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Liu L, Luo D, Zhang Y, Liu D, Yin K, Tang Q, Chou SH, He J. Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from Bacillus thuringiensis. Microbiol Spectr 2024; 12:e0045024. [PMID: 38819160 PMCID: PMC11218506 DOI: 10.1128/spectrum.00450-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
A riboswitch generally regulates the expression of its downstream genes through conformational change in its expression platform (EP) upon ligand binding. The cyclic diguanosine monophosphate (c-di-GMP) class I riboswitch Bc1 is widespread and conserved among Bacillus cereus group species. In this study, we revealed that Bc1 has a long EP with two typical ρ-independent terminator sequences 28 bp apart. The upstream terminator T1 is dominant in vitro, while downstream terminator T2 is more efficient in vivo. Through mutation analysis, we elucidated that Bc1 exerts a rare and incoherent "transcription-translation" dual regulation with T2 playing a crucial role. However, we found that Bc1 did not respond to c-di-GMP under in vitro transcription conditions, and the expressions of downstream genes did not change with fluctuation in intracellular c-di-GMP concentration. To explore this puzzle, we conducted SHAPE-MaP and confirmed the interaction of Bc1 with c-di-GMP. This shows that as c-di-GMP concentration increases, T1 unfolds but T2 remains almost intact and functional. The presence of T2 masks the effect of T1 unwinding, resulting in no response of Bc1 to c-di-GMP. The high Shannon entropy values of EP region imply the potential alternative structures of Bc1. We also found that zinc uptake regulator can specifically bind to the dual terminator coding sequence and slightly trigger the response of Bc1 to c-di-GMP. This work will shed light on the dual-regulation riboswitch and enrich our understanding of the RNA world.IMPORTANCEIn nature, riboswitches are involved in a variety of metabolic regulation, most of which preferentially regulate transcription termination or translation initiation of downstream genes in specific ways. Alternatively, the same or different riboswitches can exist in tandem to enhance regulatory effects or respond to multiple ligands. However, many putative conserved riboswitches have not yet been experimentally validated. Here, we found that the c-di-GMP riboswitch Bc1 with a long EP could form a dual terminator and exhibit non-canonical and incoherent "transcription-translation" dual regulation. Besides, zinc uptake regulator specifically bound to the coding sequence of the Bc1 EP and slightly mediated the action of Bc1. The application of SHAPE-MaP to the dual regulation mechanism of Bc1 may establish the foundation for future studies of such complex untranslated regions in other bacterial genomes.
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Affiliation(s)
- Lu Liu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dehua Luo
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongji Zhang
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dingqi Liu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kang Yin
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing Tang
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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2
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Huang SW, Lim SK, Yu YA, Pan YC, Lien WJ, Mou CY, Hu CMJ, Mou KY. Overcoming the nutritional immunity by engineering iron-scavenging bacteria for cancer therapy. eLife 2024; 12:RP90798. [PMID: 38747577 PMCID: PMC11095936 DOI: 10.7554/elife.90798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Certain bacteria demonstrate the ability to target and colonize the tumor microenvironment, a characteristic that positions them as innovative carriers for delivering various therapeutic agents in cancer therapy. Nevertheless, our understanding of how bacteria adapt their physiological condition to the tumor microenvironment remains elusive. In this work, we employed liquid chromatography-tandem mass spectrometry to examine the proteome of E. coli colonized in murine tumors. Compared to E. coli cultivated in the rich medium, we found that E. coli colonized in tumors notably upregulated the processes related to ferric ions, including the enterobactin biosynthesis and iron homeostasis. This finding indicated that the tumor is an iron-deficient environment to E. coli. We also found that the colonization of E. coli in the tumor led to an increased expression of lipocalin 2 (LCN2), a host protein that can sequester the enterobactin. We therefore engineered E. coli in order to evade the nutritional immunity provided by LCN2. By introducing the IroA cluster, the E. coli synthesizes the glycosylated enterobactin, which creates steric hindrance to avoid the LCN2 sequestration. The IroA-E. coli showed enhanced resistance to LCN2 and significantly improved the anti-tumor activity in mice. Moreover, the mice cured by the IroA-E. coli treatment became resistant to the tumor re-challenge, indicating the establishment of immunological memory. Overall, our study underscores the crucial role of bacteria's ability to acquire ferric ions within the tumor microenvironment for effective cancer therapy.
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Affiliation(s)
- Sin-Wei Huang
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - See-Khai Lim
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Yao-An Yu
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia SinicaTaipeiTaiwan
| | - Yi-Chung Pan
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Wan-Ju Lien
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan UniversityTaipeiTaiwan
| | - Che-Ming Jack Hu
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia SinicaTaipeiTaiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
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3
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Wenzl SJ, de Oliveira Mann CC. How enzyme-centered approaches are advancing research on cyclic oligo-nucleotides. FEBS Lett 2024; 598:839-863. [PMID: 38453162 DOI: 10.1002/1873-3468.14838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
Cyclic nucleotides are the most diversified category of second messengers and are found in all organisms modulating diverse pathways. While cAMP and cGMP have been studied over 50 years, cyclic di-nucleotide signaling in eukaryotes emerged only recently with the anti-viral molecule 2´3´cGAMP. Recent breakthrough discoveries have revealed not only the astonishing chemical diversity of cyclic nucleotides but also surprisingly deep-rooted evolutionary origins of cyclic oligo-nucleotide signaling pathways and structural conservation of the proteins involved in their synthesis and signaling. Here we discuss how enzyme-centered approaches have paved the way for the identification of several cyclic nucleotide signals, focusing on the advantages and challenges associated with deciphering the activation mechanisms of such enzymes.
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Affiliation(s)
- Simon J Wenzl
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Carina C de Oliveira Mann
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
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4
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Torres-Sánchez L, Sana TG, Decossas M, Hashem Y, Krasteva PV. Structures of the P. aeruginosa FleQ-FleN master regulators reveal large-scale conformational switching in motility and biofilm control. Proc Natl Acad Sci U S A 2023; 120:e2312276120. [PMID: 38051770 PMCID: PMC10723142 DOI: 10.1073/pnas.2312276120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
Pseudomonas aeruginosa can cause a wide array of chronic and acute infections associated with its ability to rapidly switch between planktonic, biofilm, and dispersed lifestyles, each with a specific arsenal for bacterial survival and virulence. At the cellular level, many of the physiological transitions are orchestrated by the intracellular second messenger c-di-GMP and its receptor-effector FleQ. A bacterial enhancer binding protein, FleQ acts as a master regulator of both flagellar motility and adherence factor secretion and uses remarkably different transcription activation mechanisms depending on its dinucleotide loading state, adenosine triphosphatase (ATPase) activity, interactions with polymerase sigma (σ) factors, and complexation with a second ATPase, FleN. How the FleQ-FleN tandem can exert diverse effects through recognition of a conserved FleQ binding consensus has remained enigmatic. Here, we provide cryogenic electron microscopy (cryo-EM) structures of both c-di-GMP-bound and c-di-GMP-free FleQ-FleN complexes which deepen our understanding of the proteins' (di)nucleotide-dependent conformational switching and fine-tuned roles in gene expression regulation.
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Affiliation(s)
- Lucía Torres-Sánchez
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, PessacF-33600, France
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology, PessacF-33600, France
- Doctoral School of Therapeutic Innovation (ITFA), Université Paris-Saclay, Gif-sur-YvetteF-91190, France
| | - Thibault Géry Sana
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, PessacF-33600, France
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology, PessacF-33600, France
| | - Marion Decossas
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, PessacF-33600, France
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology, PessacF-33600, France
| | - Yaser Hashem
- ARNA Laboratory, European Institute of Chemistry and Biology, U1212 INSERM, UMR5320 CNRS, Université de Bordeaux, PessacF-33600, France
| | - Petya Violinova Krasteva
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, PessacF-33600, France
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology, PessacF-33600, France
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5
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Scribani Rossi C, Eckartt K, Scarchilli E, Angeli S, Price-Whelan A, Di Matteo A, Chevreuil M, Raynal B, Arcovito A, Giacon N, Fiorentino F, Rotili D, Mai A, Espinosa-Urgel M, Cutruzzolà F, Dietrich LEP, Paone A, Paiardini A, Rinaldo S. Molecular insights into RmcA-mediated c-di-GMP consumption: Linking redox potential to biofilm morphogenesis in Pseudomonas aeruginosa. Microbiol Res 2023; 277:127498. [PMID: 37776579 DOI: 10.1016/j.micres.2023.127498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
The ability of many bacteria to form biofilms contributes to their resilience and makes infections more difficult to treat. Biofilm growth leads to the formation of internal oxygen gradients, creating hypoxic subzones where cellular reducing power accumulates, and metabolic activities can be limited. The pathogen Pseudomonas aeruginosa counteracts the redox imbalance in the hypoxic biofilm subzones by producing redox-active electron shuttles (phenazines) and by secreting extracellular matrix, leading to an increased surface area-to-volume ratio, which favors gas exchange. Matrix production is regulated by the second messenger bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP) in response to different environmental cues. RmcA (Redox modulator of c-di-GMP) from P. aeruginosa is a multidomain phosphodiesterase (PDE) that modulates c-di-GMP levels in response to phenazine availability. RmcA can also sense the fermentable carbon source arginine via a periplasmic domain, which is linked via a transmembrane domain to four cytoplasmic Per-Arnt-Sim (PAS) domains followed by a diguanylate cyclase (DGC) and a PDE domain. The biochemical characterization of the cytoplasmic portion of RmcA reported in this work shows that the PAS domain adjacent to the catalytic domain tunes RmcA PDE activity in a redox-dependent manner, by differentially controlling protein conformation in response to FAD or FADH2. This redox-dependent mechanism likely links the redox state of phenazines (via FAD/FADH2 ratio) to matrix production as indicated by a hyperwrinkling phenotype in a macrocolony biofilm assay. This study provides insights into the role of RmcA in transducing cellular redox information into a structural response of the biofilm at the population level. Conditions of resource (i.e. oxygen and nutrient) limitation arise during chronic infection, affecting the cellular redox state and promoting antibiotic tolerance. An understanding of the molecular linkages between condition sensing and biofilm structure is therefore of crucial importance from both biological and engineering standpoints.
