCR receptors, but also discussing less-studied receptors from both families for a broad understanding of context of expansile interactions, repertoire of cellular signaling, and disease consequences. Attention is given to cell type, level of chronicity, and disease context given that transactivation and comorbidities, including diabetes, hypertension, coronavirus infection, impact cardiovascular disease and health outcomes.
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Affiliation(s)
| | - Carolyn Xue
- University of California, Los Angeles, 101 Hershey Hall, 612 Charles E. Young Drive South, Los Angeles, CA 90095, USA.
| | - Shun Ishiyama
- Sidney Kimmel Cancer Center, Department of Surgery, Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Coloproctological Surgery, Juntendo University School of Medicine, Tokyo, Japan.
| | - Sathyamangla Venkata Naga Prasad
- NB50, Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, 1, Cleveland, OH 44195, USA.
| | - Kathleen Gabrielson
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University, School of Medicine, 733 North Broadway, Miller Research Building, Room 807, Baltimore, MD 21205-2196, USA.
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45
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Maruta N, Trusov Y, Urano D, Chakravorty D, Assmann SM, Jones AM, Botella JR. GTP binding by Arabidopsis extra-large G protein 2 is not essential for its functions. PLANT PHYSIOLOGY 2021; 186:1240-1253. [PMID: 33729516 PMCID: PMC8195506 DOI: 10.1093/plphys/kiab119] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 05/06/2023]
Abstract
The extra-large guanosine-5'-triphosphate (GTP)-binding protein 2, XLG2, is an unconventional Gα subunit of the Arabidopsis (Arabidopsis thaliana) heterotrimeric GTP-binding protein complex with a major role in plant defense. In vitro biochemical analyses and molecular dynamic simulations show that affinity of XLG2 for GTP is two orders of magnitude lower than that of the conventional Gα, AtGPA1. Here we tested the physiological relevance of GTP binding by XLG2. We generated an XLG2(T476N) variant with abolished GTP binding, as confirmed by in vitro GTPγS binding assay. Yeast three-hybrid, bimolecular fluorescence complementation, and split firefly-luciferase complementation assays revealed that the nucleotide-depleted XLG2(T476N) retained wild-type XLG2-like interactions with the Gβγ dimer and defense-related receptor-like kinases. Both wild-type and nucleotide-depleted XLG2(T476N) restored the defense responses against Fusarium oxysporum and Pseudomonas syringae compromised in the xlg2 xlg3 double mutant. Additionally, XLG2(T476N) was fully functional restoring stomatal density, root growth, and sensitivity to NaCl, but failed to complement impaired germination and vernalization-induced flowering. We conclude that XLG2 is able to function in a GTP-independent manner and discuss its possible mechanisms of action.
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Affiliation(s)
- Natsumi Maruta
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuri Trusov
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - David Chakravorty
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alan M Jones
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
- Author for communication:
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46
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Martemyanov KA. Mechanisms of Gβγ Release upon GPCR Activation. Trends Biochem Sci 2021; 46:703-704. [PMID: 34034924 DOI: 10.1016/j.tibs.2021.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022]
Abstract
Gβγ release is a key event in the transduction of GPCR signals. However, the molecular mechanisms of this process have been unclear. A recent report by Knight et al. provides important clues into the sequence of events that lead to the liberation of Gβγ upon G protein activation by GPCRs.
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Affiliation(s)
- Kirill A Martemyanov
- Department of Neuroscience, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, USA.
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47
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The GNAQ T96S Mutation Affects Cell Signaling and Enhances the Oncogenic Properties of Hepatocellular Carcinoma. Int J Mol Sci 2021; 22:ijms22063284. [PMID: 33807071 PMCID: PMC8004934 DOI: 10.3390/ijms22063284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the most common malignant tumor in the liver, grows and metastasizes rapidly. Despite advances in treatment modalities, the five-year survival rate of HCC remains less than 30%. We sought genetic mutations that may affect the oncogenic properties of HCC, using The Cancer Genome Atlas (TCGA) data analysis. We found that the GNAQ T96S mutation (threonine 96 to serine alteration of the Gαq protein) was present in 12 out of 373 HCC patients (3.2%). To examine the effect of the GNAQ T96S mutation on HCC, we transfected the SK-Hep-1 cell line with the wild-type or the mutant GNAQ T96S expression vector. Transfection with the wild-type GNAQ expression vector enhanced anchorage-independent growth, migration, and the MAPK pathways in the SK-Hep-1 cells compared to control vector transfection. Moreover, cell proliferation, anchorage-independent growth, migration, and the MAPK pathways were further enhanced in the SK-Hep-1 cells transfected with the GNAQ T96S expression vector compared to the wild-type GNAQ-transfected cells. In silico structural analysis shows that the substitution of the GNAQ amino acid threonine 96 with a serine may destabilize the interaction between the regulator of G protein signaling (RGS) protein and GNAQ. This may reduce the inhibitory effect of RGS on GNAQ signaling, enhancing the GNAQ signaling pathway. Single nucleotide polymorphism (SNP) genotyping analysis for Korean HCC patients shows that the GNAQ T96S mutation was found in only one of the 456 patients (0.22%). Our data suggest that the GNAQ T96S hotspot mutation may play an oncogenic role in HCC by potentiating the GNAQ signal transduction pathway.
