1
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Zhang S, Zhang T, Fu Y. Proteome-wide structural analysis quantifies structural conservation across distant species. Genome Res 2023; 33:1975-1993. [PMID: 37993136 PMCID: PMC10760455 DOI: 10.1101/gr.277771.123] [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: 02/03/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
Traditional evolutionary biology research mainly relies on sequence information to infer evolutionary relationships between genes or proteins. In contrast, protein structural information has long been overlooked, although structures are more conserved and closely linked to the functions than the sequences. To address this gap, we conducted a proteome-wide structural analysis using experimental and computed protein structures for organisms from the three distinct domains, including Homo sapiens (eukarya), Escherichia coli (bacteria), and Methanocaldococcus jannaschii (archaea). We reveal the distribution of structural similarity and sequence identity at the genomic level and characterize the twilight zone, where signals obtained from sequence alignment are blurred and evolutionary relationships cannot be inferred unambiguously. We find that structurally similar homologous protein pairs in the twilight zone account for ∼0.004%-0.021% of all possible protein pair combinations, which translates to ∼8%-32% of the protein-coding genes, depending on the species under comparison. In addition, by comparing the structural homologs, we show that human proteins involved in the energy supply are more similar to their E. coli homologs, whereas proteins relating to the central dogma are more similar to their M. jannaschii homologs. We also identify a bacterial GPCR homolog in the E. coli proteome that displays distinctive domain architecture. Our results shed light on the characteristics of the twilight zone and the origin of different pathways from a protein structure perspective, highlighting an exciting new frontier in evolutionary biology.
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Affiliation(s)
- Shijie Zhang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Teng Zhang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yuan Fu
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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2
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Borgo GM, Burke TP, Tran CJ, Lo NTN, Engström P, Welch MD. A patatin-like phospholipase mediates Rickettsia parkeri escape from host membranes. Nat Commun 2022; 13:3656. [PMID: 35760786 PMCID: PMC9237051 DOI: 10.1038/s41467-022-31351-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/15/2022] [Indexed: 12/25/2022] Open
Abstract
Rickettsia species of the spotted fever group are arthropod-borne obligate intracellular bacteria that can cause mild to severe human disease. These bacteria invade host cells, replicate in the cell cytosol, and spread from cell to cell. To access the host cytosol and avoid immune detection, they escape membrane-bound vacuoles by expressing factors that disrupt host membranes. Here, we show that a patatin-like phospholipase A2 enzyme (Pat1) facilitates Rickettsia parkeri infection by promoting escape from host membranes and cell-cell spread. Pat1 is important for infection in a mouse model and, at the cellular level, is crucial for efficiently escaping from single and double membrane-bound vacuoles into the host cytosol, and for avoiding host galectins that mark damaged membranes. Pat1 is also important for avoiding host polyubiquitin, preventing recruitment of autophagy receptor p62, and promoting actin-based motility and cell-cell spread. Pathogenic Rickettsia species are arthropod-borne, obligate intracellular bacteria that invade host cells, replicate in the cell cytosol, and spread from cell to cell. Here, Borgo et al. identify a Rickettsia phospholipase enzyme that is important for infection by helping the bacteria escape from host cell vacuoles into the host cytosol, preventing targeting by autophagy, and promoting bacterial motility and spread to other cells.
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Affiliation(s)
- Gina M Borgo
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Thomas P Burke
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Cuong J Tran
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T N Lo
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Patrik Engström
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Primordial Genetics, San Diego, CA, USA
| | - Matthew D Welch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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3
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Chatelain P, Astier J, Wendehenne D, Rosnoblet C, Jeandroz S. Identification of Partner Proteins of the Algae Klebsormidium nitens NO Synthases: Toward a Better Understanding of NO Signaling in Eukaryotic Photosynthetic Organisms. FRONTIERS IN PLANT SCIENCE 2021; 12:797451. [PMID: 35003186 PMCID: PMC8728061 DOI: 10.3389/fpls.2021.797451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
In animals, NO is synthesized from L-arginine by three isoforms of nitric oxide synthase (NOS) enzyme. NO production and effects have also been reported in plants but the identification of its sources, especially the enzymatic ones, remains one of the critical issues in the field. NOS-like activities have been reported, although there are no homologs of mammalian NOS in the land plant genomes sequenced so far. However, several NOS homologs have been found in algal genomes and transcriptomes. A first study has characterized a functional NOS in the chlorophyte Ostreococcus tauri and the presence of NOS homologs was later confirmed in a dozen algae. These results raise the questions of the significance of the presence of NOS and their molecular diversity in algae. We hypothesize that comparisons among protein structures of the two KnNOS, together with the identification of their interacting partner proteins, might allow a better understanding of the molecular diversification and functioning of NOS in different physiological contexts and, more generally, new insights into NO signaling in photosynthetic organisms. We recently identified two NOS homologs sequences in the genome of the streptophyte Klebsormidium nitens, a model alga in the study of plant adaptation to terrestrial life. The first sequence, named KnNOS1, contains canonical NOS signatures while the second, named KnNOS2, presents a large C-ter extension including a globin domain. In order to identify putative candidates for KnNOSs partner proteins, we draw the protein-protein interaction networks of the three human NOS using the BioGRID database and hypothesized on the biological role of K. nitens orthologs. Some of these conserved partners are known to be involved in mammalian NOSs regulation and functioning. In parallel, our methodological strategy for the identification of partner proteins of KnNOS1 and KnNOS2 by in vitro pull-down assay is presented.
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4
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Orth B, Sander B, Möglich A, Diederichs K, Eilers M, Lorenz S. Identification of an atypical interaction site in the BTB domain of the MYC-interacting zinc-finger protein 1. Structure 2021; 29:1230-1240.e5. [PMID: 34186024 DOI: 10.1016/j.str.2021.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/26/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
The repurposing of structurally conserved protein domains in different functional contexts is thought to be a driving force in the evolution of complex protein interaction networks. The BTB/POZ domain is such a versatile binding module that occurs over 200 times in the human proteome with diverse protein-specific adaptations. In BTB-zinc-finger transcription factors, the BTB domain drives homo- and heterodimerization as well as interactions with non-BTB-domain-containing proteins. Which mechanisms encode specificity in these interactions at a structural level is incompletely understood. Here, we uncover an atypical peptide-binding site in the BTB domain of the MYC-interacting zinc-finger protein 1 (MIZ1) that arises from local flexibility of the core BTB fold and may provide a target site for MIZ1-directed therapeutic approaches. Intriguingly, the identified binding mode requires the BTB domain to be in a homodimeric state, thus holding opportunities for functional discrimination between homo- and heterodimers of MIZ1 in the cell.
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Affiliation(s)
- Barbara Orth
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany; Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Bodo Sander
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, University of Bayreuth, 95447 Bayreuth, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Martin Eilers
- Lehrstuhl für Biochemie, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sonja Lorenz
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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5
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Wittenborn EC, Marletta MA. Structural Perspectives on the Mechanism of Soluble Guanylate Cyclase Activation. Int J Mol Sci 2021; 22:ijms22115439. [PMID: 34064029 PMCID: PMC8196705 DOI: 10.3390/ijms22115439] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/30/2022] Open
Abstract
The enzyme soluble guanylate cyclase (sGC) is the prototypical nitric oxide (NO) receptor in humans and other higher eukaryotes and is responsible for transducing the initial NO signal to the secondary messenger cyclic guanosine monophosphate (cGMP). Generation of cGMP in turn leads to diverse physiological effects in the cardiopulmonary, vascular, and neurological systems. Given these important downstream effects, sGC has been biochemically characterized in great detail in the four decades since its discovery. Structures of full-length sGC, however, have proven elusive until very recently. In 2019, advances in single particle cryo–electron microscopy (cryo-EM) enabled visualization of full-length sGC for the first time. This review will summarize insights revealed by the structures of sGC in the unactivated and activated states and discuss their implications in the mechanism of sGC activation.
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6
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Ferkey DM, Sengupta P, L’Etoile ND. Chemosensory signal transduction in Caenorhabditis elegans. Genetics 2021; 217:iyab004. [PMID: 33693646 PMCID: PMC8045692 DOI: 10.1093/genetics/iyab004] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Chemosensory neurons translate perception of external chemical cues, including odorants, tastants, and pheromones, into information that drives attraction or avoidance motor programs. In the laboratory, robust behavioral assays, coupled with powerful genetic, molecular and optical tools, have made Caenorhabditis elegans an ideal experimental system in which to dissect the contributions of individual genes and neurons to ethologically relevant chemosensory behaviors. Here, we review current knowledge of the neurons, signal transduction molecules and regulatory mechanisms that underlie the response of C. elegans to chemicals, including pheromones. The majority of identified molecules and pathways share remarkable homology with sensory mechanisms in other organisms. With the development of new tools and technologies, we anticipate that continued study of chemosensory signal transduction and processing in C. elegans will yield additional new insights into the mechanisms by which this animal is able to detect and discriminate among thousands of chemical cues with a limited sensory neuron repertoire.