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Affiliation(s)
- Chiara Scribani Rossi
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Kelly Eckartt
- Department of Biological Sciences, Columbia University, New York, USA
| | - Elisabetta Scarchilli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Simone Angeli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | | | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, I-00185 Rome, Italy
| | - Maelenn Chevreuil
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
| | - Noah Giacon
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection. Estación Experimental del Zaidin, CSIC, Granada, Spain
| | - Francesca Cutruzzolà
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, USA
| | - Alessio Paone
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Alessandro Paiardini
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
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6
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Seebach E, Sonnenmoser G, Kubatzky KF. Staphylococcus aureus planktonic but not biofilm environment induces an IFN-β macrophage immune response via the STING/IRF3 pathway. Virulence 2023; 14:2254599. [PMID: 37655977 PMCID: PMC10496530 DOI: 10.1080/21505594.2023.2254599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/05/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023] Open
Abstract
Chronic implant-related bone infections are a severe complication in orthopaedic surgery. Biofilm formation on the implant impairs the immune response, leading to bacterial persistence. In a previous study, we found that Staphylococcus aureus (SA) induced interferon regulatory factor 3 (IRF3) activation and Ifnb expression only in its planktonic form but not in the biofilm. The aim of this study was to clarify the role of the stimulator of interferon genes (STING) in this process. We treated RAW 264.7 macrophages with conditioned media (CM) generated from planktonic or biofilm cultured SA in combination with agonists or inhibitors of the cyclic GMP-AMP synthase (cGAS)/STING pathway. We further evaluated bacterial gene expression of planktonic and biofilm SA to identify potential mediators. STING inhibition resulted in the loss of IRF3 activation and Ifnb induction in SA planktonic CM, whereas STING activation induced an IRF3 dependent IFN-β response in SA biofilm CM. The expression levels of virulence-associated genes decreased during biofilm formation, but genes associated with cyclic dinucleotide (CDN) synthesis did not correlate with Ifnb induction. We further observed that cGAS contributed to Ifnb induction by SA planktonic CM, although cGAS activation was not sufficient to induce Ifnb expression in SA biofilm CM. Our data indicate that the different degrees of virulence associated with SA planktonic and biofilm environments result in an altered induction of the IRF3 mediated IFN-β response via the STING pathway. This finding suggests that the STING/IRF3/IFN-β axis is a potential candidate as an immunotherapeutic target for implant-related bone infections.
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Affiliation(s)
- Elisabeth Seebach
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University, Heidelberg, Germany
| | - Gabriele Sonnenmoser
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University, Heidelberg, Germany
| | - Katharina F. Kubatzky
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University, Heidelberg, Germany
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7
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Hou Y, Wang Z, Liu P, Wei X, Zhang Z, Fan S, Zhang L, Han F, Song Y, Chu L, Zhang C. SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing. Immunity 2023; 56:2492-2507.e10. [PMID: 37890481 DOI: 10.1016/j.immuni.2023.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/19/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
Lipid metabolism has been associated with the cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS) stimulator of interferon genes (STING) DNA-sensing pathway, but our understanding of how these signals are integrated into a cohesive immunometabolic program is lacking. Here, we have identified liver X receptor (LXR) agonists as potent inhibitors of STING signaling. We show that stimulation of lipid metabolism by LXR agonists specifically suppressed cyclic GMP-AMP (cGAMP)-STING signaling. Moreover, we developed cyclic dinucleotide-conjugated beads to biochemically isolate host effectors for cGAMP inhibition, and we found that LXR ligands stimulated the expression of sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A), which is a 2'3'-cGAMP-degrading enzyme. Results of crystal structures suggest that cGAMP analog induces dimerization of SMPDL3A, and the dimerization is critical for cGAMP degradation. Additionally, we have provided evidence that SMPDL3A cleaves cGAMP to restrict STING signaling in cell culture and mouse models. Our results reveal SMPDL3A as a cGAMP-specific nuclease and demonstrate a mechanism for how LXR-associated lipid metabolism modulates STING-mediated innate immunity.
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Affiliation(s)
- Yanfei Hou
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Zhimeng Wang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Peiyuan Liu
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xubiao Wei
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhengyin Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Shilong Fan
- Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Lulu Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Fangping Han
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yikang Song
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Ling Chu
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Conggang Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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8
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Scribani Rossi C, Parisi G, Paiardini A, Rinaldo S. Exploring Innovative Approaches to Isolate a One-Component c-di-GMP Transducer: A Pilot Study. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37608242 DOI: 10.1007/5584_2023_787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Environmental nutrients control bacterial biofilm homeostasis, by regulating the intracellular levels of c-di-GMP. One component transducers can sense different classes of small molecules through a periplasmic domain; the nutrient recognition triggers the subsequent regulation of the downstream cytosolic diguanylate cyclase (GGDEF) or phosphodiesterase (EAL) domains, via transmembrane helix(ces), to finally change c-di-GMP levels.Protein studies on such transducers have been mainly carried out on isolated domains due to the presence of the transmembrane portion. Nevertheless, the cleavage of GGDEF and EAL-containing proteins could be detrimental since both tertiary and quaternary structures could be allosterically controlled; to by-pass this limitation, studies on the corresponding full-length proteins are highly desired.We have in silico selected a GGDEF-EAL transducer from Dyella thiooxydans (ann. A0A160N0B7), whose periplasmic binding domain was predicted to bind to arginine, a nutrient often associated with chronic infections and biofilm. This protein has been used as an in vitro tool for the identification of the best approach for its isolation, including (i) protein engineering to produce a water-soluble version via QTY (Glutamine, Threonine, and Tyrosine) code or (ii) nanodiscs assembly. The results on this "prototype" may represent the proof-of-concept for future isolation of other transmembrane proteins sharing the same architecture, including more complex nutrient-based transducers controlling c-di-GMP levels.
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Affiliation(s)
- Chiara Scribani Rossi
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Alessandro Paiardini
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
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9
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Li Y, Slavik KM, Toyoda HC, Morehouse BR, de Oliveira Mann CC, Elek A, Levy S, Wang Z, Mears KS, Liu J, Kashin D, Guo X, Mass T, Sebé-Pedrós A, Schwede F, Kranzusch PJ. cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell 2023; 186:3261-3276.e20. [PMID: 37379839 PMCID: PMC10527820 DOI: 10.1016/j.cell.2023.05.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/03/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is an enzyme in human cells that controls an immune response to cytosolic DNA. Upon binding DNA, cGAS synthesizes a nucleotide signal 2'3'-cGAMP that activates STING-dependent downstream immunity. Here, we discover that cGAS-like receptors (cGLRs) constitute a major family of pattern recognition receptors in innate immunity. Building on recent analysis in Drosophila, we identify >3,000 cGLRs present in nearly all metazoan phyla. A forward biochemical screening of 150 animal cGLRs reveals a conserved mechanism of signaling including response to dsDNA and dsRNA ligands and synthesis of isomers of the nucleotide signals cGAMP, c-UMP-AMP, and c-di-AMP. Combining structural biology and in vivo analysis in coral and oyster animals, we explain how synthesis of distinct nucleotide signals enables cells to control discrete cGLR-STING signaling pathways. Our results reveal cGLRs as a widespread family of pattern recognition receptors and establish molecular rules that govern nucleotide signaling in animal immunity.
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Affiliation(s)
- Yao Li
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kailey M Slavik
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Hunter C Toyoda
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Benjamin R Morehouse
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shani Levy
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Zhenwei Wang
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Kepler S Mears
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Liu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dmitry Kashin
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Barcelona, Spain
| | - Frank Schwede
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, 28199 Bremen, Germany
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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10
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Xie W, Patel DJ. Structure-based mechanisms of 2'3'-cGAMP intercellular transport in the cGAS-STING immune pathway. Trends Immunol 2023; 44:450-467. [PMID: 37147228 DOI: 10.1016/j.it.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/07/2023]
Abstract
Upon activation by double-stranded DNA (dsDNA), the cytosolic dsDNA sensor cyclic GMP-AMP synthase (cGAS) synthesizes the diffusible cyclic dinucleotide 2'3'-cGAMP (cyclic GMP-AMP), which subsequently binds to the adaptor STING, triggering a cascade of events leading to an inflammatory response. Recent studies have highlighted the role of 2'3'-cGAMP as an 'immunotransmitter' between cells, a process facilitated by gap junctions as well as by specialized membrane-spanning importer and exporter channels. This review highlights recent advances from a structural perspective of intercellular trafficking of 2'3'-cGAMP, with particular emphasis on the binding of importer SLC19A1 to 2'3'-cGAMP, as well as the significance of associated folate nutrients and antifolate therapeutics. This provides a path forward for structure-guided understanding of the transport cycle in immunology, as well as for candidate targeting approaches towards therapeutic intervention in inflammation.
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Affiliation(s)
- Wei Xie
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 311027, China; Department of Infectious Diseases, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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11
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Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization. Sci Rep 2023; 13:2727. [PMID: 36810577 PMCID: PMC9944927 DOI: 10.1038/s41598-023-29110-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Bacterial second messengers c-di-GMP and (p)ppGpp have broad functional repertoires ranging from growth and cell cycle control to the regulation of biofilm formation and virulence. The recent identification of SmbA, an effector protein from Caulobacter crescentus that is jointly targeted by both signaling molecules, has opened up studies on how these global bacterial networks interact. C-di-GMP and (p)ppGpp compete for the same SmbA binding site, with a dimer of c-di-GMP inducing a conformational change that involves loop 7 of the protein that leads to downstream signaling. Here, we report a crystal structure of a partial loop 7 deletion mutant, SmbA∆loop in complex with c-di-GMP determined at 1.4 Å resolution. SmbA∆loop binds monomeric c-di-GMP indicating that loop 7 is required for c-di-GMP dimerization. Thus the complex probably represents the first step of consecutive c-di-GMP binding to form an intercalated dimer as has been observed in wild-type SmbA. Considering the prevalence of intercalated c-di-GMP molecules observed bound to proteins, the proposed mechanism may be generally applicable to protein-mediated c-di-GMP dimerization. Notably, in the crystal, SmbA∆loop forms a 2-fold symmetric dimer via isologous interactions with the two symmetric halves of c-di-GMP. Structural comparisons of SmbA∆loop with wild-type SmbA in complex with dimeric c-di-GMP or ppGpp support the idea that loop 7 is critical for SmbA function by interacting with downstream partners. Our results also underscore the flexibility of c-di-GMP, to allow binding to the symmetric SmbA∆loop dimer interface. It is envisaged that such isologous interactions of c-di-GMP could be observed in hitherto unrecognized targets.
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12
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Liposomal Delivery of MIW815 (ADU-S100) for Potentiated STING Activation. Pharmaceutics 2023; 15:pharmaceutics15020638. [PMID: 36839960 PMCID: PMC9966736 DOI: 10.3390/pharmaceutics15020638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Stimulator of interferon genes (STING) agonists can improve the anticancer efficacy of immune checkpoint blockade by amplifying tumor immunogenicity. However, the clinical translation of cyclic dinucleotides (CDNs) as STING agonists is hindered by their poor drug-like properties. In this study, we investigated the design criteria for DOTAP/cholesterol liposomes for the systemic delivery of ADU-S100 and delineated the impact of key formulation factors on the loading efficiency, serum stability, and STING agonistic activity of ADU-S100. Our findings demonstrate that the cationic liposomal formulation of ADU-S100 can be optimized to greatly potentiate STING activation in antigen-presenting cells.
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13
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Lu Z, Fu Y, Zhou X, Du H, Chen Q. Cyclic dinucleotides mediate bacterial immunity by dinucleotide cyclase in Vibrio. Front Microbiol 2022; 13:1065945. [PMID: 36619988 PMCID: PMC9813507 DOI: 10.3389/fmicb.2022.1065945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
The cyclic GMP-AMP (cGAMP) synthase (cGAS) recognizes cytosolic DNA and synthesizes the second messenger, cGAMP, thus activating the adaptor protein stimulator of interferon genes (STING) and initiating the innate immune responses against microbial infections. cGAS-STING pathway has been crucially implicated in autoimmune diseases, cellular senescence, and cancer immunotherapy, while the cGAS-like receptors in bacteria can protect it against viral infections. Dinucleotide cyclase in Vibrio (DncV) is a dinucleotide cyclase originally identified in Vibrio cholerae. The synthesis of cyclic nucleotides by DncV, including c-di-GMP, c-di-AMP, and cGAMP mediates bacterial colonization, cell membrane formation, and virulence. DncV is a structural and functional homolog of the mammalian cytoplasmic DNA sensor, cGAS, implicating cGAS-STING signaling cascades may have originated in the bacterial immune system. Herein, we summarize the roles of DncV in bacterial immunity, which are expected to provide insights into the evolution of cGAS-STING signaling.