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WDR35 is involved in subcellular localization of acetylated tubulin in 293T cells. Biochem Biophys Res Commun 2021; 547:169-175. [PMID: 33610917 DOI: 10.1016/j.bbrc.2021.01.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 11/23/2022]
Abstract
WDR35/IFT121 is an intraflagellar transport protein in primary cilia, which is associated with RagA, an mTORC1-activating protein. To elucidate the functions of the interaction between WDR35 and RagA in primary cilia, as well as mTOR signaling, we identified WDR35-interacting proteins using mass spectrometry. We found that WDR35 associates with CCT complex proteins including TCP1/CCT1, which act as molecular chaperones for α-tubulin folding. Immunostaining showed that acetylated α-tubulin was concentrated in the vicinity of primary cilia in 293T cells. In contrast, acetylated tubulin was dispersed in WDR35 partial knockout cells established from 293T cells. Similarly, scattered subcellular localization of acetylated tubulin was observed in RagA knockout cells. RagA was present in the primary cilia of NIH3T3 cells, and the GDP form of RagA exhibited strong binding to WDR35 and negative regulation of primary cilium formation. These results suggest that WDR35 is involved in the subcellular localization of acetylated tubulin in primary cilia via its interactions with TCP1 and/or RagA family proteins.
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Takagi J, Cho C, Duvalyan A, Yan Y, Halloran M, Hanson-Smith V, Thorner J, Finnigan GC. Reconstructed evolutionary history of the yeast septins Cdc11 and Shs1. G3-GENES GENOMES GENETICS 2021; 11:6025175. [PMID: 33561226 PMCID: PMC7849910 DOI: 10.1093/g3journal/jkaa006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/13/2020] [Indexed: 11/21/2022]
Abstract
Septins are GTP-binding proteins conserved across metazoans. They can polymerize into extended filaments and, hence, are considered a component of the cytoskeleton. The number of individual septins varies across the tree of life—yeast (Saccharomyces cerevisiae) has seven distinct subunits, a nematode (Caenorhabditis elegans) has two, and humans have 13. However, the overall geometric unit (an apolar hetero-octameric protomer and filaments assembled there from) has been conserved. To understand septin evolutionary variation, we focused on a related pair of yeast subunits (Cdc11 and Shs1) that appear to have arisen from gene duplication within the fungal clade. Either Cdc11 or Shs1 occupies the terminal position within a hetero-octamer, yet Cdc11 is essential for septin function and cell viability, whereas Shs1 is not. To discern the molecular basis of this divergence, we utilized ancestral gene reconstruction to predict, synthesize, and experimentally examine the most recent common ancestor (“Anc.11-S”) of Cdc11 and Shs1. Anc.11-S was able to occupy the terminal position within an octamer, just like the modern subunits. Although Anc.11-S supplied many of the known functions of Cdc11, it was unable to replace the distinct function(s) of Shs1. To further evaluate the history of Shs1, additional intermediates along a proposed trajectory from Anc.11-S to yeast Shs1 were generated and tested. We demonstrate that multiple events contributed to the current properties of Shs1: (1) loss of Shs1–Shs1 self-association early after duplication, (2) co-evolution of heterotypic Cdc11–Shs1 interaction between neighboring hetero-octamers, and (3) eventual repurposing and acquisition of novel function(s) for its C-terminal extension domain. Thus, a pair of duplicated proteins, despite constraints imposed by assembly into a highly conserved multi-subunit structure, could evolve new functionality via a complex evolutionary pathway.
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Affiliation(s)
- Julie Takagi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Christina Cho
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Angela Duvalyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Yao Yan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Megan Halloran
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Victor Hanson-Smith
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA
| | - Jeremy Thorner
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202, USA
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
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Cross-Kingdom Activation of Vibrio Toxins by ADP-Ribosylation Factor Family GTPases. J Bacteriol 2020; 202:JB.00278-20. [PMID: 32900828 DOI: 10.1128/jb.00278-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic Vibrio species use many different approaches to subvert, attack, and undermine the host response. The toxins they produce are often responsible for the devastating effects associated with their diseases. These toxins target a variety of host proteins, which leads to deleterious effects, including dissolution of cell organelle integrity and inhibition of protein secretion. Becoming increasingly prevalent as cofactors for Vibrio toxins are proteins of the small GTPase families. ADP-ribosylation factor small GTPases (ARFs) in particular are emerging as a common host cofactor necessary for full activation of Vibrio toxins. While ARFs are not the direct target of Vibrio cholerae cholera toxin (CT), ARF binding is required for its optimal activity as an ADP-ribosyltransferase. The makes caterpillars floppy (MCF)-like and the domain X (DmX) effectors of the Vibrio vulnificus multifunctional autoprocessing repeats-in-toxin (MARTX) toxin also both require ARFs to initiate autoprocessing and activation as independent effectors. ARFs are ubiquitously expressed in eukaryotes and are key regulators of many cellular processes, and as such they are ideal cofactors for Vibrio pathogens that infect many host species. In this review, we cover in detail the known Vibrio toxins that use ARFs as cross-kingdom activators to both stimulate and optimize their activity. We further discuss how these contrast to toxins and effectors from other bacterial species that coactivate, stimulate, or directly modify host ARFs as their mechanisms of action.
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