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Affiliation(s)
- Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Noelle D L’Etoile
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
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7
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Astier J, Rossi J, Chatelain P, Klinguer A, Besson-Bard A, Rosnoblet C, Jeandroz S, Nicolas-Francès V, Wendehenne D. Nitric oxide production and signalling in algae. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:781-792. [PMID: 32910824 DOI: 10.1093/jxb/eraa421] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/07/2020] [Indexed: 05/27/2023]
Abstract
Nitric oxide (NO) was the first identified gaseous messenger and is now well established as a major ubiquitous signalling molecule. The rapid development of our understanding of NO biology in embryophytes came with the partial characterization of the pathways underlying its production and with the decrypting of signalling networks mediating its effects. Notably, the identification of proteins regulated by NO through nitrosation greatly enhanced our perception of NO functions. In comparison, the role of NO in algae has been less investigated. Yet, studies in Chlamydomonas reinhardtii have produced key insights into NO production through the identification of NO-forming nitrite reductase and of S-nitrosated proteins. More intriguingly, in contrast to embryophytes, a few algal species possess a conserved nitric oxide synthase, the main enzyme catalysing NO synthesis in metazoans. This latter finding paves the way for a deeper characterization of novel members of the NO synthase family. Nevertheless, the typical NO-cyclic GMP signalling module transducing NO effects in metazoans is not conserved in algae, nor in embryophytes, highlighting a divergent acquisition of NO signalling between the green and the animal lineages.
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Affiliation(s)
- Jeremy Astier
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Jordan Rossi
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Pauline Chatelain
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Agnès Klinguer
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Angélique Besson-Bard
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Sylvain Jeandroz
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - David Wendehenne
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne Franche-Comté, Dijon, France
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8
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Manna D, Cordara G, Krengel U. Crystal structure of MOA in complex with a peptide fragment: A protease caught in flagranti. Curr Res Struct Biol 2020; 2:56-67. [PMID: 34235469 PMCID: PMC8244254 DOI: 10.1016/j.crstbi.2020.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/28/2020] [Accepted: 04/06/2020] [Indexed: 11/20/2022] Open
Abstract
The Marasmius oreades agglutinin (MOA) is the holotype of an emerging family of fungal chimerolectins and an active Ca2+/Mn2+-dependent protease, which exhibits a unique papain-like fold with special active site features. Here we investigated the functional significance of the structural elements differentiating MOA from other papain-like cysteine proteases. X-ray crystal structures of MOA co-crystallized with two synthetic substrates reveal cleaved peptides bound to the catalytic site, corresponding to the final products of the proteolytic reaction. Anomalous diffraction data on crystals grown in the presence of calcium and manganese, cadmium or zinc resolve the calcium/manganese preference of MOA and elucidate the inhibitory roles of zinc and cadmium towards papain-like cysteine proteases in general. The reported structures, together with activity data of MOA active site variants, point to a conservation of the general proteolysis mechanism established for papain. Ultimately, the findings suggest that papain and the papain-like domain of MOA are the product of convergent evolution.
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Affiliation(s)
- Dipankar Manna
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
| | - Gabriele Cordara
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, 0315, Oslo, Norway
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9
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Bose A, Banerjee S, Visweswariah SS. Mutational landscape of receptor guanylyl cyclase C: Functional analysis and disease-related mutations. IUBMB Life 2020; 72:1145-1159. [PMID: 32293781 DOI: 10.1002/iub.2283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/18/2022]
Abstract
Guanylyl cyclase C (GC-C) is the receptor for the heat-stable enterotoxin, which causes diarrhea, and the endogenous ligands, guanylin and uroguanylin. GC-C is predominantly expressed in the intestinal epithelium and regulates fluid and ion secretion in the gut. The receptor has a complex domain organization, and in the absence of structural information, mutational analysis provides clues to mechanisms of regulation of this protein. Here, we review the mutational landscape of this receptor that reveals regulatory features critical for its activity. We also summarize the available information on mutations in GC-C that have been reported in humans and contribute to severe gastrointestinal abnormalities. Since GC-C is also expressed in extra-intestinal tissues, it is likely that mutations thus far reported in humans may also affect other organ systems, warranting a close observation of these patients in future.
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Affiliation(s)
- Avipsa Bose
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sanghita Banerjee
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
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10
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Butryn A, Raza H, Rada H, Moraes I, Owens RJ, Orville AM. Molecular basis for GTP recognition by light-activated guanylate cyclase RhGC. FEBS J 2019; 287:2797-2807. [PMID: 31808997 PMCID: PMC7384201 DOI: 10.1111/febs.15167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/23/2019] [Accepted: 12/05/2019] [Indexed: 11/27/2022]
Abstract
Cyclic guanosine 3',5'-monophosphate (cGMP) is an intracellular signalling molecule involved in many sensory and developmental processes. Synthesis of cGMP from GTP is catalysed by guanylate cyclase (GC) in a reaction analogous to cAMP formation by adenylate cyclase (AC). Although detailed structural information is available on the catalytic region of nucleotidyl cyclases (NCs) in various states, these atomic models do not provide a sufficient explanation for the substrate selectivity between GC and AC family members. Detailed structural information on the GC domain in its active conformation is largely missing, and no crystal structure of a GTP-bound wild-type GC domain has been published to date. Here, we describe the crystal structure of the catalytic domain of rhodopsin-GC (RhGC) from Catenaria anguillulae in complex with GTP at 1.7 Å resolution. Our study reveals the organization of a eukaryotic GC domain in its active conformation. We observe that the binding mode of the substrate GTP is similar to that of AC-ATP interaction, although surprisingly not all of the interactions predicted to be responsible for base recognition are present. The structure provides insights into potential mechanisms of substrate discrimination and activity regulation that may be common to all class III purine NCs. DATABASE: Structural data are available in Protein Data Bank database under the accession number 6SIR. ENZYMES: EC4.6.1.2.
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Affiliation(s)
- Agata Butryn
- Diamond Light Source Limited, Didcot, UK.,Research Complex at Harwell, Didcot, UK
| | - Hadeeqa Raza
- Diamond Light Source Limited, Didcot, UK.,Research Complex at Harwell, Didcot, UK
| | - Heather Rada
- Protein Production UK, Research Complex at Harwell, Didcot, UK
| | - Isabel Moraes
- Research Complex at Harwell, Didcot, UK.,Membrane Protein Laboratory, Diamond Light Source Limited, Didcot, UK
| | - Raymond J Owens
- Protein Production UK, Research Complex at Harwell, Didcot, UK
| | - Allen M Orville
- Diamond Light Source Limited, Didcot, UK.,Research Complex at Harwell, Didcot, UK
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11
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Evasion of autophagy mediated by Rickettsia surface protein OmpB is critical for virulence. Nat Microbiol 2019; 4:2538-2551. [PMID: 31611642 PMCID: PMC6988571 DOI: 10.1038/s41564-019-0583-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/10/2019] [Indexed: 01/05/2023]
Abstract
Rickettsia are obligate intracellular bacteria that evade antimicrobial autophagy in the host cell cytosol by unknown mechanisms. Other cytosolic pathogens block different steps of autophagy targeting, including the initial step of polyubiquitin-coat formation. One mechanism of evasion is to mobilize actin to the bacterial surface. Here, we show that actin mobilization is insufficient to block autophagy recognition of the pathogen Rickettsia parkeri. Instead, R. parkeri employs outer membrane protein B (OmpB) to block ubiquitylation of the bacterial surface proteins, including OmpA, and subsequent recognition by autophagy receptors. OmpB is also required for the formation of a capsule-like layer. Although OmpB is dispensable for bacterial growth in endothelial cells, it is essential for R. parkeri to block autophagy in macrophages and to colonize mice because of its ability to promote autophagy evasion in immune cells. Our results indicate that OmpB acts as a protective shield to obstruct autophagy recognition, thereby revealing a distinctive bacterial mechanism to evade antimicrobial autophagy.
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12
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Horst BG, Yokom AL, Rosenberg DJ, Morris KL, Hammel M, Hurley JH, Marletta MA. Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy. eLife 2019; 8:e50634. [PMID: 31566566 PMCID: PMC6839917 DOI: 10.7554/elife.50634] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/27/2019] [Indexed: 12/14/2022] Open
Abstract
Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length Manduca sexta sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.
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Affiliation(s)
- Benjamin G Horst
- Department of ChemistryUniversity of California, BerkeleyBerkeleyUnited States
| | - Adam L Yokom
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyUnited States
- California Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyUnited States
| | - Kyle L Morris
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
| | - Michal Hammel
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - James H Hurley
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyUnited States
- California Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyUnited States
| | - Michael A Marletta
- Department of ChemistryUniversity of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
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13
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Weichsel A, Kievenaar JA, Curry R, Croft JT, Montfort WR. Instability in a coiled-coil signaling helix is conserved for signal transduction in soluble guanylyl cyclase. Protein Sci 2019; 28:1830-1839. [PMID: 31411784 DOI: 10.1002/pro.3707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/01/2023]
Abstract
How nitric oxide (NO) activates its primary receptor, α1/β1 soluble guanylyl cyclase (sGC or GC-1), remains unknown. Likewise, how stimulatory compounds enhance sGC activity is poorly understood, hampering development of new treatments for cardiovascular disease. NO binding to ferrous heme near the N-terminus in sGC activates cyclase activity near the C-terminus, yielding cGMP production and physiological response. CO binding can also stimulate sGC, but only weakly in the absence of stimulatory small-molecule compounds, which together lead to full activation. How ligand binding enhances catalysis, however, has yet to be discovered. Here, using a truncated version of sGC from Manduca sexta, we demonstrate that the central coiled-coil domain, the most highly conserved region of the ~150,000 Da protein, not only provides stability to the heterodimer but is also conformationally active in signal transduction. Sequence conservation in the coiled coil includes the expected heptad-repeating pattern for coiled-coil motifs, but also invariant positions that disfavor coiled-coil stability. Full-length coiled coil dampens CO affinity for heme, while shortening of the coiled coil leads to enhanced CO binding. Introducing double mutation αE447L/βE377L, predicted to replace two destabilizing glutamates with leucines, lowers CO binding affinity while increasing overall protein stability. Likewise, introduction of a disulfide bond into the coiled coil results in reduced CO affinity. Taken together, we demonstrate that the heme domain is greatly influenced by coiled-coil conformation, suggesting communication between heme and catalytic domains is through the coiled coil. Highly conserved structural imperfections in the coiled coil provide needed flexibility for signal transduction.