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14
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Abidi W, Decossas M, Torres-Sánchez L, Puygrenier L, Létoffé S, Ghigo JM, Krasteva PV. Bacterial crystalline cellulose secretion via a supramolecular BcsHD scaffold. SCIENCE ADVANCES 2022; 8:eadd1170. [PMID: 36525496 PMCID: PMC9757748 DOI: 10.1126/sciadv.add1170] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Cellulose, the most abundant biopolymer on Earth, is not only the predominant constituent of plants but also a key extracellular polysaccharide in the biofilms of many bacterial species. Depending on the producers, chemical modifications, and three-dimensional assemblies, bacterial cellulose (BC) can present diverse degrees of crystallinity. Highly ordered, or crystalline, cellulose presents great economical relevance due to its ever-growing number of biotechnological applications. Even if some acetic acid bacteria have long been identified as BC superproducers, the molecular mechanisms determining the secretion of crystalline versus amorphous cellulose remain largely unknown. Here, we present structural and mechanistic insights into the role of the accessory subunits BcsH (CcpAx) and BcsD (CesD) that determine crystalline BC secretion in the Gluconacetobacter lineage. We show that oligomeric BcsH drives the assembly of BcsD into a supramolecular cytoskeletal scaffold that likely stabilizes the cellulose-extruding synthase nanoarrays through an unexpected inside-out mechanism for secretion system assembly.
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Affiliation(s)
- Wiem Abidi
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- ‘Structural Biology of Biofilms’ Group, European Institute of Chemistry and Biology (IECB), Pessac, France
- Doctoral School of Therapeutic Innovation ITFA, Université Paris-Saclay, Orsay, France
| | - Marion Decossas
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- ‘Structural Biology of Biofilms’ Group, European Institute of Chemistry and Biology (IECB), Pessac, France
| | - Lucía Torres-Sánchez
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- ‘Structural Biology of Biofilms’ Group, European Institute of Chemistry and Biology (IECB), Pessac, France
- Doctoral School of Therapeutic Innovation ITFA, Université Paris-Saclay, Orsay, France
| | - Lucie Puygrenier
- ‘Structural Biology of Biofilms’ Group, European Institute of Chemistry and Biology (IECB), Pessac, France
| | - Sylvie Létoffé
- Institut Pasteur, Université de Paris, UMR CNRS2001, ‘Genetics of Biofilms’ laboratory, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris, UMR CNRS2001, ‘Genetics of Biofilms’ laboratory, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Petya V. Krasteva
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- ‘Structural Biology of Biofilms’ Group, European Institute of Chemistry and Biology (IECB), Pessac, France
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15
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Koppenhöfer S, Lang AS. Patterns of abundance, chromosomal localization, and domain organization among c-di-GMP-metabolizing genes revealed by comparative genomics of five alphaproteobacterial orders. BMC Genomics 2022; 23:834. [PMID: 36522693 PMCID: PMC9756655 DOI: 10.1186/s12864-022-09072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/17/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a bacterial second messenger that affects diverse processes in different bacteria, including the cell cycle, motility, and biofilm formation. Its cellular levels are controlled by the opposing activities of two types of enzymes, with synthesis by diguanylate cyclases containing a GGDEF domain and degradation by phosphodiesterases containing either an HD-GYP or an EAL domain. These enzymes are ubiquitous in bacteria with up to 50 encoded in some genomes, the specific functions of which are mostly unknown. RESULTS We used comparative analyses to identify genomic patterns among genes encoding proteins with GGDEF, EAL, and HD-GYP domains in five orders of the class Alphaproteobacteria. GGDEF-containing sequences and GGDEF-EAL hybrids were the most abundant and had the highest diversity of co-occurring auxiliary domains while EAL and HD-GYP containing sequences were less abundant and less diverse with respect to auxiliary domains. There were striking patterns in the chromosomal localizations of the genes found in two of the orders. The Rhodobacterales' EAL-encoding genes and Rhizobiales' GGDEF-EAL-encoding genes showed opposing patterns of distribution compared to the GGDEF-encoding genes. In the Rhodobacterales, the GGDEF-encoding genes showed a tri-modal distribution with peaks mid-way between the origin (ori) and terminus (ter) of replication and at ter while the EAL-encoding genes peaked near ori. The patterns were more complex in the Rhizobiales, but the GGDEF-encoding genes were biased for localization near ter. CONCLUSIONS The observed patterns in the chromosomal localizations of these genes suggest a coupling of synthesis and hydrolysis of c-di-GMP with the cell cycle. Moreover, the higher proportions and diversities of auxiliary domains associated with GGDEF domains and GGDEF-EAL hybrids compared to EAL or HD-GYP domains could indicate that more stimuli affect synthesis compared to hydrolysis of c-di-GMP.
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Affiliation(s)
- Sonja Koppenhöfer
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
| | - Andrew S. Lang
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
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16
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Takahama S, Ishige K, Nogimori T, Yasutomi Y, Appay V, Yamamoto T. Model for predicting age-dependent safety and immunomodulatory effects of STING ligands in non-human primates. Mol Ther Methods Clin Dev 2022; 28:99-115. [PMID: 36620070 PMCID: PMC9813482 DOI: 10.1016/j.omtm.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Stimulator of interferon genes (STING) is a cytoplasmic dinucleotide sensor used as an immunomodulatory agent for cancer treatment. The efficacy of the STING ligand (STING-L) against various tumors has been evaluated in mouse models; however, its safety and efficacy in non-human primates have not been reported. We examined the effects of escalating doses of cyclic-di-adenosine monophosphate (c-di-AMP) or cyclic [G (3',5')pA (3',5'p] (3'-3'-cGAMP) administered intramuscularly or intravenously to cynomolgus macaques. Both ligands induced transient local and systemic inflammatory responses and systemic immunomodulatory responses, including the upregulation of interferon-α (IFN-α) and IFN-γ expression and the activation of multiple immunocompetent cell subsets. Better immunological responses were observed in animals that received c-di-AMP compared with those that received 3'-3'-cGAMP. Multi-parameter analysis using a dataset obtained before administering the ligands predicted the efficacy outcome partially. Importantly, the efficacy of these ligands was reduced in older macaques. We propose that 0.5 mg/kg c-di-AMP via intramuscular administration should be the optimal starting point for clinical studies. Our study is the first to demonstrate the age-dependent safety and efficacy of STING-L in non-human primates and supports the potential of STING-L use as a direct immunomodulator in vivo.
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Affiliation(s)
- Shokichi Takahama
- Laboratory of Immunosenescence, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Kazuya Ishige
- Biochemicals Division, Yamasa Corporation, Chiba 288-0056, Japan
| | - Takuto Nogimori
- Laboratory of Immunosenescence, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Yasuhiro Yasutomi
- Laboratory of Immunoregulation and Vaccine Research, Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki 305-0843, Japan
| | - Victor Appay
- Laboratory of Immunosenescence, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan,Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, 33000 Bordeaux, France
| | - Takuya Yamamoto
- Laboratory of Immunosenescence, Center for Vaccine and Adjuvant Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan,Laboratory of Aging and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan,Department of Virology and Immunology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan,Laboratory of Translational Cancer Immunology and Biology, Next-generation Precision Medicine Research Center, Osaka International Cancer Institute, Osaka 541-8567, Japan,Corresponding author: Takuya Yamamoto, Laboratory of Immunosenescence, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan.
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17
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Chauhan S, Marotta NJ, Karls AC, Weinert EE. Binding of 2',3'-Cyclic Nucleotide Monophosphates to Bacterial Ribosomes Inhibits Translation. ACS CENTRAL SCIENCE 2022; 8:1518-1526. [PMID: 36439312 PMCID: PMC9686202 DOI: 10.1021/acscentsci.2c00681] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 06/16/2023]
Abstract
The intracellular small molecules 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have recently been rediscovered within both prokaryotes and eukaryotes. Studies in bacteria have demonstrated that 2',3'-cNMP levels affect bacterial phenotypes, such as biofilm formation, motility, and growth, and modulate expression of numerous genes, suggesting that 2',3'-cNMP levels are monitored by cells. In this study, 2',3'-cNMP-linked affinity chromatography resins were used to identify Escherichia coli proteins that bind 2',3'-cNMPs, with the top hits including all of the ribosomal proteins, and to confirm direct binding of purified ribosomes. Using in vitro translation assays, we have demonstrated that 2',3'-cNMPs inhibit translation at concentrations found in amino acid-starved cells. In addition, a genetically encoded tool to increase cellular 2',3'-cNMP levels was developed and was demonstrated to decrease E. coli growth rates. Taken together, this work suggests a mechanism for 2',3-cNMP levels to modulate bacterial phenotypes by rapidly affecting translation.
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Affiliation(s)
- Shikha
S. Chauhan
- Department
of Biochemistry and Molecular Biology, Penn
State University, University
Park, Pennsylvania 16802, United States
| | - Nick J. Marotta
- Graduate
Program in Molecular, Cellular, and Integrative Biosciences, Penn State University, University Park, Pennsylvania 16802, United States
| | - Anna C. Karls
- Department
of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Emily E. Weinert
- Department
of Biochemistry and Molecular Biology, Penn
State University, University
Park, Pennsylvania 16802, United States
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
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18
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Vavřina Z, Perlíková P, Milisavljević N, Chevrier F, Smola M, Smith J, Dejmek M, Havlíček V, Buděšínský M, Liboska R, Vaneková L, Brynda J, Boura E, Řezáčová P, Hocek M, Birkuš G. Design, Synthesis, and Biochemical and Biological Evaluation of Novel 7-Deazapurine Cyclic Dinucleotide Analogues as STING Receptor Agonists. J Med Chem 2022; 65:14082-14103. [PMID: 36201304 PMCID: PMC9620234 DOI: 10.1021/acs.jmedchem.2c01305] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 11/28/2022]
Abstract
Cyclic dinucleotides (CDNs) are second messengers that activate stimulator of interferon genes (STING). The cGAS-STING pathway plays a promising role in cancer immunotherapy. Here, we describe the synthesis of CDNs containing 7-substituted 7-deazapurine moiety. We used mouse cyclic GMP-AMP synthase and bacterial dinucleotide synthases for the enzymatic synthesis of CDNs. Alternatively, 7-(het)aryl 7-deazapurine CDNs were prepared by Suzuki-Miyaura cross-couplings. New CDNs were tested in biochemical and cell-based assays for their affinity to human STING. Eight CDNs showed better activity than 2'3'-cGAMP, the natural ligand of STING. The effect on cytokine and chemokine induction was also evaluated. The best activities were observed for CDNs bearing large aromatic substituents that point above the CDN molecule. We solved four X-ray structures of complexes of new CDNs with human STING. We observed π-π stacking interactions between the aromatic substituents and Tyr240 that are involved in the stabilization of CDN-STING complexes.
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Affiliation(s)
- Zdeněk Vavřina
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Pavla Perlíková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Technicka 5, Prague 166 28, Czech Republic
| | - Nemanja Milisavljević
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Florian Chevrier
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Miroslav Smola
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Joshua Smith
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- First
Faculty of Medicine, Charles University, Katerinska 1660/32, Prague 121 08, Czech Republic
| | - Milan Dejmek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Vojtěch Havlíček
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Miloš Buděšínský
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Radek Liboska
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Lenka Vaneková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Cell Biology, Faculty of Science, Charles
University, Vinicna 1594/7, Prague 128 43, Czech Republic
| | - Jiří Brynda
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Evzen Boura
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Pavlína Řezáčová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Gabriel Birkuš
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
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19
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Lee VT, Sondermann H, Winkler WC. Nano-RNases: oligo- or dinucleases? FEMS Microbiol Rev 2022; 46:6677394. [PMID: 36026528 PMCID: PMC9779919 DOI: 10.1093/femsre/fuac038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 01/07/2023] Open
Abstract
Diribonucleotides arise from two sources: turnover of RNA transcripts (rRNA, tRNA, mRNA, and others) and linearization of cyclic-di-nucleotide signaling molecules. In both cases, there appears to be a requirement for a dedicated set of enzymes that will cleave these diribonucleotides into mononucleotides. The first enzyme discovered to mediate this activity is oligoribonuclease (Orn) from Escherichia coli. In addition to being the enzyme that cleaves dinucleotides and potentially other short oligoribonucleotides, Orn is also the only known exoribonuclease enzyme that is essential for E. coli, suggesting that removal of the shortest RNAs is an essential cellular function. Organisms naturally lacking the orn gene encode other nanoRNases (nrn) that can complement the conditional E. coli orn mutant. This review covers the history and recent advances in our understanding of these enzymes and their substrates. In particular, we focus on (i) the sources of diribonucleotides; (ii) the discovery of exoribonucleases; (iii) the structural features of Orn, NrnA/NrnB, and NrnC; (iv) the enzymatic activity of these enzymes against diribonucleotides versus other substrates; (v) the known physiological consequences of accumulation of linear dinucleotides; and (vi) outstanding biological questions for diribonucleotides and diribonucleases.
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20
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Rangarajan AA, Waters CM. Double take: A dual-functional Hypr GGDEF synthesizes both cyclic di-GMP and cyclic GMP—AMP to control predation in Bdellovibrio bacteriovorus. PLoS Genet 2022; 18:e1010263. [PMID: 35862299 PMCID: PMC9302825 DOI: 10.1371/journal.pgen.1010263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Aathmaja Anandhi Rangarajan
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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21
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Yanase Y, Tsuji G, Nakamura M, Shibata N, Demizu Y. Control of STING Agonistic/Antagonistic Activity Using Amine-Skeleton-Based c-di-GMP Analogues. Int J Mol Sci 2022; 23:ijms23126847. [PMID: 35743289 PMCID: PMC9224868 DOI: 10.3390/ijms23126847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/15/2022] [Accepted: 06/18/2022] [Indexed: 02/05/2023] Open
Abstract
Stimulator of Interferon Genes (STING) is a type of endoplasmic reticulum (ER)-membrane receptor. STING is activated by a ligand binding, which leads to an enhancement of the immune-system response. Therefore, a STING ligand can be used to regulate the immune system in therapeutic strategies. However, the natural (or native) STING ligand, cyclic-di-nucleotide (CDN), is unsuitable for pharmaceutical use because of its susceptibility to degradation by enzymes and its low cell-membrane permeability. In this study, we designed and synthesized CDN derivatives by replacing the sugar-phosphodiester moiety, which is responsible for various problems of natural CDNs, with an amine skeleton. As a result, we identified novel STING ligands that activate or inhibit STING. The cyclic ligand 7, with a cyclic amine structure containing two guanines, was found to have agonistic activity, whereas the linear ligand 12 showed antagonistic activity. In addition, these synthetic ligands were more chemically stable than the natural ligands.
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Affiliation(s)
- Yuta Yanase
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki 210-9501, Japan; (Y.Y.); (M.N.); (N.S.)
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Genichiro Tsuji
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki 210-9501, Japan; (Y.Y.); (M.N.); (N.S.)
- Correspondence: (G.T.); (Y.D.); Tel.: +81-44-270-6579 (G.T.); +81-44-270-6578 (Y.D.)
| | - Miki Nakamura
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki 210-9501, Japan; (Y.Y.); (M.N.); (N.S.)
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Division of Pharmaceutical Science of Okayama University, 1-1-1 Tsushimanaka, Kita 700-8530, Japan
| | - Norihito Shibata
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki 210-9501, Japan; (Y.Y.); (M.N.); (N.S.)
| | - Yosuke Demizu
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki 210-9501, Japan; (Y.Y.); (M.N.); (N.S.)
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Division of Pharmaceutical Science of Okayama University, 1-1-1 Tsushimanaka, Kita 700-8530, Japan
- Correspondence: (G.T.); (Y.D.); Tel.: +81-44-270-6579 (G.T.); +81-44-270-6578 (Y.D.)
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22
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Hou L, Yu X, Zhang Y, Du L, Zhang Y, Cheng H, Zheng Q, Chen J, Hou J. Enhanced Immune Responses in Mice Induced by the c-di-GMP Adjuvanted Inactivated Vaccine for Pseudorabies Virus. Front Immunol 2022; 13:845680. [PMID: 35432301 PMCID: PMC9009373 DOI: 10.3389/fimmu.2022.845680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/07/2022] [Indexed: 11/30/2022] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) is a bacterial second messenger with immunomodulatory activities in mice, suggesting potential applications as a vaccine immunopotentiator or therapeutic agent. In this study, we evaluated the efficacy of c-di-GMP as an immunopotentiator for pseudorabies virus (PRV) inactivated vaccine in a murine model. We found that c-di-GMP improved the humoral and cellular immune responses induced by PRV inactivated vaccine and its effects on immunity reached the level comparable to that of a live attenuated vaccine. Furthermore, c-di-GMP enhanced the murine antibody response against the viral glycoprotein gB up to 120 days after immunization. The c-di-GMP–adjuvanted PRV inactivated vaccine induced long-term humoral immunity by promoting a potent T follicular helper cell response, which is known to directly control the magnitude of the germinal center B cell response. Furthermore, the c-di-GMP enhanced the response of bone marrow plasma cells and upregulated the expression of Bcl-2 and Mcl-1, which have been identified as anti-apoptotic regulatory genes of germinal center and memory B cells. Our findings open a new avenue for improving the immune efficacy of PRV inactivated vaccines.
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Affiliation(s)
- Liting Hou
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Xiaoming Yu
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Yuanyuan Zhang
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Luping Du
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Yuanpeng Zhang
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Haiwei Cheng
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Qisheng Zheng
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Jin Chen
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
| | - Jibo Hou
- National Research Center of Veterinary Biological Engineering and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
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23
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Bacterial origins of human cell-autonomous innate immune mechanisms. Nat Rev Immunol 2022; 22:629-638. [PMID: 35396464 DOI: 10.1038/s41577-022-00705-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2022] [Indexed: 12/11/2022]
Abstract
The cell-autonomous innate immune system enables animal cells to resist viral infection. This system comprises an array of sensors that, after detecting viral molecules, activate the expression of antiviral proteins and the interferon response. The repertoire of immune sensors and antiviral proteins has long been considered to be derived from extensive evolutionary innovation in vertebrates, but new data challenge this dogma. Recent studies show that central components of the cell-autonomous innate immune system have ancient evolutionary roots in prokaryotic genes that protect bacteria from phages. These include the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, Toll/IL-1 receptor (TIR) domain-containing pathogen receptors, the viperin family of antiviral proteins, SAMHD1-like nucleotide-depletion enzymes, gasdermin proteins and key components of the RNA interference pathway. This Perspective details current knowledge of the elements of antiviral immunity that are conserved from bacteria to humans, and presents possible evolutionary scenarios to explain the observed conservation.
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24
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Analysis of HubP-dependent cell pole protein targeting in Vibrio cholerae uncovers novel motility regulators. PLoS Genet 2022; 18:e1009991. [PMID: 35020734 PMCID: PMC8789113 DOI: 10.1371/journal.pgen.1009991] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/25/2022] [Accepted: 12/14/2021] [Indexed: 11/25/2022] Open
Abstract
In rod-shaped bacteria, the emergence and maintenance of long-axis cell polarity is involved in key cellular processes such as cell cycle, division, environmental sensing and flagellar motility among others. Many bacteria achieve cell pole differentiation through the use of polar landmark proteins acting as scaffolds for the recruitment of functional macromolecular assemblies. In Vibrio cholerae a large membrane-tethered protein, HubP, specifically interacts with proteins involved in chromosome segregation, chemotaxis and flagellar biosynthesis. Here we used comparative proteomics, genetic and imaging approaches to identify additional HubP partners and demonstrate that at least six more proteins are subject to HubP-dependent polar localization. These include a cell-wall remodeling enzyme (DacB), a likely chemotaxis sensory protein (HlyB), two presumably cytosolic proteins of unknown function (VC1210 and VC1380) and two membrane-bound proteins, named here MotV and MotW, that exhibit distinct effects on chemotactic motility. We show that while both ΔmotW and ΔmotV mutants retain monotrichous flagellation, they present significant to severe motility defects when grown in soft agar. Video-tracking experiments further reveal that ΔmotV cells can swim in liquid environments but are unable to tumble or penetrate a semisolid matrix, whereas a motW deletion affects both tumbling frequency and swimming speed. Motility suppressors and gene co-occurrence analyses reveal co-evolutionary linkages between MotV, a subset of non-canonical CheV proteins and flagellar C-ring components FliG and FliM, whereas MotW regulatory inputs appear to intersect with specific c-di-GMP signaling pathways. Together, these results reveal an ever more versatile role for the landmark cell pole organizer HubP and identify novel mechanisms of motility regulation. Cell polarity is the result of controlled asymmetric distribution of protein macrocomplexes, genetic material, membrane lipids and cellular metabolites, and can play crucial physiological roles not only in multicellular organisms but also in unicellular bacteria. In the opportunistic cholera pathogen Vibrio cholerae, the polar landmark protein HubP tethers key actors in chromosome segregation, chemotaxis and flagellar biosynthesis and thus converts the cell pole into an important functional microdomain for cell proliferation, environmental sensing and adaptation between free-living and pathogenic life-styles. Using a comparative proteomics approach, we here-in present a comprehensive analysis of HubP-dependent cell pole protein sorting and identify novel HubP partners including ones likely involved in cell wall remodeling (DacB), chemotaxis (HlyB) and motility regulation (MotV and MotW). Unlike previous studies which have identified early roles for HubP in flagellar assembly, functional, genetic and phylogenetic analyses of its MotV and MotW partners suggest a direct role in flagellar rotary mechanics and provide new insights into the coevolution and functional interdependence of chemotactic signaling, bacterial motility and biofilm formation.