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Affiliation(s)
- Andrzej Weichsel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Jessica A Kievenaar
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Roslyn Curry
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Jacob T Croft
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
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14
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Cirri E, De Decker S, Bilcke G, Werner M, Osuna-Cruz CM, De Veylder L, Vandepoele K, Werz O, Vyverman W, Pohnert G. Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom. Front Microbiol 2019; 10:1790. [PMID: 31428077 PMCID: PMC6688387 DOI: 10.3389/fmicb.2019.01790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/19/2019] [Indexed: 01/23/2023] Open
Abstract
Diatoms are unicellular algae with a fundamental role in global biogeochemical cycles as major primary producers at the base of aquatic food webs. In recent years, chemical communication between diatoms and associated bacteria has emerged as a key factor in diatom ecology, spurred by conceptual and technological advancements to study the mechanisms underlying these interactions. Here, we use a combination of physiological, transcriptomic, and metabolomic approaches to study the influence of naturally co-existing bacteria, Maribacter sp. and Roseovarius sp., on the sexual reproduction of the biofilm inhabiting marine pennate diatom Seminavis robusta. While Maribacter sp. severely reduces the reproductive success of S. robusta cultures, Roseovarius sp. slightly enhances it. Contrary to our expectation, we demonstrate that the effect of the bacterial exudates is not caused by altered cell-cycle regulation prior to the switch to meiosis. Instead, Maribacter sp. exudates cause a reduced production of diproline, the sexual attraction pheromone of S. robusta. Transcriptomic analyses show that this is likely an indirect consequence of altered intracellular metabolic fluxes in the diatom, especially those related to amino acid biosynthesis, oxidative stress response, and biosynthesis of defense molecules. This study provides the first insights into the influence of bacteria on diatom sexual reproduction and adds a new dimension to the complexity of a still understudied phenomenon in natural diatom populations.
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Affiliation(s)
- Emilio Cirri
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Sam De Decker
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Gust Bilcke
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Markus Werner
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
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15
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Mukherjee S, Hegemann P, Broser M. Enzymerhodopsins: novel photoregulated catalysts for optogenetics. Curr Opin Struct Biol 2019; 57:118-126. [PMID: 30954887 DOI: 10.1016/j.sbi.2019.02.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 12/22/2022]
Abstract
Enzymerhodopsins are a recently discovered class of natural rhodopsin-based photoreceptors with light-regulated enzyme activity. Currently, three different types of these fusion proteins with an N-terminal type-1 rhodopsin and a C-terminal enzyme domain have been identified, but their physiological relevance is mostly unknown. Among these, histidine kinase rhodopsins (HKR) are photo-regulated two-component-like signaling systems that trigger a phosphorylation cascade, whereas rhodopsin phosphodiesterase (RhoPDE) or rhodopsin guanylyl cyclase (RhGC) show either light-activated hydrolysis or production of cyclic nucleotides. RhGC, the best characterized enzymerhodopsin, is involved in the phototaxis of fungal zoospores and allows for optically controlled production of cyclic nucleotides in different cell-types. These photoreceptors have great optogenetic potential and possess several advantages over the hitherto existing tools to manipulate cyclic-nucleotide dynamics in living cells.
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Affiliation(s)
- Shatanik Mukherjee
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Germany.
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Germany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Germany.
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16
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Rehkamp A, Tänzler D, Iacobucci C, Golbik RP, Ihling CH, Sinz A. Molecular Details of Retinal Guanylyl Cyclase 1/GCAP-2 Interaction. Front Mol Neurosci 2018; 11:330. [PMID: 30283299 PMCID: PMC6156451 DOI: 10.3389/fnmol.2018.00330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/27/2018] [Indexed: 12/13/2022] Open
Abstract
The rod outer segment guanylyl cyclase 1 (ROS-GC1) is an essential component of photo-transduction in the retina. In the light-induced signal cascade, membrane-bound ROS-GC1 restores cGMP levels in the dark in a calcium-dependent manner. With decreasing calcium concentration in the intracellular compartment, ROS-GC1 is activated via the intracellular site by guanylyl cyclase-activating proteins (GCAP-1/-2). Presently, the exact activation mechanism is elusive. To obtain structural insights into the ROS-GC1 regulation by GCAP-2, chemical cross-linking/mass spectrometry studies using GCAP-2 and three ROS-GC1 peptides were performed in the presence and absence of calcium. The majority of cross-links were identified with the C-terminal lobe of GCAP-2 and a peptide comprising parts of ROS-GC1's catalytic domain and C-terminal extension. Consistently with the cross-linking results, surface plasmon resonance and fluorescence measurements confirmed specific binding of this ROS-GC peptide to GCAP-2 with a dissociation constant in the low micromolar range. These results imply that a region of the catalytic domain of ROS-GC1 can participate in the interaction with GCAP-2. Additional binding surfaces upstream of the catalytic domain, in particular the juxtamembrane domain, can currently not be excluded.
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Affiliation(s)
- Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dirk Tänzler
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ralph P Golbik
- Department of Microbial Biotechnology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
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17
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Gao H, Yang Z, Wang X, Qian P, Hong R, Chen X, Su XZ, Cui H, Yuan J. ISP1-Anchored Polarization of GCβ/CDC50A Complex Initiates Malaria Ookinete Gliding Motility. Curr Biol 2018; 28:2763-2776.e6. [PMID: 30146157 DOI: 10.1016/j.cub.2018.06.069] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/28/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022]
Abstract
Ookinete gliding motility is essential for penetration of the mosquito midgut wall and transmission of malaria parasites. Cyclic guanosine monophosphate (cGMP) signaling has been implicated in ookinete gliding. However, the upstream mechanism of how the parasites activate cGMP signaling and thus initiate ookinete gliding remains unknown. Using real-time imaging to visualize Plasmodium yoelii guanylate cyclase β (GCβ), we show that cytoplasmic GCβ translocates and polarizes to the parasite plasma membrane at "ookinete extrados site" (OES) during zygote-to-ookinete differentiation. The polarization of enzymatic active GCβ at OES initiates gliding of matured ookinete. Both the P4-ATPase-like domain and guanylate cyclase domain are required for GCβ polarization and ookinete gliding. CDC50A, a co-factor of P4-ATPase, binds to and stabilizes GCβ during ookinete development. Screening of inner membrane complex proteins identifies ISP1 as a key molecule that anchors GCβ/CDC50A complex at the OES of mature ookinetes. This study defines a spatial-temporal mechanism for the initiation of ookinete gliding, where GCβ polarization likely elevates local cGMP levels and activates cGMP-dependent protein kinase signaling.
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Affiliation(s)
- Han Gao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhenke Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xu Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Pengge Qian
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Renjie Hong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xin Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Huiting Cui
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jing Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
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18
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Horst BG, Marletta MA. Physiological activation and deactivation of soluble guanylate cyclase. Nitric Oxide 2018; 77:65-74. [PMID: 29704567 PMCID: PMC6919197 DOI: 10.1016/j.niox.2018.04.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/24/2023]
Abstract
Soluble guanylate cyclase (sGC) is responsible for transducing the gaseous signaling molecule nitric oxide (NO) into the ubiquitous secondary signaling messenger cyclic guanosine monophosphate in eukaryotic organisms. sGC is exquisitely tuned to respond to low levels of NO, allowing cells to respond to non-toxic levels of NO. In this review, the structure of sGC is discussed in the context of sGC activation and deactivation. The sequence of events in the activation pathway are described into a comprehensive model of in vivo sGC activation as elucidated both from studies with purified enzyme and those done in cells. This model is then used to discuss the deactivation of sGC, as well as the molecular mechanisms of pathophysiological deactivation.
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Affiliation(s)
- Benjamin G Horst
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
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19
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Scheib U, Broser M, Constantin OM, Yang S, Gao S, Mukherjee S, Stehfest K, Nagel G, Gee CE, Hegemann P. Rhodopsin-cyclases for photocontrol of cGMP/cAMP and 2.3 Å structure of the adenylyl cyclase domain. Nat Commun 2018; 9:2046. [PMID: 29799525 PMCID: PMC5967339 DOI: 10.1038/s41467-018-04428-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/26/2018] [Indexed: 12/17/2022] Open
Abstract
The cyclic nucleotides cAMP and cGMP are important second messengers that orchestrate fundamental cellular responses. Here, we present the characterization of the rhodopsin-guanylyl cyclase from Catenaria anguillulae (CaRhGC), which produces cGMP in response to green light with a light to dark activity ratio >1000. After light excitation the putative signaling state forms with τ = 31 ms and decays with τ = 570 ms. Mutations (up to 6) within the nucleotide binding site generate rhodopsin-adenylyl cyclases (CaRhACs) of which the double mutated YFP-CaRhAC (E497K/C566D) is the most suitable for rapid cAMP production in neurons. Furthermore, the crystal structure of the ligand-bound AC domain (2.25 Å) reveals detailed information about the nucleotide binding mode within this recently discovered class of enzyme rhodopsin. Both YFP-CaRhGC and YFP-CaRhAC are favorable optogenetic tools for non-invasive, cell-selective, and spatio-temporally precise modulation of cAMP/cGMP with light. Cyclic AMP and cGMP orchestrate a variety of cellular responses. Here, authors characterize the cGMP producing rhodopsin-guanylyl cyclase from C. anguillulae and derived adenylyl cyclase by a biochemical and structural approach which demonstrates the usability of these cyclases for optogenetic applications.