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25
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Bjelić D, Finšgar M. Bioactive coatings with anti-osteoclast therapeutic agents for bone implants: Enhanced compliance and prolonged implant life. Pharmacol Res 2022; 176:106060. [PMID: 34998972 DOI: 10.1016/j.phrs.2022.106060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 12/18/2022]
Abstract
The use of therapeutic agents that inhibit bone resorption is crucial to prolong implant life, delay revision surgery, and reduce the burden on the healthcare system. These therapeutic agents include bisphosphonates, various nucleic acids, statins, proteins, and protein complexes. Their use in systemic treatment has several drawbacks, such as side effects and insufficient efficacy in terms of concentration, which can be eliminated by local treatment. This review focuses on the incorporation of osteoclast inhibitors (antiresorptive agents) into bioactive coatings for bone implants. The ability of bioactive coatings as systems for local delivery of antiresorptive agents to achieve optimal loading of the bioactive coating and its release is described in detail. Various parameters such as the suitable concentrations, release times, and the effects of the antiresorptive agents on nearby cells or bone tissue are discussed. However, further research is needed to support the optimization of the implant, as this will enable subsequent personalized design of the coating in terms of the design and selection of the coating material, the choice of an antiresorptive agent and its amount in the coating. In addition, therapeutic agents that have not yet been incorporated into bioactive coatings but appear promising are also mentioned. From this work, it can be concluded that therapeutic agents contribute to the biocompatibility of the bioactive coating by enhancing its beneficial properties.
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Affiliation(s)
- Dragana Bjelić
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia.
| | - Matjaž Finšgar
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia.
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26
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Cutruzzolà F, Paiardini A, Scribani Rossi C, Spizzichino S, Paone A, Giardina G, Rinaldo S. A conserved scaffold with heterogeneous metal ion binding site: the multifaceted example of HD-GYP proteins. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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27
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Onyedibe KI, Elmanfi S, Aryal UK, Könönen E, Gürsoy UK, Sintim HO. Global proteomics of fibroblast cells treated with bacterial cyclic dinucleotides, c-di-GMP and c-di-AMP. J Oral Microbiol 2021; 14:2003617. [PMID: 34992733 PMCID: PMC8725719 DOI: 10.1080/20002297.2021.2003617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/04/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Constant exposure of human gingival fibroblasts (HGFs) to oral pathogens trigger selective immune responses. Recently, the activation of immune response to cyclic dinucleotides (CDNs) via STING has come to the forefront. Reports show that other proteins outside the STING-TBK1-IRF3 axis respond to CDNs but a global view of impacted proteome in diverse cells is lacking. HGFs are constantly exposed to bacterial-derived cyclic-di-adenosine monophosphate (c-di-AMP) and cyclic-di-guanosine monophosphate (c-di-GMP). AIM To understand the response of HGFs to bacterial-derived CDNs, we carried out a global proteomics analysis of HGFs treated with c-di-AMP or c-di-GMP. METHODS The expression levels of several proteins modulated by CDNs were examined. RESULTS Interferon signaling proteins such as Ubiquitin-like protein ISG15 (ISG15), Interferon-induced GTP-binding protein Mx1 (MX1), Interferon-induced protein with tetratricopeptide repeats (IFIT) 1 (IFIT1), and (IFIT3) were significantly upregulated. Interestingly, other pathways not fully characterized to be regulated by CDNs, such as necroptosis signaling, iron homeostasis signaling, protein ubiquitination, EIF2 signaling, sumoylation and nucleotide excision repair pathways were also modulated by the bacterial-derived CDNs. CONCLUSION This study has added to the increasing appreciation that beyond the regulation of cytokine production via STING, cyclic dinucleotides also broadly affect many critical processes in human cells.
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Affiliation(s)
- Kenneth I. Onyedibe
- Department of Chemistry, Purdue University, West Lafayette, USA
- Immunology and Infectious Disease, Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Purdue University, West Lafayette, USA
| | - Samira Elmanfi
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Uma K. Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, USA
| | - Eija Könönen
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Ulvi Kahraman Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Herman O. Sintim
- Department of Chemistry, Purdue University, West Lafayette, USA
- Immunology and Infectious Disease, Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Purdue University, West Lafayette, USA
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28
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Impact of STING Inflammatory Signaling during Intracellular Bacterial Infections. Cells 2021; 11:cells11010074. [PMID: 35011636 PMCID: PMC8750390 DOI: 10.3390/cells11010074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 12/15/2022] Open
Abstract
The early detection of bacterial pathogens through immune sensors is an essential step in innate immunity. STING (Stimulator of Interferon Genes) has emerged as a key mediator of inflammation in the setting of infection by connecting pathogen cytosolic recognition with immune responses. STING detects bacteria by directly recognizing cyclic dinucleotides or indirectly by bacterial genomic DNA sensing through the cyclic GMP-AMP synthase (cGAS). Upon activation, STING triggers a plethora of powerful signaling pathways, including the production of type I interferons and proinflammatory cytokines. STING activation has also been associated with the induction of endoplasmic reticulum (ER) stress and the associated inflammatory responses. Recent reports indicate that STING-dependent pathways participate in the metabolic reprogramming of macrophages and contribute to the establishment and maintenance of a robust inflammatory profile. The induction of this inflammatory state is typically antimicrobial and related to pathogen clearance. However, depending on the infection, STING-mediated immune responses can be detrimental to the host, facilitating bacterial survival, indicating an intricate balance between immune signaling and inflammation during bacterial infections. In this paper, we review recent insights regarding the role of STING in inducing an inflammatory profile upon intracellular bacterial entry in host cells and discuss the impact of STING signaling on the outcome of infection. Unraveling the STING-mediated inflammatory responses can enable a better understanding of the pathogenesis of certain bacterial diseases and reveal the potential of new antimicrobial therapy.
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29
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Shang M, Lu K, Guan W, Cao S, Ren M, Zhou C. 2',3'-Cyclic GMP-AMP Dinucleotides for STING-Mediated Immune Modulation: Principles, Immunotherapeutic Potential, and Synthesis. ChemMedChem 2021; 17:e202100671. [PMID: 34807508 DOI: 10.1002/cmdc.202100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 11/09/2022]
Abstract
The cGAS-STING pathway discovered ten years ago is an important component of the innate immune system. Activation of cGAS-STING triggers downstream signalling, such as TBK1-IRF3, NF-κB and autophagy, which in turn leads to antipathogen responses, durable antitumour immunity or autoimmune diseases. 2',3'-Cyclic GMP-AMP dinucleotides (2',3'-cGAMP), the key second messengers produced by cGAS, play a pivotal role in cGAS-STING signalling by binding and activating STING. Thus, 2',3'-cGAMP has immunotherapeutic potential, which in turn has stimulated research on the design and synthesis of 2',3'-cGAMP analogues for clinical applications over the past ten years. This review presents the discovery, metabolism, and function of 2',3'-cGAMP in the cGAS-STING innate immune signalling axis. The enzymatic and chemical syntheses of 2',3'-cGAMP analogues as STING-targeting therapeutics are also summarized.
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Affiliation(s)
- Mengdi Shang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Wenli Guan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Shujie Cao
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Mengtian Ren
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology College of Chemistry, Nankai University, Tianjin, 300071, China
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30
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Lamprokostopoulou A, Römling U. Yin and Yang of Biofilm Formation and Cyclic di-GMP Signaling of the Gastrointestinal Pathogen Salmonella enterica Serovar Typhimurium. J Innate Immun 2021; 14:275-292. [PMID: 34775379 PMCID: PMC9275015 DOI: 10.1159/000519573] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022] Open
Abstract
Within the last 60 years, microbiological research has challenged many dogmas such as bacteria being unicellular microorganisms directed by nutrient sources; these investigations produced new dogmas such as cyclic diguanylate monophosphate (cyclic di-GMP) second messenger signaling as a ubiquitous regulator of the fundamental sessility/motility lifestyle switch on the single-cell level. Successive investigations have not yet challenged this view; however, the complexity of cyclic di-GMP as an intracellular bacterial signal, and, less explored, as an extracellular signaling molecule in combination with the conformational flexibility of the molecule, provides endless opportunities for cross-kingdom interactions. Cyclic di-GMP-directed microbial biofilms commonly stimulate the immune system on a lower level, whereas host-sensed cyclic di-GMP broadly stimulates the innate and adaptive immune responses. Furthermore, while the intracellular second messenger cyclic di-GMP signaling promotes bacterial biofilm formation and chronic infections, oppositely, Salmonella Typhimurium cellulose biofilm inside immune cells is not endorsed. These observations only touch on the complexity of the interaction of biofilm microbial cells with its host. In this review, we describe the Yin and Yang interactive concepts of biofilm formation and cyclic di-GMP signaling using S. Typhimurium as an example.
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Affiliation(s)
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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31
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Pathania M, Tosi T, Millership C, Hoshiga F, Morgan RML, Freemont PS, Gründling A. Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM. J Biol Chem 2021; 297:101317. [PMID: 34678313 PMCID: PMC8573169 DOI: 10.1016/j.jbc.2021.101317] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Cyclic-di-adenosine monophosphate (c-di-AMP) is an important nucleotide signaling molecule that plays a key role in osmotic regulation in bacteria. c-di-AMP is produced from two molecules of ATP by proteins containing a diadenylate cyclase (DAC) domain. In Bacillus subtilis, the main c-di-AMP cyclase, CdaA, is a membrane-linked cyclase with an N-terminal transmembrane domain followed by the cytoplasmic DAC domain. As both high and low levels of c-di-AMP have a negative impact on bacterial growth, the cellular levels of this signaling nucleotide are tightly regulated. Here we investigated how the activity of the B. subtilis CdaA is regulated by the phosphoglucomutase GlmM, which has been shown to interact with the c-di-AMP cyclase. Using the soluble B. subtilis CdaACD catalytic domain and purified full-length GlmM or the GlmMF369 variant lacking the C-terminal flexible domain 4, we show that the cyclase and phosphoglucomutase form a stable complex in vitro and that GlmM is a potent cyclase inhibitor. We determined the crystal structure of the individual B. subtilis CdaACD and GlmM homodimers and of the CdaACD:GlmMF369 complex. In the complex structure, a CdaACD dimer is bound to a GlmMF369 dimer in such a manner that GlmM blocks the oligomerization of CdaACD and formation of active head-to-head cyclase oligomers, thus suggesting a mechanism by which GlmM acts as a cyclase inhibitor. As the amino acids at the CdaACD:GlmM interphase are conserved, we propose that the observed mechanism of inhibition of CdaA by GlmM may also be conserved among Firmicutes.
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Affiliation(s)
- Monisha Pathania
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Tommaso Tosi
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Charlotte Millership
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Fumiya Hoshiga
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhodri M L Morgan
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paul S Freemont
- London Biofoundry, Imperial College Translation and Innovation Hub, White City Campus, London, United Kingdom; Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom.
| | - Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.
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32
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Abidi W, Torres-Sánchez L, Siroy A, Krasteva PV. Weaving of bacterial cellulose by the Bcs secretion systems. FEMS Microbiol Rev 2021; 46:6388354. [PMID: 34634120 PMCID: PMC8892547 DOI: 10.1093/femsre/fuab051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Cellulose is the most abundant biological compound on Earth and while it is the predominant building constituent of plants, it is also a key extracellular matrix component in many diverse bacterial species. While bacterial cellulose was first described in the 19th century, it was not until this last decade that a string of structural works provided insights into how the cellulose synthase BcsA, assisted by its inner-membrane partner BcsB, senses c-di-GMP to simultaneously polymerize its substrate and extrude the nascent polysaccharide across the inner bacterial membrane. It is now established that bacterial cellulose can be produced by several distinct types of cellulose secretion systems and that in addition to BcsAB, they can feature multiple accessory subunits, often indispensable for polysaccharide production. Importantly, the last years mark significant progress in our understanding not only of cellulose polymerization per se but also of the bigger picture of bacterial signaling, secretion system assembly, biofilm formation and host tissue colonization, as well as of structural and functional parallels of this dominant biosynthetic process between the bacterial and eukaryotic domains of life. Here, we review current mechanistic knowledge on bacterial cellulose secretion with focus on the structure, assembly and cooperativity of Bcs secretion system components.
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Affiliation(s)
- Wiem Abidi
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.,École doctorale 'Innovation thérapeutique: du fundamental à l'appliqué' (ITFA), Université Paris-Saclay, 92296, Chatenay-Malabry, France
| | - Lucía Torres-Sánchez
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.,École doctorale 'Innovation thérapeutique: du fundamental à l'appliqué' (ITFA), Université Paris-Saclay, 92296, Chatenay-Malabry, France
| | - Axel Siroy
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
| | - Petya Violinova Krasteva
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
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A rationally designed c-di-AMP FRET biosensor to monitor nucleotide dynamics. J Bacteriol 2021; 203:e0008021. [PMID: 34309402 DOI: 10.1128/jb.00080-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3'3'-cyclic di-adenosine monophosphate (c-di-AMP) is an important nucleotide second messenger found throughout the bacterial domain of life. C-di-AMP is essential in many bacteria and regulates a diverse array of effector proteins controlling pathogenesis, cell wall homeostasis, osmoregulation, and central metabolism. Despite the ubiquity and importance of c-di-AMP, methods to detect this signaling molecule are limited, particularly at single cell resolution. In this work, crystallization of the Listeria monocytogenes c-di-AMP effector protein Lmo0553 enabled structure guided design of a Förster resonance energy transfer (FRET) based biosensor, which we have named CDA5. CDA5 is a fully genetically encodable, specific, and reversible biosensor which allows for the detection of c-di-AMP dynamics both in vitro and within live cells in a nondestructive manner. Our initial studies identify a distribution of c-di-AMP in Bacillus subtilis populations first grown in Luria Broth and then resuspended in diluted Luria Broth compatible with florescence analysis. Furthermore, we find that B. subtilis mutants lacking either a c-di-AMP phosphodiesterase or cyclase have respectively higher and lower FRET responses. These findings provide novel insight into the c-di-AMP distribution within bacterial populations and establish CDA5 as a powerful platform for characterizing new aspects of c-di-AMP regulation. Importance C-di-AMP is an important nucleotide second messenger for which detection methods are severely limited. In this work we engineer and implement a c-di-AMP specific FRET biosensor to remedy this dearth. We present this biosensor, CDA5, as a versatile tool to investigate previously intractable facets of c-di-AMP biology.
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Krol E, Schäper S, Becker A. Cyclic di-GMP signaling controlling the free-living lifestyle of alpha-proteobacterial rhizobia. Biol Chem 2021; 401:1335-1348. [PMID: 32990642 DOI: 10.1515/hsz-2020-0232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger which has been associated with a motile to sessile lifestyle switch in many bacteria. Here, we review recent insights into c-di-GMP regulated processes related to environmental adaptations in alphaproteobacterial rhizobia, which are diazotrophic bacteria capable of fixing nitrogen in symbiosis with their leguminous host plants. The review centers on Sinorhizobium meliloti, which in the recent years was intensively studied for its c-di-GMP regulatory network.
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Affiliation(s)
- Elizaveta Krol
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Simon Schäper
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
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35
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Kim SK, Ngo HX, Dennis EK, Thamban Chandrika N, DeShong P, Garneau-Tsodikova S, Lee VT. Inhibition of Pseudomonas aeruginosa Alginate Synthesis by Ebselen Oxide and Its Analogues. ACS Infect Dis 2021; 7:1713-1726. [PMID: 33871968 DOI: 10.1021/acsinfecdis.1c00045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that is frequently found in the airways of cystic fibrosis (CF) patients due to the dehydrated mucus that collapses the underlying cilia and prevents mucociliary clearance. During this life-long chronic infection, P. aeruginosa cell accumulates mutations that lead to inactivation of the mucA gene that results in the constitutive expression of algD-algA operon and the production of alginate exopolysaccharide. The viscous alginate polysaccharide further occludes the airways of CF patients and serves as a protective matrix to shield P. aeruginosa from host immune cells and antibiotic therapy. Development of inhibitors of alginate production by P. aeruginosa would reduce the negative impact from this viscous polysaccharide. In addition to transcriptional regulation, alginate biosynthesis requires allosteric activation by bis (3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding to an Alg44 protein. Previously, we found that ebselen (Eb) and ebselen oxide (EbO) inhibited diguanylate cyclase from synthesizing c-di-GMP. In this study, we show that EbO, Eb, ebsulfur (EbS), and their analogues inhibit alginate production. Eb and EbS can covalently modify the cysteine 98 (C98) residue of Alg44 and prevent its ability to bind c-di-GMP. However, P. aeruginosa with Alg44 C98 substituted with alanine or serine was still inhibited for alginate production by Eb and EbS. Our results indicate that EbO, Eb, and EbS are lead compounds for reducing alginate production by P. aeruginosa. Future development of these inhibitors could provide a potential treatment for CF patients infected with mucoid P. aeruginosa.
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Affiliation(s)
- Soo-Kyoung Kim
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, Maryland 20742, United States
| | - Huy X. Ngo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Emily K. Dennis
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Philip DeShong
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Vincent T. Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, Maryland 20742, United States
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36
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c-di-AMP, a likely master regulator of bacterial K + homeostasis machinery, activates a K + exporter. Proc Natl Acad Sci U S A 2021; 118:2020653118. [PMID: 33790011 DOI: 10.1073/pnas.2020653118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
bis-(3',5')-cyclic diadenosine monophosphate (c-di-AMP) is a second messenger with roles in virulence, cell wall and biofilm formation, and surveillance of DNA integrity in many bacterial species, including pathogens. Strikingly, it has also been proposed to coordinate the activity of the components of K+ homeostasis machinery, inhibiting K+ import, and activating K+ export. However, there is a lack of quantitative evidence supporting the direct functional impact of c-di-AMP on K+ transporters. To gain a detailed understanding of the role of c-di-AMP on the activity of a component of the K+ homeostasis machinery in B. subtilis, we have characterized the impact of c-di-AMP on the functional, biochemical, and physiological properties of KhtTU, a K+/H+ antiporter composed of the membrane protein KhtU and the cytosolic protein KhtT. We have confirmed c-di-AMP binding to KhtT and determined the crystal structure of this complex. We have characterized in vitro the functional properties of KhtTU and KhtU alone and quantified the impact of c-di-AMP and of pH on their activity, demonstrating that c-di-AMP activates KhtTU and that pH increases its sensitivity to this nucleotide. Based on our functional and structural data, we were able to propose a mechanism for the activation of KhtTU by c-di-AMP. In addition, we have analyzed the impact of KhtTU in its native bacterium, providing a physiological context for the regulatory function of c-di-AMP and pH. Overall, we provide unique information that supports the proposal that c-di-AMP is a master regulator of K+ homeostasis machinery.
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37
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π-Helix controls activity of oxygen-sensing diguanylate cyclases. Biosci Rep 2021; 40:222070. [PMID: 32039439 PMCID: PMC7033309 DOI: 10.1042/bsr20193602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 11/18/2022] Open
Abstract
The ability of organisms to sense and adapt to oxygen levels in their environment leads to changes in cellular phenotypes, including biofilm formation and virulence. Globin coupled sensors (GCSs) are a family of heme proteins that regulate diverse functions in response to O2 levels, including modulating synthesis of cyclic dimeric guanosine monophosphate (c-di-GMP), a bacterial second messenger that regulates biofilm formation. While GCS proteins have been demonstrated to regulate O2-dependent pathways, the mechanism by which the O2 binding event is transmitted from the globin domain to the cyclase domain is unknown. Using chemical cross-linking and subsequent liquid chromatography-tandem mass spectrometry, diguanylate cyclase (DGC)-containing GCS proteins from Bordetella pertussis (BpeGReg) and Pectobacterium carotovorum (PccGCS) have been demonstrated to form direct interactions between the globin domain and a middle domain π-helix. Additionally, mutation of the π-helix caused major changes in oligomerization and loss of DGC activity. Furthermore, results from assays with isolated globin and DGC domains found that DGC activity is affected by the cognate globin domain, indicating unique interactions between output domain and cognate globin sensor. Based on these studies a compact GCS structure, which depends on the middle domain π-helix for orienting the three domains, is needed for DGC activity and allows for direct sensor domain interactions with both middle and output domains to transmit the O2 binding signal. The insights from the present study improve our understanding of DGC regulation and provide insight into GCS signaling that may lead to the ability to rationally control O2-dependent GCS activity.
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38
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Kim DS, Endo A, Fang FG, Huang KC, Bao X, Choi HW, Majumder U, Shen YY, Mathieu S, Zhu X, Sanders K, Noland T, Hao MH, Chen Y, Wang JY, Yasui S, TenDyke K, Wu J, Ingersoll C, Loiacono KA, Hutz JE, Sarwar N. E7766, a Macrocycle-Bridged Stimulator of Interferon Genes (STING) Agonist with Potent Pan-Genotypic Activity. ChemMedChem 2021; 16:1740-1743. [PMID: 33522135 DOI: 10.1002/cmdc.202100068] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Indexed: 01/01/2023]
Abstract
A strategy for creating potent and pan-genotypic stimulator of interferon genes (STING) agonists is described. Locking a bioactive U-shaped conformation of cyclic dinucleotides by introducing a transannular macrocyclic bridge between the nucleic acid bases leads to a topologically novel macrocycle-bridged STING agonist (MBSA). In addition to substantially enhanced potency, the newly designed MBSAs, exemplified by clinical candidate E7766, exhibit broad pan-genotypic activity in all major human STING variants. E7766 is shown to have potent antitumor activity with long lasting immune memory response in a mouse liver metastatic tumor model. Two complementary stereoselective synthetic routes to E7766 are also described.