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Affiliation(s)
- Ulrike Scheib
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Oana M Constantin
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Shang Yang
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany
| | - Shiqiang Gao
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany
| | - Shatanik Mukherjee
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Katja Stehfest
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Georg Nagel
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany
| | - Christine E Gee
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
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20
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Sömmer A, Behrends S. Methods to investigate structure and activation dynamics of GC-1/GC-2. Nitric Oxide 2018; 78:S1089-8603(17)30348-8. [PMID: 29705716 DOI: 10.1016/j.niox.2018.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/19/2018] [Accepted: 04/23/2018] [Indexed: 12/18/2022]
Abstract
Soluble guanylyl cyclase (sGC) is a heterodimeric enzyme consisting of one α and one β subunit. The α1β1 (GC-1) and α2β1 (GC-2) heterodimers are important for NO signaling in humans and catalyse the conversion from GTP to cGMP. Each sGC subunit consists of four domains. Several crystal structures of the isolated domains are available. However, crystals of full-length sGC have failed to materialise. In consequence, the detailed three dimensional structure of sGC remains unknown to date. Different techniques including stopped-flow spectroscopy, Förster-resonance energy transfer, direct fluorescence, analytical ultracentrifugation, chemical cross-linking, small-angle X-ray scattering, electron microscopy, hydrogen-deuterium exchange and protein thermal shift assays, were used to collect indirect information. Taken together, this circumstantial evidence from different groups brings forth a plausible model of sGC domain arrangement, spatial orientation and dynamic rearrangement upon activation. For analysis of the active conformation the stable binding mode of sGC activators has a significant methodological advantage over the transient, elusive, complex and highly concentration dependent effects of NO in many applications. The methods used and the results obtained are reviewed and discussed in this article.
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Affiliation(s)
- Anne Sömmer
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig - Institute of Technology, Germany.
| | - Sönke Behrends
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig - Institute of Technology, Germany.
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21
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Childers KC, Garcin ED. Structure/function of the soluble guanylyl cyclase catalytic domain. Nitric Oxide 2018; 77:53-64. [PMID: 29702251 PMCID: PMC6005667 DOI: 10.1016/j.niox.2018.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
Abstract
Soluble guanylyl cyclase (GC-1) is the primary receptor of nitric oxide (NO) in smooth muscle cells and maintains vascular function by inducing vasorelaxation in nearby blood vessels. GC-1 converts guanosine 5′-triphosphate (GTP) into cyclic guanosine 3′,5′-monophosphate (cGMP), which acts as a second messenger to improve blood flow. While much work has been done to characterize this pathway, we lack a mechanistic understanding of how NO binding to the heme domain leads to a large increase in activity at the C-terminal catalytic domain. Recent structural evidence and activity measurements from multiple groups have revealed a low-activity cyclase domain that requires additional GC-1 domains to promote a catalytically-competent conformation. How the catalytic domain structurally transitions into the active conformation requires further characterization. This review focuses on structure/function studies of the GC-1 catalytic domain and recent advances various groups have made in understanding how catalytic activity is regulated including small molecules interactions, Cys-S-NO modifications and potential interactions with the NO-sensor domain and other proteins.
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Affiliation(s)
- Kenneth C Childers
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA
| | - Elsa D Garcin
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA.
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22
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Shah RC, Sanker S, Wood KC, Durgin BG, Straub AC. Redox regulation of soluble guanylyl cyclase. Nitric Oxide 2018; 76:97-104. [PMID: 29578056 DOI: 10.1016/j.niox.2018.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/28/2018] [Accepted: 03/19/2018] [Indexed: 11/15/2022]
Abstract
The nitric oxide/soluble guanylyl cyclase (NO-sGC) signaling pathway regulates the cardiovascular, neuronal, and gastrointestinal systems. Impaired sGC signaling can result in disease and system-wide organ failure. This review seeks to examine the redox control of sGC through heme and cysteine regulation while discussing therapeutic drugs that target various conditions. Heme regulation involves mechanisms of insertion of the heme moiety into the sGC protein, the molecules and proteins that control switching between the oxidized (Fe3+) and reduced states (Fe2+), and the activity of heme degradation. Modifications to cysteine residues by S-nitrosation on the α1 and β1 subunits of sGC have been shown to be important in sGC signaling. Moreover, redox balance and localization of sGC is thought to control downstream effects. In response to altered sGC activity due to changes in the redox state, many therapeutic drugs have been developed to target decreased NO-sGC signaling. The importance and relevance of sGC continues to grow as sGC dysregulation leads to numerous disease conditions.
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Affiliation(s)
- Rohan C Shah
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Subramaniam Sanker
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Katherine C Wood
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brittany G Durgin
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adam C Straub
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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23
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Sharon D, Wimberg H, Kinarty Y, Koch KW. Genotype-functional-phenotype correlations in photoreceptor guanylate cyclase (GC-E) encoded by GUCY2D. Prog Retin Eye Res 2018; 63:69-91. [DOI: 10.1016/j.preteyeres.2017.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 01/09/2023]
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24
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Duda T, Pertzev A, Sharma RK. CO 2/bicarbonate modulates cone photoreceptor ROS-GC1 and restores its CORD6-linked catalytic activity. Mol Cell Biochem 2018; 448:91-105. [PMID: 29427171 DOI: 10.1007/s11010-018-3317-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/02/2018] [Indexed: 01/12/2023]
Abstract
This study with recombinant reconstituted system mimicking the cellular conditions of the native cones documents that photoreceptor ROS-GC1 is modulated by gaseous CO2. Mechanistically, CO2 is sensed by carbonic anhydrase (CAII), generates bicarbonate that, in turn, directly targets the core catalytic domain of ROS-GC1, and activates it to increased synthesis of cyclic GMP. This, then, functions as a second messenger for the cone phototransduction. The study demonstrates that, in contrast to the Ca2+-modulated phototransduction, the CO2 pathway is Ca2+-independent, yet is linked with it and synergizes it. It, through R787C mutation in the third heptad of the signal helix domain of ROS-GC1, affects cone-rod dystrophy, CORD6. CORD6 is caused firstly by lowered basal and GCAP1-dependent ROS-GC1 activity and secondly, by a shift in Ca2+ sensitivity of the ROS-GC1/GCAP1 complex that remains active in darkness. Remarkably, the first but not the second defect disappears with bicarbonate thus explaining the basis for CORD6 pathological severity. Because cones, but not rods, express CAII, the excessive synthesis of cyclic GMP would be most acute in cones.
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Affiliation(s)
- Teresa Duda
- Research Divisions of Biochemistry and Molecular Biology, The Unit of Regulatory and Molecular Biology, Salus University, Elkins Park, PA, USA
| | - Alexander Pertzev
- Research Divisions of Biochemistry and Molecular Biology, The Unit of Regulatory and Molecular Biology, Salus University, Elkins Park, PA, USA
| | - Rameshwar K Sharma
- Research Divisions of Biochemistry and Molecular Biology, The Unit of Regulatory and Molecular Biology, Salus University, Elkins Park, PA, USA.
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25
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Düner M, Lambertz J, Mügge C, Hemschemeier A. The soluble guanylate cyclase CYG12 is required for the acclimation to hypoxia and trophic regimes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:311-337. [PMID: 29161457 DOI: 10.1111/tpj.13779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/03/2017] [Accepted: 11/09/2017] [Indexed: 05/27/2023]
Abstract
Oxygenic phototrophs frequently encounter environmental conditions that result in intracellular energy crises. Growth of the unicellular green alga Chlamydomonas reinhardtii in hypoxia in the light depends on acclimatory responses of which the induction of photosynthetic cyclic electron flow is essential. The microalga cannot grow in the absence of molecular oxygen (O2 ) in the dark, although it possesses an elaborate fermentation metabolism. Not much is known about how the microalga senses and signals the lack of O2 or about its survival strategies during energy crises. Recently, nitric oxide (NO) has emerged to be required for the acclimation of C. reinhardtii to hypoxia. In this study, we show that the soluble guanylate cyclase (sGC) CYG12, a homologue of animal NO sensors, is also involved in this response. CYG12 is an active sGC, and post-transcriptional down-regulation of the CYG12 gene impairs hypoxic growth and gene expression in C. reinhardtii. However, it also results in a disturbed photosynthetic apparatus under standard growth conditions and the inability to grow heterotrophically. Transcriptome profiles indicate that the mis-expression of CYG12 results in a perturbation of responses that, in the wild-type, maintain the cellular energy budget. We suggest that CYG12 is required for the proper operation of the photosynthetic apparatus which, in turn, is essential for survival in hypoxia and darkness.
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Affiliation(s)
- Melis Düner
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Jan Lambertz
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Anja Hemschemeier
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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26
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Synthesis and degradation of cAMP in Giardia lamblia: possible role and characterization of a nucleotidyl cyclase with a single cyclase homology domain. Biochem J 2017; 474:4001-4017. [PMID: 29054977 DOI: 10.1042/bcj20170590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 01/25/2023]
Abstract
Despite its importance in the regulation of growth and differentiation processes of a variety of organisms, the mechanism of synthesis and degradation of cAMP (cyclic AMP) has not yet been described in Giardia lamblia In this work, we measured significant quantities of cAMP in trophozoites of G. lamblia incubated in vitro and later detected how it increases during the first hours of encystation, and how it then returns to basal levels at 24 h. Through an analysis of the genome of G. lamblia, we found sequences of three putative enzymes - one phosphodiesterase (gPDE) and two nucleotidyl cyclases (gNC1 and gNC2) - that should be responsible for the regulation of cAMP in G. lamblia Later, an RT-PCR assay confirmed that these three genes are expressed in trophozoites. The bioinformatic analysis indicated that gPDE is a transmembrane protein of 154 kDa, with a single catalytic domain in the C-terminal end; gNC1 is predicted to be a transmembrane protein of 74 kDa, with only one class III cyclase homology domain (CHD) at the C-terminal end; and gNC2 should be a transmembrane protein of 246 kDa, with two class III CHDs. Finally, we cloned and enriched the catalytic domain of gNC1 (gNC1cd) from bacteria. After that, we confirmed that gNC1cd has adenylyl cyclase (AC) activity. This enzymatic activity depends on the presence of Mn2+ and Ca2+, but no significant activity was displayed in the presence of Mg2+ Additionally, the AC activity of gNC1cd is competitively inhibited with GTP, so it is highly possible that gNC1 has guanylyl cyclase activity as well.
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Kumar RP, Morehouse BR, Fofana J, Trieu MM, Zhou DH, Lorenz MO, Oprian DD. Structure and monomer/dimer equilibrium for the guanylyl cyclase domain of the optogenetics protein RhoGC. J Biol Chem 2017; 292:21578-21589. [PMID: 29118188 DOI: 10.1074/jbc.m117.812685] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/31/2017] [Indexed: 12/23/2022] Open
Abstract
RhoGC is a fusion protein from the aquatic fungus Blastocladiella emersonii, combining a type I rhodopsin domain with a guanylyl cyclase domain. It has generated excitement as an optogenetics tool for the manipulation of cyclic nucleotide signaling pathways. To investigate the regulation of the cyclase activity, we isolated the guanylyl cyclase domain from Escherichia coli with (GCwCCRho) and without (GCRho) the coiled-coil linker. Both constructs were constitutively active but were monomeric as determined by size-exclusion chromatography and analytical ultracentrifugation, whereas other class III nucleotidyl cyclases are functional dimers. We also observed that crystals of GCRho have only a monomer in an asymmetric unit. Dimers formed when crystals were grown in the presence of the non-cyclizable substrate analog 2',3'-dideoxyguanosine-5'-triphosphate, MnCl2, and tartrate, but their quaternary structure did not conform to the canonical pairing expected for class III enzymes. Moreover, the structure contained a disulfide bond formed with an active-site Cys residue required for activity. We consider it unlikely that the disulfide would form under intracellular reducing conditions, raising the possibility that this unusual dimer might have a biologically relevant role in the regulation of full-length RhoGC. Although we did not observe it with direct methods, a functional dimer was identified as the active state by following the dependence of activity on total enzyme concentration. The low affinity observed for GCRho monomers is unusual for this enzyme class and suggests that dimer formation may contribute to light activation of the full-length protein.
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Affiliation(s)
- Ramasamy P Kumar
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Benjamin R Morehouse
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Josiane Fofana
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Melissa M Trieu
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Daniel H Zhou
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Molly O Lorenz
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Daniel D Oprian
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
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Wheeler JI, Wong A, Marondedze C, Groen AJ, Kwezi L, Freihat L, Vyas J, Raji MA, Irving HR, Gehring C. The brassinosteroid receptor BRI1 can generate cGMP enabling cGMP-dependent downstream signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:590-600. [PMID: 28482142 DOI: 10.1111/tpj.13589] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 05/24/2023]
Abstract
The brassinosteroid receptor brassinosteroid insensitive 1 (BRI1) is a member of the leucine-rich repeat receptor-like kinase family. The intracellular kinase domain of BRI1 is an active kinase and also encapsulates a guanylate cyclase catalytic centre. Using liquid chromatography tandem mass spectrometry, we confirmed that the recombinant cytoplasmic domain of BRI1 generates pmol amounts of cGMP per μg protein with a preference for magnesium over manganese as a co-factor. Importantly, a functional BRI1 kinase is essential for optimal cGMP generation. Therefore, the guanylate cyclase activity of BRI1 is modulated by the kinase while cGMP, the product of the guanylate cyclase, in turn inhibits BRI1 kinase activity. Furthermore, we show using Arabidopsis root cell cultures that cGMP rapidly potentiates phosphorylation of the downstream substrate brassinosteroid signaling kinase 1 (BSK1). Taken together, our results suggest that cGMP acts as a modulator that enhances downstream signaling while dampening signal generation from the receptor.
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Affiliation(s)
- Janet I Wheeler
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
- AgriBio, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Aloysius Wong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- College of Natural, Applied and Health Sciences, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China, 325060
| | - Claudius Marondedze
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Arnoud J Groen
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lusisizwe Kwezi
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
- Council for Scientific and Industrial Research, Biosciences, Brummeria, Pretoria, 0001, South Africa
| | - Lubna Freihat
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Jignesh Vyas
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Misjudeen A Raji
- Analytical Chemistry Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Chris Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Ravichandran S, Duda T, Pertzev A, Sharma RK. Membrane Guanylate Cyclase catalytic Subdomain: Structure and Linkage with Calcium Sensors and Bicarbonate. Front Mol Neurosci 2017; 10:173. [PMID: 28638321 PMCID: PMC5461267 DOI: 10.3389/fnmol.2017.00173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/17/2017] [Indexed: 11/30/2022] Open
Abstract
Membrane guanylate cyclase (MGC) is a ubiquitous multi-switching cyclic GMP generating signaling machine linked with countless physiological processes. In mammals it is encoded by seven distinct homologous genes. It is a single transmembrane spanning multi-modular protein; composed of integrated blocks and existing in homo-dimeric form. Its core catalytic domain (CCD) module is a common transduction center where all incoming signals are translated into the production of cyclic GMP, a cellular signal second messenger. Crystal structure of the MGC's CCD does not exist and its precise identity is ill-defined. Here, we define it at a sub-molecular level for the phototransduction-linked MGC, the rod outer segment guanylate cyclase type 1, ROS-GC1. (1) The CCD is a conserved 145-residue structural unit, represented by the segment V820-P964. (2) It exists as a homo-dimer and contains seven conserved catalytic elements (CEs) wedged into seven conserved motifs. (3) It also contains a conserved 21-residue neurocalcin δ-modulated structural domain, V836-L857. (4) Site-directed mutagenesis documents that each of the seven CEs governs the cyclase's catalytic activity. (5) In contrast to the soluble and the bacterium MGC which use Mn2+-GTP substrate for catalysis, MGC CCD uses the natural Mg2+-GTP substrate. (6) Strikingly, the MGC CCD requires anchoring by the Transmembrane Domain (TMD) to exhibit its major (∼92%) catalytic activity; in isolated form the activity is only marginal. This feature is not linked with any unique sequence of the TMD; there is minimal conservation in TMD. Finally, (7) the seven CEs control each of four phototransduction pathways- -two Ca2+-sensor GCAPs-, one Ca2+-sensor, S100B-, and one bicarbonate-modulated. The findings disclose that the CCD of ROS-GC1 has built-in regulatory elements that control its signal translational activity. Due to conservation of these regulatory elements, it is proposed that these elements also control the physiological activity of other members of MGC family.
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Affiliation(s)
- Sarangan Ravichandran
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., FredrickMD, United States
| | - Teresa Duda
- The Unit of Regulatory and Molecular Biology, Research Divisions of Biochemistry and Molecular Biology, Salus University, Elkins ParkPA, United States
| | - Alexandre Pertzev
- The Unit of Regulatory and Molecular Biology, Research Divisions of Biochemistry and Molecular Biology, Salus University, Elkins ParkPA, United States
| | - Rameshwar K. Sharma
- The Unit of Regulatory and Molecular Biology, Research Divisions of Biochemistry and Molecular Biology, Salus University, Elkins ParkPA, United States
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Probing the Molecular Mechanism of Human Soluble Guanylate Cyclase Activation by NO in vitro and in vivo. Sci Rep 2017; 7:43112. [PMID: 28230071 PMCID: PMC5322342 DOI: 10.1038/srep43112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/19/2017] [Indexed: 11/12/2022] Open
Abstract
Soluble guanylate cyclase (sGC) is a heme-containing metalloprotein in NO-sGC-cGMP signaling. NO binds to the heme of sGC to catalyze the synthesis of the second messenger cGMP, which plays a critical role in several physiological processes. However, the molecular mechanism for sGC to mediate the NO signaling remains unclear. Here fluorophore FlAsH-EDT2 and fluorescent proteins were employed to study the NO-induced sGC activation. FlAsH-EDT2 labeling study revealed that NO binding to the H-NOX domain of sGC increased the distance between H-NOX and PAS domain and the separation between H-NOX and coiled-coil domain. The heme pocket conformation changed from “closed” to “open” upon NO binding. In addition, the NO-induced conformational change of sGC was firstly investigated in vivo through fluorescence lifetime imaging microscopy. The results both in vitro and in vivo indicated the conformational change of the catalytic domain of sGC from “open” to “closed” upon NO binding. NO binding to the heme of H-NOX domain caused breaking of Fe-N coordination bond, initiated the domain moving and conformational change, induced the allosteric effect of sGC to trigger the NO-signaling from H-NOX via PAS & coiled-coil to the catalytic domain, and ultimately stimulates the cyclase activity of sGC.