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Affiliation(s)
- Dae-Shik Kim
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Atsushi Endo
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Francis G Fang
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Kuan-Chun Huang
- H3 Biomedicine, 300 Technology Square FL5, Cambridge, MA 02139, USA
| | - Xingfeng Bao
- H3 Biomedicine, 300 Technology Square FL5, Cambridge, MA 02139, USA
| | | | - Utpal Majumder
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Young Y Shen
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Steven Mathieu
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Xiaojie Zhu
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Kristen Sanders
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Thomas Noland
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Ming-Hong Hao
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Yu Chen
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - John Y Wang
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - So Yasui
- Analytical Research Laboratories, Pharmaceutical Science & Technology, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba-shi, Ibaraki, 300-2635, Japan
| | - Karen TenDyke
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Jiayi Wu
- H3 Biomedicine, 300 Technology Square FL5, Cambridge, MA 02139, USA
| | | | - Kara A Loiacono
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Janna E Hutz
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
| | - Nadeem Sarwar
- Eisai Inc., 35 Cambridgepark Drive, Cambridge, MA 02140, USA
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39
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Vavřina Z, Gutten O, Smola M, Zavřel M, Aliakbar Tehrani Z, Charvát V, Kožíšek M, Boura E, Birkuš G, Rulíšek L. Protein-Ligand Interactions in the STING Binding Site Probed by Rationally Designed Single-Point Mutations: Experiment and Theory. Biochemistry 2021; 60:607-620. [PMID: 33586948 DOI: 10.1021/acs.biochem.0c00949] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
STING protein (stimulator of interferon genes) plays an important role in the innate immune system. A number of potent compounds regulating its activity have been reported, mostly derivatives of cyclic dinucleotides (CDNs), natural STING agonists. Here, we aim to provide complementary information to large-scale "ligand-profiling" studies by probing the importance of STING-CDN protein-ligand interactions on the protein side. We examined in detail six typical CDNs each in complex with 13 rationally devised mutations in STING: S162A, S162T, Y167F, G230A, R232K, R232H, A233L, A233I, R238K, T263A, T263S, R293Q, and G230A/R293Q. The mutations switch on and off various types of protein-ligand interactions: π-π stacking, hydrogen bonding, ionic pairing, and nonpolar contacts. We correlated experimental data obtained by differential scanning fluorimetry, X-ray crystallography, and isothermal titration calorimetry with theoretical calculations. This enabled us to provide a mechanistic interpretation of the differences in the binding of representative CDNs to STING. We observed that the G230A mutation increased the thermal stability of the protein-ligand complex, indicating an increased level of ligand binding, whereas R238K and Y167F led to a complete loss of stabilization (ligand binding). The effects of the other mutations depended on the type of ligand (CDN) and varied, to some extent. A very good correlation (R2 = 0.6) between the experimental binding affinities and interaction energies computed by quantum chemical methods enabled us to explain the effect of the studied mutations in detail and evaluate specific interactions quantitatively. Our work may inspire development of high-affinity ligands against the common STING haplotypes by targeting the key (sometimes non-intuitive) protein-ligand interactions.
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Affiliation(s)
- Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague 110 00, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Zahra Aliakbar Tehrani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
| | - Vilém Charvát
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
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40
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Zaver SA, Pollock AJ, Boradia VM, Woodward JJ. A Luminescence-Based Coupled Enzyme Assay Enables High-Throughput Quantification of the Bacterial Second Messenger 3'3'-Cyclic-Di-AMP. Chembiochem 2020; 22:1030-1041. [PMID: 33142009 DOI: 10.1002/cbic.202000667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/02/2020] [Indexed: 11/12/2022]
Abstract
Cyclic dinucleotide signaling systems, which are found ubiquitously throughout nature, allow organisms to rapidly and dynamically sense and respond to alterations in their environments. In recent years, the second messenger, cyclic di-(3',5')-adenosine monophosphate (c-di-AMP), has been identified as an essential signaling molecule in a diverse array of bacterial genera. We and others have shown that defects in c-di-AMP homeostasis result in severe physiological defects and virulence attenuation in many bacterial species. Despite significant advancements in the field, there is still a major gap in the understanding of the environmental and cellular factors that influence c-di-AMP dynamics due to a lack of tools to sensitively and rapidly monitor changes in c-di-AMP levels. To address this limitation, we describe here the development of a luciferase-based coupled enzyme assay that leverages the cyclic nucleotide phosphodiesterase, CnpB, for the sensitive and high-throughput quantification of 3'3'-c-di-AMP. We also demonstrate the utility of this approach for the quantification of the cyclic oligonucleotide-based anti-phage signaling system (CBASS) effector, 3'3'-cGAMP. These findings establish CDA-Luc as a more affordable and sensitive alternative to conventional c-di-AMP detection tools with broad utility for the study of bacterial cyclic dinucleotide physiology.
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Affiliation(s)
- Shivam A Zaver
- Department of Microbiology, University of Washington, 98195, Seattle, WA, USA
| | - Alex J Pollock
- Department of Microbiology, University of Washington, 98195, Seattle, WA, USA
| | | | - Joshua J Woodward
- Department of Microbiology, University of Washington, 98195, Seattle, WA, USA
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41
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c-di-AMP Accumulation Impairs Muropeptide Synthesis in Listeria monocytogenes. J Bacteriol 2020; 202:JB.00307-20. [PMID: 33020220 DOI: 10.1128/jb.00307-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022] Open
Abstract
Cyclic di-AMP (c-di-AMP) is an essential and ubiquitous second messenger among bacteria. c-di-AMP regulates many cellular pathways through direct binding to several molecular targets in bacterial cells. c-di-AMP depletion is well known to destabilize the bacterial cell wall, resulting in increased bacteriolysis and enhanced susceptibility to cell wall targeting antibiotics. Using the human pathogen Listeria monocytogenes as a model, we found that c-di-AMP accumulation also impaired cell envelope integrity. An L. monocytogenes mutant deleted for c-di-AMP phosphodiesterases (pdeA pgpH mutant) exhibited a 4-fold increase in c-di-AMP levels and several cell wall defects. For instance, the pdeA pgpH mutant was defective for the synthesis of peptidoglycan muropeptides and was susceptible to cell wall-targeting antimicrobials. Among different muropeptide precursors, we found that the pdeA pgpH strain was particularly impaired in the synthesis of d-Ala-d-Ala, which is required to complete the pentapeptide stem associated with UDP-N-acetylmuramic acid (MurNAc). This was consistent with an increased sensitivity to d-cycloserine, which inhibits the d-alanine branch of peptidoglycan synthesis. Finally, upon examining d-Ala:d-Ala ligase (Ddl), which catalyzes the conversion of d-Ala to d-Ala-d-Ala, we found that its activity was activated by K+ Based on previous reports that c-di-AMP inhibits K+ uptake, we propose that c-di-AMP accumulation impairs peptidoglycan synthesis, partially through the deprivation of cytoplasmic K+ levels, which are required for cell wall-synthetic enzymes.IMPORTANCE The bacterial second messenger c-di-AMP is produced by a large number of bacteria and conditionally essential to many species. Conversely, c-di-AMP accumulation is also toxic to bacterial physiology and pathogenesis, but its mechanisms are largely undefined. We found that in Listeria monocytogenes, elevated c-di-AMP levels diminished muropeptide synthesis and increased susceptibility to cell wall-targeting antimicrobials. Cell wall defects might be an important mechanism for attenuated virulence in bacteria with high c-di-AMP levels.
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42
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Rosenthal K, Becker M, Rolf J, Siedentop R, Hillen M, Nett M, Lütz S. Catalytic Promiscuity of cGAS: A Facile Enzymatic Synthesis of 2'-3'-Linked Cyclic Dinucleotides. Chembiochem 2020; 21:3225-3228. [PMID: 32633874 PMCID: PMC7754487 DOI: 10.1002/cbic.202000433] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Indexed: 12/19/2022]
Abstract
Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that catalyzes the synthesis of the cyclic GMP-AMP dinucleotide 2'3'-cGAMP. 2'3'-cGAMP functions as inducer for the production of type I interferons. Derivatives of this important second messenger are highly valuable for pharmaceutical applications. However, the production of these analogues requires complex, multistep syntheses. Herein, human cGAS is shown to react with a series of unnatural nucleotides, thus leading to novel cyclic dinucleotides. Most substrate derivatives with modifications at the nucleobase, ribose, and the α-thio phosphate were accepted. These results demonstrate the catalytic promiscuity of human cGAS and its utility for the biocatalytic synthesis of cyclic dinucleotide derivatives.
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Affiliation(s)
- Katrin Rosenthal
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund University Emil-Figge-Strasse 6644227DortmundGermany
| | - Martin Becker
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund University Emil-Figge-Strasse 6644227DortmundGermany
| | - Jascha Rolf
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund University Emil-Figge-Strasse 6644227DortmundGermany
| | - Regine Siedentop
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund University Emil-Figge-Strasse 6644227DortmundGermany
| | - Michael Hillen
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund University Emil-Figge-Strasse 6644227DortmundGermany
| | - Markus Nett
- Department of Biochemical and Chemical EngineeringLaboratory of Technical BiologyTU Dortmund UniversityEmil-Figge-Strasse 6644227DortmundGermany
| | - Stephan Lütz
- Department of Biochemical and Chemical EngineeringChair for Bioprocess EngineeringTU Dortmund University Emil-Figge-Strasse 6644227DortmundGermany
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43
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Louie A, Bhandula V, Portnoy DA. Secretion of c-di-AMP by Listeria monocytogenes Leads to a STING-Dependent Antibacterial Response during Enterocolitis. Infect Immun 2020; 88:e00407-20. [PMID: 33020211 PMCID: PMC7671888 DOI: 10.1128/iai.00407-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/27/2020] [Indexed: 12/24/2022] Open
Abstract
Stimulator of interferon genes (STING) acts as a cytoplasmic signaling hub of innate immunity that is activated by host-derived or bacterially derived cyclic dinucleotides. Listeria monocytogenes is a foodborne, facultative intracellular pathogen that secretes c-di-AMP and activates STING, yet the in vivo role of the STING pathway during bacterial pathogenesis remains unclear. In this study, we found that STING-deficient mice had increased weight loss and roughly 10-fold-increased systemic bacterial burden during L. monocytogenes-induced enterocolitis. Infection with a L. monocytogenes mutant impaired in c-di-AMP secretion failed to elicit a protective response, whereas a mutant with increased c-di-AMP secretion triggered enhanced protection. Type I interferon (IFN) is a major output of STING signaling; however, disrupting IFN signaling during L. monocytogenes-induced enterocolitis did not recapitulate STING deficiency. In the absence of STING, the intestinal immune response was associated with a reduced influx of inflammatory monocytes. These studies suggest that in barrier sites such as the intestinal tract, where pathogen-associated molecular patterns are abundant, cytosolic surveillance systems such as STING are well positioned to detect pathogenic bacteria.
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Affiliation(s)
- Alexander Louie
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Varaang Bhandula
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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44
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Liu K, Lan Y, Li X, Li M, Cui L, Luo H, Luo L. Development of small molecule inhibitors/agonists targeting STING for disease. Biomed Pharmacother 2020; 132:110945. [PMID: 33254439 DOI: 10.1016/j.biopha.2020.110945] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 01/07/2023] Open
Abstract
Cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) -stimulator of interferon genes (STING) signaling pathway is the primary immune response pathway in the cytoplasm. Pharmacological regulation of the STING pathway has good characteristics in both structure and function, which plays a significant role in the immunotherapy of autoimmune diseases, autoinflammatory diseases, and cancer. In this review, we summarized the activation of STING signaling pathway, the STING-related diseases, the development principle and the latest progress of inhibitors and agonists targeting STING. Our review demonstrates that STING signal pathway is a promising drug target, providing effective clues and correct guidance for the discovery of novel small molecule inhibitors/agonists that targeted STING for cancer, autoimmune, and inflammatory diseases.
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Affiliation(s)
- Kaifeng Liu
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China
| | - Yongqi Lan
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China
| | - Xiaoling Li
- Animal Experiment Center of Guangdong Medical University, Zhanjiang, 524023, China
| | - Mingyue Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Liao Cui
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Hui Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, Guangdong, 524023, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, Guangdong, 524023, China.
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Liu Y, Lee C, Li F, Trček J, Bähre H, Guo RT, Chen CC, Chernobrovkin A, Zubarev R, Römling U. A Cyclic di-GMP Network Is Present in Gram-Positive Streptococcus and Gram-Negative Proteus Species. ACS Infect Dis 2020; 6:2672-2687. [PMID: 32786278 PMCID: PMC7551669 DOI: 10.1021/acsinfecdis.0c00314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 01/16/2023]
Abstract
The ubiquitous cyclic di-GMP (c-di-GMP) network is highly redundant with numerous GGDEF domain proteins as diguanylate cyclases and EAL domain proteins as c-di-GMP specific phosphodiesterases comprising those domains as two of the most abundant bacterial domain superfamilies. One hallmark of the c-di-GMP network is its exalted plasticity as c-di-GMP turnover proteins can rapidly vanish from species within a genus and possess an above average transmissibility. To address the evolutionary forces of c-di-GMP turnover protein maintenance, conservation, and diversity, we investigated a Gram-positive and a Gram-negative species, which preserved only one single clearly identifiable GGDEF domain protein. Species of the family Morganellaceae of the order Enterobacterales exceptionally show disappearance of the c-di-GMP signaling network, but Proteus spp. still retained one diguanylate cyclase. As another example, in species of the bovis, pyogenes, and salivarius subgroups as well as Streptococcus suis and Streptococcus henryi of the genus Streptococcus, one candidate diguanylate cyclase was frequently identified. We demonstrate that both proteins encompass PAS (Per-ARNT-Sim)-GGDEF domains, possess diguanylate cyclase catalytic activity, and are suggested to signal via a PilZ receptor domain at the C-terminus of type 2 glycosyltransferase constituting BcsA cellulose synthases and a cellulose synthase-like protein CelA, respectively. Preservation of the ancient link between production of cellulose(-like) exopolysaccharides and c-di-GMP signaling indicates that this functionality is even of high ecological importance upon maintenance of the last remnants of a c-di-GMP signaling network in some of today's free-living bacteria.
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Affiliation(s)
- Ying Liu
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Changhan Lee
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Fengyang Li
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Janja Trček
- Faculty
of Natural Sciences and Mathematics, Department of Biology, University
of Maribor, 2000 Maribor, Slovenia
| | - Heike Bähre
- Research
Core Unit Metabolomics, Hannover Medical
School, D-30625 Hannover, Germany
| | - Rey-Ting Guo
- State
Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative
Innovation Center for Green Transformation of Bio-Resources, Hubei
Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P.R. China
| | - Chun-Chi Chen
- State
Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative
Innovation Center for Green Transformation of Bio-Resources, Hubei
Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P.R. China
| | - Alexey Chernobrovkin
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Roman Zubarev
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Department
of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
| | - Ute Römling
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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Autotransporters Drive Biofilm Formation and Autoaggregation in the Diderm Firmicute Veillonella parvula. J Bacteriol 2020; 202:JB.00461-20. [PMID: 32817093 PMCID: PMC7549365 DOI: 10.1128/jb.00461-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Veillonella parvula is an anaerobic commensal and opportunistic pathogen whose ability to adhere to surfaces or other bacteria and form biofilms is critical for it to inhabit complex human microbial communities such as the gut and oral microbiota. Although the adhesive capacity of V. parvula has been previously described, very little is known about the underlying molecular mechanisms due to a lack of genetically amenable Veillonella strains. In this study, we took advantage of a naturally transformable V. parvula isolate and newly adapted genetic tools to identify surface-exposed adhesins called autotransporters as the main molecular determinants of adhesion in this bacterium. This work therefore provides new insights on an important aspect of the V. parvula lifestyle, opening new possibilities for mechanistic studies of the contribution of biofilm formation to the biology of this major commensal of the oral-digestive tract. The Negativicutes are a clade of the Firmicutes that have retained the ancestral diderm character and possess an outer membrane. One of the best studied Negativicutes, Veillonella parvula, is an anaerobic commensal and opportunistic pathogen inhabiting complex human microbial communities, including the gut and the dental plaque microbiota. Whereas the adhesion and biofilm capacities of V. parvula are expected to be crucial for its maintenance and development in these environments, studies of V. parvula adhesion have been hindered by the lack of efficient genetic tools to perform functional analyses in this bacterium. Here, we took advantage of a recently described naturally transformable V. parvula isolate, SKV38, and adapted tools developed for the closely related Clostridia spp. to perform random transposon and targeted mutagenesis to identify V. parvula genes involved in biofilm formation. We show that type V secreted autotransporters, typically found in diderm bacteria, are the main determinants of V. parvula autoaggregation and biofilm formation and compete with each other for binding either to cells or to surfaces, with strong consequences for V. parvula biofilm formation capacity. The identified trimeric autotransporters have an original structure compared to classical autotransporters identified in Proteobacteria, with an additional C-terminal domain. We also show that inactivation of the gene coding for a poorly characterized metal-dependent phosphohydrolase HD domain protein conserved in the Firmicutes and their closely related diderm phyla inhibits autotransporter-mediated biofilm formation. This study paves the way for further molecular characterization of V. parvula interactions with other bacteria and the host within complex microbiota environments. IMPORTANCEVeillonella parvula is an anaerobic commensal and opportunistic pathogen whose ability to adhere to surfaces or other bacteria and form biofilms is critical for it to inhabit complex human microbial communities such as the gut and oral microbiota. Although the adhesive capacity of V. parvula has been previously described, very little is known about the underlying molecular mechanisms due to a lack of genetically amenable Veillonella strains. In this study, we took advantage of a naturally transformable V. parvula isolate and newly adapted genetic tools to identify surface-exposed adhesins called autotransporters as the main molecular determinants of adhesion in this bacterium. This work therefore provides new insights on an important aspect of the V. parvula lifestyle, opening new possibilities for mechanistic studies of the contribution of biofilm formation to the biology of this major commensal of the oral-digestive tract.
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Kawai M, Ota A, Takemura T, Nakai T, Maruyama F. Continuation and replacement of Vibrio cholerae non-O1 clonal genomic groups isolated from Plecoglossus altivelis fish in freshwaters. Environ Microbiol 2020; 22:4473-4484. [PMID: 33448654 DOI: 10.1111/1462-2920.15199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 01/14/2023]
Abstract
The dissemination and abundances of Vibrio species in aquatic environments are of interest, as some species cause emerging diseases in humans and in aquatic organisms like fish. It is suggested that Vibrio cholerae non-O1 infections of Plecoglossus altivelis ('ayu') were spread to various parts of Japan through the annual transplantation of juvenile fish. To investigate this, we used genome-aided tracing of 17 V. cholerae strains isolated from ayu between the 1970s and 1990s in different Japanese freshwater systems. The strains formed a genomic clade distinct from all known clades, which we designate as the Ayu clade. Two clonal genomic groups identified within the clade, Ayu-1 and Ayu-2, persisted for a few years (between 1977 to 1979 and 1987 to 1990, respectively), and clonal replacement of Ayu-1 by Ayu-2 took place over an 8-year period. Despite the high similarity between Ayu-1 and Ayu-2 (> 99.9% identity and > 97% fraction of genomes shared), differences in their gene repertoires were found, raising the possibility that they are phenotypically distinct. These results highlight the importance of genome-based studies for understanding the long-term dynamics of populations over the timescale of years.
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Affiliation(s)
- Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Atsushi Ota
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashihiroshima, Japan
| | - Taichiro Takemura
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Higashihiroshima, Japan
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Abstract
Most bacteria respond to surfaces by biogenesis of intracellular c-di-GMP, which inhibits motility and induces secretion of biofilm-promoting adherence factors. Bacterial cellulose is a widespread biofilm component whose secretion in Gram-negative species requires an inner membrane, c-di-GMP-dependent synthase tandem (BcsAB), an outer membrane porin (BcsC), and various accessory subunits that regulate synthase assembly and function as well as the exopolysaccharide's chemical composition and mechanical properties. We recently showed that in Escherichia coli, most Bcs proteins form a megadalton-sized secretory nanomachine, but the role and structure of individual regulatory components remained enigmatic. Here, we demonstrate that essential-for-secretion BcsR and BcsQ regulate each other's folding and stability and are recruited to the inner membrane via c-di-GMP-sensing BcsE and its intraoperon partner BcsF. Crystallographic and solution-based data show that BcsE's predicted GIL domain is a degenerate receiver-GGDEF domain tandem (BcsEREC*-GGDEF*), where the divergent diguanylate cyclase module binds both dimeric c-di-GMP and BcsQ through mutually independent interfaces. In addition, we reveal that a third N-terminal domain (BcsENTD) determines the protein's homooligomerization and targeting of BcsERQ to the membrane as well as previously unreported interactions with transcription antitermination complex components. Together, the data suggest that BcsE acts on multiple levels to fine-tune bacterial cellulose secretion, from the early stages of secretion system assembly to the maintenance of a membrane-proximal pool of dimeric c-di-GMP for processive synthase activation.IMPORTANCE Bacterial cellulose is a widespread biofilm component that can modulate microbial fitness and virulence both in the environment and infected hosts. Whereas its secretion generally involves an inner membrane c-di-GMP-dependent synthase tandem (BcsAB) across the bacterial domain of life, enterobacteria feature sophisticated Escherichia coli-like Bcs secretion systems, where multiple additional subunits are either required for secretion or contribute to the maximal production of the polysaccharide in vivo. Here, we demonstrate that essential-for-secretion BcsR and BcsQ regulate each other's folding and stability and are recruited to the inner membrane via c-di-GMP-sensing BcsE and its intraoperon partner, BcsF. Crystallographic and functional data reveal that BcsE features unexpected domain architecture and likely acts on multiple levels to fine-tune bacterial cellulose production, from the early stages of secretion system assembly to the maintenence of a membrane-proximal pool of dimeric c-di-GMP for processive synthase activation.
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Pollock AJ, Zaver SA, Woodward JJ. A STING-based biosensor affords broad cyclic dinucleotide detection within single living eukaryotic cells. Nat Commun 2020; 11:3533. [PMID: 32669552 PMCID: PMC7363834 DOI: 10.1038/s41467-020-17228-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Cyclic dinucleotides (CDNs) are second messengers conserved across all three domains of life. Within eukaryotes they mediate protective roles in innate immunity against malignant, viral, and bacterial disease, and exert pathological effects in autoimmune disorders. Despite their ubiquitous role in diverse biological contexts, CDN detection methods are limited. Here, using structure guided design of the murine STING CDN binding domain, we engineer a Förster resonance energy transfer (FRET) based biosensor deemed BioSTING. Recombinant BioSTING affords real-time detection of CDN synthase activity and inhibition. Expression of BioSTING in live human cells allows quantification of localized bacterial and eukaryotic CDN levels in single cells with low nanomolar sensitivity. These findings establish BioSTING as a powerful kinetic in vitro platform amenable to high throughput screens and as a broadly applicable cellular tool to interrogate the temporal and spatial dynamics of CDN signaling in a variety of infectious, malignant, and autoimmune contexts.
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Affiliation(s)
- Alex J Pollock
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Shivam A Zaver
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
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Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication. Biochem J 2020; 476:3333-3353. [PMID: 31647518 DOI: 10.1042/bcj20190399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 01/02/2023]
Abstract
Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3'3'-cyclic GMP-AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5'-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5'-pGpG-Ca2+ structure, β5-α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5'-pGpG-Ca2+ structure quite different from other 5'-pGpG bound structures reported earlier.
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