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31
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Montfort WR, Wales JA, Weichsel A. Structure and Activation of Soluble Guanylyl Cyclase, the Nitric Oxide Sensor. Antioxid Redox Signal 2017; 26:107-121. [PMID: 26979942 PMCID: PMC5240008 DOI: 10.1089/ars.2016.6693] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE Soluble guanylyl/guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) and is central to the physiology of blood pressure regulation, wound healing, memory formation, and other key physiological activities. sGC is increasingly implicated in disease and is targeted by novel therapeutic compounds. The protein displays a rich evolutionary history and a fascinating signal transduction mechanism, with NO binding to an N-terminal heme-containing domain, which activates the C-terminal cyclase domains. Recent Advances: Crystal structures of individual sGC domains or their bacterial homologues coupled with small-angle x-ray scattering, electron microscopy, chemical cross-linking, and Förster resonance energy transfer measurements are yielding insight into the overall structure for sGC, which is elongated and likely quite dynamic. Transient kinetic measurements reveal a role for individual domains in lowering NO affinity for heme. New sGC stimulatory drugs are now in the clinic and appear to function through binding near or directly to the sGC heme domain, relieving inhibitory contacts with other domains. New sGC-activating drugs show promise for recovering oxidized sGC in diseases with high inflammation by replacing lost heme. CRITICAL ISSUES Despite the many recent advances, sGC regulation, NO activation, and mechanisms of drug binding remain unclear. Here, we describe the molecular evolution of sGC, new molecular models, and the linked equilibria between sGC NO binding, drug binding, and catalytic activity. FUTURE DIRECTIONS Recent results and ongoing studies lay the foundation for a complete understanding of structure and mechanism, and they open the door for new drug discovery targeting sGC. Antioxid. Redox Signal. 26, 107-121.
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Affiliation(s)
- William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona
| | - Jessica A Wales
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona
| | - Andrzej Weichsel
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona
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Lamason RL, Bastounis E, Kafai NM, Serrano R, Del Álamo JC, Theriot JA, Welch MD. Rickettsia Sca4 Reduces Vinculin-Mediated Intercellular Tension to Promote Spread. Cell 2016; 167:670-683.e10. [PMID: 27768890 DOI: 10.1016/j.cell.2016.09.023] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/22/2016] [Accepted: 09/13/2016] [Indexed: 12/12/2022]
Abstract
Spotted fever group (SFG) rickettsiae are human pathogens that infect cells in the vasculature. They disseminate through host tissues by a process of cell-to-cell spread that involves protrusion formation, engulfment, and vacuolar escape. Other bacterial pathogens rely on actin-based motility to provide a physical force for spread. Here, we show that SFG species Rickettsia parkeri typically lack actin tails during spread and instead manipulate host intercellular tension and mechanotransduction to promote spread. Using transposon mutagenesis, we identified surface cell antigen 4 (Sca4) as a secreted effector of spread that specifically promotes protrusion engulfment. Sca4 interacts with the cell-adhesion protein vinculin and blocks association with vinculin's binding partner, α-catenin. Using traction and monolayer stress microscopy, we show that Sca4 reduces vinculin-dependent mechanotransduction at cell-cell junctions. Our results suggest that Sca4 relieves intercellular tension to promote protrusion engulfment, which represents a distinctive strategy for manipulating cytoskeletal force generation to enable spread.
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Affiliation(s)
- Rebecca L Lamason
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Effie Bastounis
- Departments of Biochemistry, Microbiology, and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Natasha M Kafai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ricardo Serrano
- Mechanical and Aerospace Engineering Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Juan C Del Álamo
- Mechanical and Aerospace Engineering Department, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Julie A Theriot
- Departments of Biochemistry, Microbiology, and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew D Welch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Bharambe NG, Barathy DV, Syed W, Visweswariah SS, Colaςo M, Misquith S, Suguna K. Substrate specificity determinants of class III nucleotidyl cyclases. FEBS J 2016; 283:3723-3738. [PMID: 27542992 DOI: 10.1111/febs.13837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/08/2016] [Accepted: 08/18/2016] [Indexed: 12/30/2022]
Abstract
The two second messengers in signalling, cyclic AMP and cyclic GMP, are produced by adenylyl and guanylyl cyclases respectively. Recognition and discrimination of the substrates ATP and GTP by the nucleotidyl cyclases are vital in these reactions. Various apo-, substrate- or inhibitor-bound forms of adenylyl cyclase (AC) structures from transmembrane and soluble ACs have revealed the catalytic mechanism of ATP cyclization reaction. Previously reported structures of guanylyl cyclases represent ligand-free forms and inactive open states of the enzymes and thus do not provide information regarding the exact mode of substrate binding. The structures we present here of the cyclase homology domain of a class III AC from Mycobacterium avium (Ma1120) and its mutant in complex with ATP and GTP in the presence of calcium ion, provide the structural basis for substrate selection by the nucleotidyl cyclases at the atomic level. Precise nature of the enzyme-substrate interactions, novel modes of substrate binding and the ability of the binding pocket to accommodate diverse conformations of the substrates have been revealed by the present crystallographic analysis. This is the first report to provide structures of both the nucleotide substrates bound to a nucleotidyl cyclase. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank with accession numbers: 5D15 (Ma1120CHD +ATP.Ca2+ ), 5D0E (Ma1120CHD +GTP.Ca2+ ), 5D0H (Ma1120CHD (KDA→EGY)+ATP.Ca2+ ), 5D0G (Ma1120CHD (KDA→EGY)+GTP.Ca2+ ). ENZYMES Adenylyl cyclase (EC number: 4.6.1.1).
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Affiliation(s)
- Nikhil G Bharambe
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Wajeed Syed
- Department of Chemistry, St. Joseph's College, Bangalore, India
| | - Sandhya S Visweswariah
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Melwin Colaςo
- Department of Chemistry, St. Joseph's College, Bangalore, India
| | - Sandra Misquith
- Department of Chemistry, St. Joseph's College, Bangalore, India
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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Phosphorylation of the dimeric cytoplasmic domain of the phytosulfokine receptor, PSKR1. Biochem J 2016; 473:3081-98. [PMID: 27487840 DOI: 10.1042/bcj20160593] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/03/2016] [Indexed: 11/17/2022]
Abstract
Phytosulfokines (PSKs) are plant peptide hormones that co-regulate plant growth, differentiation and defense responses. PSKs signal through a plasma membrane localized leucine-rich repeat receptor-like kinase (phytosulfokine receptor 1, PSKR1) that also contains a functional cytosolic guanylate cyclase with its cyclase catalytic center embedded within the kinase domain. To functionally characterize this novel type of overlapping dual catalytic function, we investigated the phosphorylation of PSKR1 in vitro Tandem mass spectrometry of the cytoplasmic domain of PSKR1 (PSKR1cd) revealed at least 11 phosphorylation sites (8 serines, 2 threonines and 1 tyrosine) within the PSKR1cd. Phosphomimetic mutations of three serine residues (Ser686, Ser696 and Ser698) in tandem at the juxta-membrane position resulted in enhanced kinase activity in the on-mutant that was suppressed in the off-mutant, but both mutations reduced guanylate cyclase activity. Both the on and off phosphomimetic mutations of the phosphotyrosine (Tyr888) residue in the activation loop suppressed kinase activity, while neither mutation affected guanylate cyclase activity. Size exclusion and analytical ultracentrifugation analysis of the PSKR1cd suggest that it is reversibly dimeric in solution, which was further confirmed by biflourescence complementation. Taken together, these data suggest that in this novel type of receptor domain architecture, specific phosphorylation and dimerization are possibly essential mechanisms for ligand-mediated catalysis and signaling.
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Agulló L, Buch I, Gutiérrez-de-Terán H, Garcia-Dorado D, Villà-Freixa J. Computational exploration of the binding mode of heme-dependent stimulators into the active catalytic domain of soluble guanylate cyclase. Proteins 2016; 84:1534-48. [PMID: 27364190 DOI: 10.1002/prot.25096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 06/22/2016] [Accepted: 06/28/2016] [Indexed: 11/08/2022]
Abstract
Soluble guanylate cyclase (sGC), the main target of nitric oxide (NO), has been proven to have a significant role in coronary artery disease, pulmonary hypertension, erectile dysfunction, and myocardial infarction. One of its agonists, BAY 41-2272 (Riociguat), has been recently approved for treatment of pulmonary arterial hypertension (PHA), while some others are in clinical phases of development. However, the location of the binding sites for the two known types of agonists, heme-dependent stimulators and heme-independent activators, is a matter of debate, particularly for the first group where both a location on the regulatory (H-NOX) and on the catalytic domain have been suggested by different authors. Here, we address its potential location on the catalytic domain, the unique well characterized at the structural level, by an "in silico" approach. Homology models of the catalytic domain of sGC in "inactive" or "active" conformations were constructed using the structure of previously described crystals of the catalytic domains of "inactive" sGCs (2WZ1, 3ET6) and of "active" adenylate cyclase (1CJU). Each model was submitted to six independent molecular dynamics simulations of about 1 μs. Docking of YC-1, a classic heme-dependent stimulator, to all frames of representative trajectories of "inactive" and "active" conformations, followed by calculation of absolute binding free energies with the linear interaction energy (LIE) method, revealed a potential high-affinity binding site on the "active" structure. The site, located between the pseudo-symmetric and the catalytic site just over the loop β2 -β3 , does not overlap with the forskolin binding site on adenylate cyclases. Proteins 2016; 84:1534-1548. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Luis Agulló
- Department of Systems Biology, U Science Tech, University of Vic - Central University of Catalonia (UVIC-UCC), Vic, 08500, Spain.
| | - Ignasi Buch
- Computational Biophysics Laboratory, Hospital Del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedicinska Centrum BMC, Uppsala, 75124, Sweden
| | - David Garcia-Dorado
- Cardiocirculatory Pathology Group, Vall D'Hebron Research Institute (VHIR), Barcelona, 08035, Spain
| | - Jordi Villà-Freixa
- Department of Systems Biology, U Science Tech, University of Vic - Central University of Catalonia (UVIC-UCC), Vic, 08500, Spain
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Sunahara RK, Insel PA. The Molecular Pharmacology of G Protein Signaling Then and Now: A Tribute to Alfred G. Gilman. Mol Pharmacol 2016; 89:585-92. [PMID: 26984025 PMCID: PMC11037445 DOI: 10.1124/mol.116.104216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
The recent, unfortunate death of Alfred G. ("Al") Gilman, M.D., Ph.D., represents a sad signpost for an era spanning over 40 years in molecular pharmacology. Gilman's discoveries, influence, and persona were dominant forces in research and training in pharmacology. Here, we review the progression of ideas and knowledge that spawned early work by Gilman and collaborators (among them, one of the authors) and later efforts (including those of the other author) that have recently yielded a comprehensive and precise structural understanding of fundamental topics in pharmacology: the binding of ligands to G protein-coupled receptors (GPCRs) and the interaction of GPCRs with heterotrimeric G proteins and effector molecules. Those data provide new and important insights into the molecular basis that underlies affinity and efficacy, two of the most important features of drug action, which represent the latest chapter in the saga that Al Gilman's work helped launch.
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Affiliation(s)
- Roger K Sunahara
- Department of Pharmacology (R.K.S., P.A.I.) and Department of Medicine (P.A.I.), University of California, San Diego, La Jolla, California
| | - Paul A Insel
- Department of Pharmacology (R.K.S., P.A.I.) and Department of Medicine (P.A.I.), University of California, San Diego, La Jolla, California
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37
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Lorenz S, Bhattacharyya M, Feiler C, Rape M, Kuriyan J. Crystal Structure of a Ube2S-Ubiquitin Conjugate. PLoS One 2016; 11:e0147550. [PMID: 26828794 PMCID: PMC4734694 DOI: 10.1371/journal.pone.0147550] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/04/2016] [Indexed: 12/18/2022] Open
Abstract
Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a "donor" ubiquitin and a primary amino group of an "acceptor" ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface.
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Affiliation(s)
- Sonja Lorenz
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Moitrayee Bhattacharyya
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Christian Feiler
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Michael Rape
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - John Kuriyan
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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Duda T, Pertzev A, Makino CL, Sharma RK. Bicarbonate and Ca(2+) Sensing Modulators Activate Photoreceptor ROS-GC1 Synergistically. Front Mol Neurosci 2016; 9:5. [PMID: 26858600 PMCID: PMC4729890 DOI: 10.3389/fnmol.2016.00005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
Photoreceptor ROS-GC1, a prototype subfamily member of the membrane guanylate cyclase family, is a central component of phototransduction. It is a single transmembrane-spanning protein, composed of modular blocks. In rods, guanylate cyclase activating proteins (GCAPs) 1 and 2 bind to its juxtamembrane domain (JMD) and the C-terminal extension, respectively, to accelerate cyclic GMP synthesis when Ca(2+) levels are low. In cones, the additional expression of the Ca(2+)-dependent guanylate cyclase activating protein (CD-GCAP) S100B which binds to its C-terminal extension, supports acceleration of cyclic GMP synthesis at high Ca(2+) levels. Independent of Ca(2+), ROS-GC1 activity is also stimulated directly by bicarbonate binding to the core catalytic domain (CCD). Several enticing molecular features of this transduction system are revealed in the present study. In combination, bicarbonate and Ca(2+)-dependent modulators raised maximal ROS-GC activity to levels that exceeded the sum of their individual effects. The F(514)S mutation in ROS-GC1 that causes blindness in type 1 Leber's congenital amaurosis (LCA) severely reduced basal ROS-GC1 activity. GCAP2 and S100B Ca(2+) signaling modes remained functional, while the GCAP1-modulated mode was diminished. Bicarbonate nearly restored basal activity as well as GCAP2- and S100B-stimulated activities of the F(514)S mutant to normal levels but could not resurrect GCAP1 stimulation. We conclude that GCAP1 and GCAP2 forge distinct pathways through domain-specific modules of ROS-GC1 whereas the S100B and GCAP2 pathways may overlap. The synergistic interlinking of bicarbonate to GCAPs- and S100B-modulated pathways intensifies and tunes the dependence of cyclic GMP synthesis on intracellular Ca(2+). Our study challenges the recently proposed GCAP1 and GCAP2 "overlapping" phototransduction model (Peshenko et al., 2015b).
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Affiliation(s)
- Teresa Duda
- Research Divisions of Biochemistry and Molecular Biology, The Unit of Regulatory and Molecular Biology, Salus University Elkins Park, PA, USA
| | - Alexandre Pertzev
- Research Divisions of Biochemistry and Molecular Biology, The Unit of Regulatory and Molecular Biology, Salus University Elkins Park, PA, USA
| | - Clint L Makino
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School Boston, MA, USA
| | - Rameshwar K Sharma
- Research Divisions of Biochemistry and Molecular Biology, The Unit of Regulatory and Molecular Biology, Salus University Elkins Park, PA, USA
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Gross I, Durner J. In Search of Enzymes with a Role in 3', 5'-Cyclic Guanosine Monophosphate Metabolism in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:576. [PMID: 27200049 PMCID: PMC4858519 DOI: 10.3389/fpls.2016.00576] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/14/2016] [Indexed: 05/07/2023]
Abstract
In plants, nitric oxide (NO)-mediated 3', 5'-cyclic guanosine monophosphate (cGMP) synthesis plays an important role during pathogenic stress response, stomata closure upon osmotic stress, the development of adventitious roots and transcript regulation. The NO-cGMP dependent pathway is well characterized in mammals. The binding of NO to soluble guanylate cyclase enzymes (GCs) initiates the synthesis of cGMP from guanosine triphosphate. The produced cGMP alters various cellular responses, such as the function of protein kinase activity, cyclic nucleotide gated ion channels and cGMP-regulated phosphodiesterases. The signal generated by the second messenger is terminated by 3', 5'-cyclic nucleotide phosphodiesterase (PDEs) enzymes that hydrolyze cGMP to a non-cyclic 5'-guanosine monophosphate. To date, no homologues of mammalian cGMP-synthesizing and degrading enzymes have been found in higher plants. In the last decade, six receptor proteins from Arabidopsis thaliana have been reported to have guanylate cyclase activity in vitro. Of the six receptors, one was shown to be a NO dependent guanylate cyclase enzyme (NOGC1). However, the role of these proteins in planta remains to be elucidated. Enzymes involved in the degradation of cGMP remain elusive, albeit, PDE activity has been detected in crude protein extracts from various plants. Additionally, several research groups have partially purified and characterized PDE enzymatic activity from crude protein extracts. In this review, we focus on presenting advances toward the identification of enzymes involved in the cGMP metabolism pathway in higher plants.
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Affiliation(s)
- Inonge Gross
- Nitric Oxide Production and Signalling Group, Institute of Biochemical Plant Pathology, Helmholtz Center MunichGermany
- *Correspondence: Inonge Gross,
| | - Jörg Durner
- Nitric Oxide Production and Signalling Group, Institute of Biochemical Plant Pathology, Helmholtz Center MunichGermany
- Chair of Biochemical Plant Pathology, Technische Universität München, FreisingGermany
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Maruyama IN. Receptor Guanylyl Cyclases in Sensory Processing. Front Endocrinol (Lausanne) 2016; 7:173. [PMID: 28123378 PMCID: PMC5225109 DOI: 10.3389/fendo.2016.00173] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 12/28/2016] [Indexed: 11/18/2022] Open
Abstract
Invertebrate models have generated many new insights into transmembrane signaling by cell-surface receptors. This review focuses on receptor guanylyl cyclases (rGCs) and describes recent advances in understanding their roles in sensory processing in the nematode, Caenorhabditis elegans. A complete analysis of the C. elegans genome elucidated 27 rGCs, an unusually large number compared with mammalian genomes, which encode 7 rGCs. Most C. elegans rGCs are expressed in sensory neurons and play roles in sensory processing, including gustation, thermosensation, olfaction, and phototransduction, among others. Recent studies have found that by producing a second messenger, guanosine 3',5'-cyclic monophosphate, some rGCs act as direct sensor molecules for ions and temperatures, while others relay signals from G protein-coupled receptors. Interestingly, genetic and biochemical analyses of rGCs provide the first example of an obligate heterodimeric rGC. Based on recent structural studies of rGCs in mammals and other organisms, molecular mechanisms underlying activation of rGCs are also discussed in this review.
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Affiliation(s)
- Ichiro N. Maruyama
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- *Correspondence: Ichiro N. Maruyama,
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Abstract
Over 30 receptor-like kinases contain a guanylate cyclase (GC) catalytic centre embedded within the C-terminal region of their kinase domain in the model plant Arabidopsis. A number of the kinase GCs contain both functional kinase and GC activity in vitro and the natural ligands of these receptors stimulate increases in cGMP within isolated protoplasts. The GC activity could be described as a minor or moonlighting activity. We have also identified mammalian proteins that contain the novel GC centre embedded within kinase domains. One example is the interleukin 1 receptor-associated kinase 3 (IRAK3). We compare the GC functionality of the mammalian protein IRAK3 with the cytoplasmic domain of the plant prototype molecule, the phytosulfokine receptor 1 (PSKR1). We have developed homology models of these molecules and have undertaken in vitro experiments to compare their functionality and structural features. Recombinant IRAK3 produces cGMP at levels comparable to those produced by PSKR1, suggesting that IRAK3 contains GC activity. Our findings raise the possibility that kinase-GCs may switch between downstream kinase-mediated or cGMP-mediated signalling cascades to elicit desired outputs to particular stimuli. The challenge now lies in understanding the interaction between the GC and kinase domains and how these molecules utilize their dual functionality within cells.
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Virulent Burkholderia species mimic host actin polymerases to drive actin-based motility. Cell 2015; 161:348-60. [PMID: 25860613 DOI: 10.1016/j.cell.2015.02.044] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/22/2014] [Accepted: 02/05/2015] [Indexed: 11/23/2022]
Abstract
Burkholderia pseudomallei and B. mallei are bacterial pathogens that cause melioidosis and glanders, whereas their close relative B. thailandensis is non-pathogenic. All use the trimeric autotransporter BimA to facilitate actin-based motility, host cell fusion, and dissemination. Here, we show that BimA orthologs mimic different host actin-polymerizing proteins. B. thailandensis BimA activates the host Arp2/3 complex. In contrast, B. pseudomallei and B. mallei BimA mimic host Ena/VASP actin polymerases in their ability to nucleate, elongate, and bundle filaments by associating with barbed ends, as well as in their use of WH2 motifs and oligomerization for activity. Mechanistic differences among BimA orthologs resulted in distinct actin filament organization and motility parameters, which affected the efficiency of cell fusion during infection. Our results identify bacterial Ena/VASP mimics and reveal that pathogens imitate the full spectrum of host actin-polymerizing pathways, suggesting that mimicry of different polymerization mechanisms influences key parameters of infection.
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Barathy DV, Bharambe NG, Syed W, Zaveri A, Visweswariah SS, Colaςo M, Misquith S, Suguna K. Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase. J Struct Biol 2015; 190:304-13. [PMID: 25916753 DOI: 10.1016/j.jsb.2015.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/15/2015] [Accepted: 04/20/2015] [Indexed: 01/02/2023]
Abstract
An adenylyl cyclase from Mycobacterium avium, Ma1120, is a functional orthologue of a pseudogene Rv1120c from Mycobacterium tuberculosis. We report the crystal structure of Ma1120 in a monomeric form and its truncated construct as a dimer. Ma1120 exists as a monomer in solution and crystallized as a monomer in the absence of substrate or inhibitor. An additional α-helix present at the N-terminus of the monomeric structure blocks the active site by interacting with the substrate binding residues and occupying the dimer interface region. However, the enzyme has been found to be active in solution, indicating the movement of the helix away from the interface to facilitate the formation of active dimers in conditions favourable for catalysis. Thus, the N-terminal helix of Ma1120 keeps the enzyme in an autoinhibited state when it is not active. Deletion of this helix enabled us to crystallize the molecule as an active homodimer in the presence of a P-site inhibitor 2',5'-dideoxy-3'-ATP, or pyrophosphate along with metal ions. The substrate specifying lysine residue plays a dual role of interacting with the substrate and stabilizing the dimer. The dimerization loop region harbouring the second substrate specifying residue, an aspartate, shows significant differences in conformation and position between the monomeric and dimeric structures. Thus, this study has not only revealed that significant structural transitions are required for the interconversion of the inactive and the active forms of the enzyme, but also provided precise nature of these transitions.
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Affiliation(s)
| | - Nikhil G Bharambe
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Wajeed Syed
- Department of Chemistry, St. Joseph's College, Bangalore 560 027, India
| | - Anisha Zaveri
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
| | - Sandhya S Visweswariah
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
| | - Melwin Colaςo
- Department of Chemistry, St. Joseph's College, Bangalore 560 027, India
| | - Sandra Misquith
- Department of Chemistry, St. Joseph's College, Bangalore 560 027, India
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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Abstract
In the last few years, advances in algal research have identified the participation of haemoglobins in nitrogen metabolism and the management of reactive nitrogen and oxygen species. This chapter summarises the state of knowledge concerning algal haemoglobins with a focus on the most widely used model system, namely, Chlamydomonas reinhardtii. Genetic, physiologic, structural, and chemical information is compiled to provide a framework for further studies.
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Affiliation(s)
- Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
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Steegborn C. Structure, mechanism, and regulation of soluble adenylyl cyclases — similarities and differences to transmembrane adenylyl cyclases. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2535-47. [DOI: 10.1016/j.bbadis.2014.08.012] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/19/2014] [Accepted: 08/26/2014] [Indexed: 12/14/2022]
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Syed W, Colaςo M, Misquith S. Mutational analysis gives insight into substrate preferences of a nucleotidyl cyclase from Mycobacterium avium. PLoS One 2014; 9:e109358. [PMID: 25360748 PMCID: PMC4215837 DOI: 10.1371/journal.pone.0109358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/04/2014] [Indexed: 01/02/2023] Open
Abstract
Mutational, crystallographic and phylogenetic analysis of nucleotidyl cyclases have been used to understand how these enzymes discriminate between substrates. Ma1120, a class III adenylyl cyclase (AC) from Mycobacterium avium, was used as a model to study the amino acid residues that determine substrate preference, by systematically replacing ATP specifying residues with those known to specify GTP. This enzyme was found to possess residual guanylyl cyclase (GC) activity at alkaline pH. Replacement of key residues lysine (101) and aspartate (157) with residues conserved across GCs by site directed mutagenesis, led to a marked improvement in GC activity and a decrease in AC activity. This could be correlated to the presence and strength of the hydrogen bond between the second substrate binding residue (157) and the base of the nucleotide triphosphate. This is substantiated by the fact that the pH optimum is highly dependent on the amino acid residues present at positions 101 and 157.
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Affiliation(s)
- Wajeed Syed
- Department of Chemistry, St. Joseph's College, Bangalore, India
| | - Melwin Colaςo
- Department of Chemistry, St. Joseph's College, Bangalore, India
| | - Sandra Misquith
- Department of Chemistry, St. Joseph's College, Bangalore, India
- * E-mail:
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Structures of soluble guanylate cyclase: implications for regulatory mechanisms and drug development. Biochem Soc Trans 2014; 42:108-13. [PMID: 24450636 PMCID: PMC3901396 DOI: 10.1042/bst20130228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Activation of cGMP synthesis leads to vasodilation, and is an important mechanism in clinical treatment of angina, heart failure, and severe peripheral and pulmonary hypertension. The nitric oxide-responsive sGC (soluble guanylate cyclase) has been the target of recent drug discovery efforts. The present review surveys recent data on the structure and regulation of sGC, and the prospects of new avenues for therapeutic intervention.
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Barathy D, Mattoo R, Visweswariah S, Suguna K. New structural forms of a mycobacterial adenylyl cyclase Rv1625c. IUCRJ 2014; 1:338-48. [PMID: 25295175 PMCID: PMC4174876 DOI: 10.1107/s2052252514016741] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/19/2014] [Indexed: 06/03/2023]
Abstract
Rv1625c is one of 16 adenylyl cyclases encoded in the genome of Mycobacterium tuberculosis. In solution Rv1625c exists predominantly as a monomer, with a small amount of dimer. It has been shown previously that the monomer is active and the dimeric fraction is inactive. Both fractions of wild-type Rv1625c crystallized as head-to-head inactive domain-swapped dimers as opposed to the head-to-tail dimer seen in other functional adenylyl cyclases. About half of the molecule is involved in extensive domain swapping. The strain created by a serine residue located on a hinge loop and the crystallization condition might have led to this unusual domain swapping. The inactivity of the dimeric form of Rv1625c could be explained by the absence of the required catalytic site in the swapped dimer. A single mutant of the enzyme was also generated by changing a phenylalanine predicted to occur at the functional dimer interface to an arginine. This single mutant exists as a dimer in solution but crystallized as a monomer. Analysis of the structure showed that a salt bridge formed between a glutamate residue in the N-terminal segment and the mutated arginine residue hinders dimer formation by pulling the N-terminal region towards the dimer interface. Both structures reported here show a change in the dimerization-arm region which is involved in formation of the functional dimer. It is concluded that the dimerization arm along with other structural elements such as the N-terminal region and certain loops are vital for determining the oligomeric nature of the enzyme, which in turn dictates its activity.
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Affiliation(s)
- Deivanayaga Barathy
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnataka 560 012, India
| | - Rohini Mattoo
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnataka 560 012, India
| | - Sandhya Visweswariah
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnataka 560 012, India
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnataka 560 012, India
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A rhodopsin-guanylyl cyclase gene fusion functions in visual perception in a fungus. Curr Biol 2014; 24:1234-40. [PMID: 24835457 PMCID: PMC4046227 DOI: 10.1016/j.cub.2014.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 03/03/2014] [Accepted: 04/03/2014] [Indexed: 12/23/2022]
Abstract
Sensing light is the fundamental property of visual systems, with vision in animals being based almost exclusively on opsin photopigments [1]. Rhodopsin also acts as a photoreceptor linked to phototaxis in green algae [2, 3] and has been implicated by chemical means as a light sensor in the flagellated swimming zoospores of the fungus Allomyces reticulatus [4]; however, the signaling mechanism in these fungi remains unknown. Here we use a combination of genome sequencing and molecular inhibition experiments with light-sensing phenotype studies to examine the signaling pathway involved in visual perception in the closely related fungus Blastocladiella emersonii. Our data show that in these fungi, light perception is accomplished by the function of a novel gene fusion (BeGC1) of a type I (microbial) rhodopsin domain and guanylyl cyclase catalytic domain. Photobleaching of rhodopsin function prevents accumulation of cGMP levels and phototaxis of fungal zoospores exposed to green light, whereas inhibition of guanylyl cyclase activity negatively affects fungal phototaxis. Immunofluorescence microscopy localizes the BeGC1 protein to the external surface of the zoospore eyespot positioned close to the base of the swimming flagellum [4, 5], demonstrating this is a photoreceptive organelle composed of lipid droplets. Taken together, these data indicate that Blastocladiomycota fungi have a cGMP signaling pathway involved in phototaxis similar to the vertebrate vision-signaling cascade but composed of protein domain components arranged as a novel gene fusion architecture and of distant evolutionary ancestry to type II rhodopsins of animals.
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