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Zhan X, Zhang K, Wang C, Fan Q, Tang X, Zhang X, Wang K, Fu Y, Liang H. A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa. Nat Commun 2024; 15:1860. [PMID: 38424057 PMCID: PMC10904736 DOI: 10.1038/s41467-024-46149-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous studies have conducted comprehensive analysis of c-di-GMP. However, the mechanisms by which certain environmental signals such as iron control intracellular c-di-GMP levels are unclear. Here, we show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein, IsmP, and a diguanylate cyclase, ImcA. Binding of iron to the CHASE4 domain of IsmP inhibits the IsmP-ImcA interaction, which leads to increased c-di-GMP synthesis by ImcA, thus promoting biofilm formation and reducing bacterial motility. Structural characterization of the apo-CHASE4 domain and its binding to iron allows us to pinpoint residues defining its specificity. In addition, the cryo-electron microscopy structure of ImcA in complex with a c-di-GMP analog (GMPCPP) suggests a unique conformation in which the compound binds to the catalytic pockets and to the membrane-proximal side located at the cytoplasm. Thus, our results indicate that a CHASE4 domain directly senses iron and modulates the crosstalk between c-di-GMP metabolic enzymes.
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Affiliation(s)
- Xueliang Zhan
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Kuo Zhang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Chenchen Wang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Qiao Fan
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Xiujia Tang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xi Zhang
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Ke Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yang Fu
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Haihua Liang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China.
- University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
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Chen T, Pu M, Subramanian S, Kearns D, Rowe-Magnus D. PlzD modifies Vibrio vulnificus foraging behavior and virulence in response to elevated c-di-GMP. mBio 2023; 14:e0153623. [PMID: 37800901 PMCID: PMC10653909 DOI: 10.1128/mbio.01536-23] [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: 06/23/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Many free-swimming bacteria propel themselves through liquid using rotary flagella, and mounting evidence suggests that the inhibition of flagellar rotation initiates biofilm formation, a sessile lifestyle that is a nearly universal surface colonization paradigm in bacteria. In general, motility and biofilm formation are inversely regulated by the intracellular second messenger bis-(3´-5´)-cyclic dimeric guanosine monophosphate (c-di-GMP). Here, we identify a protein, PlzD, bearing a conserved c-di-GMP binding PilZ domain that localizes to the flagellar pole in a c-di-GMP-dependent manner and alters the foraging behavior, biofilm, and virulence characteristics of the opportunistic human pathogen, Vibrio vulnificus. Our data suggest that PlzD interacts with components of the flagellar stator to decrease bacterial swimming speed and changes in swimming direction, and these activities are enhanced when cellular c-di-GMP levels are elevated. These results reveal a physical link between a second messenger (c-di-GMP) and an effector (PlzD) that promotes transition from a motile to a sessile state in V. vulnificus.
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Affiliation(s)
- Tianyi Chen
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Meng Pu
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Dan Kearns
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Dean Rowe-Magnus
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Bloomington, Indiana, USA
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Yao Y, Xi N, Hai E, Zhang X, Guo J, Lin Z, Huang W. PA0575 (RmcA) interacts with other c-di-GMP metabolizing proteins in Pseudomonas aeruginosa PAO1. J GEN APPL MICROBIOL 2023; 68:232-241. [PMID: 35732459 DOI: 10.2323/jgam.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
As a central signaling molecule, c-di-GMP (bis-(3,5)-cyclic diguanosine monophosphate) is becoming the focus for research in bacteria physiology. Pseudomonas aeruginosa PAO1 genome contains highly complicated c-di-GMP metabolizing genes and a number of these proteins have been identified and investigated. Especially, a sophisticated network of these proteins is emerging. In current study, mainly through Bacteria-2-Hybrid assay, we found PA0575 (RmcA), a GGDEF-EAL dual protein, to interact with two other dual proteins of PA4601 (MorA) and PA4959 (FimX). These observations imply the intricacy of c-di-GMP metabolizing protein interactions. Our work thus provides one piece of data to increase the understandings to c-di-GMP signaling.
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Affiliation(s)
- Yanxiang Yao
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - Naren Xi
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - E Hai
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - Xiaomin Zhang
- Research Center of Medical Science and Technology, Ningxia Medical University
| | - Jiayi Guo
- Research Center of Medical Science and Technology, Ningxia Medical University
| | - Zhi Lin
- School of Life Sciences, Tianjin University
| | - Weidong Huang
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
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Vávra J, Sergunin A, Jeřábek P, Shimizu T, Martínková M. Signal transduction mechanisms in heme-based globin-coupled oxygen sensors with a focus on a histidine kinase ( AfGcHK) and a diguanylate cyclase (YddV or EcDosC). Biol Chem 2022; 403:1031-1042. [PMID: 36165459 DOI: 10.1515/hsz-2022-0185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/08/2022] [Indexed: 01/19/2023]
Abstract
Heme is a vital cofactor of proteins with roles in oxygen transport (e.g. hemoglobin), storage (e.g. myoglobin), and activation (e.g. P450) as well as electron transfer (e.g. cytochromes) and many other functions. However, its structural and functional role in oxygen sensing proteins differs markedly from that in most other enzymes, where it serves as a catalytic or functional center. This minireview discusses the mechanism of signal transduction in two heme-based oxygen sensors: the histidine kinase AfGcHK and the diguanylate cyclase YddV (EcDosC), both of which feature a heme-binding domain containing a globin fold resembling that of hemoglobin and myoglobin.
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Affiliation(s)
- Jakub Vávra
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Artur Sergunin
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Petr Jeřábek
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
| | - Markéta Martínková
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, 128 43 Czech Republic
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Rick T, Kreiling V, Höing A, Fiedler S, Glatter T, Steinchen W, Hochberg G, Bähre H, Seifert R, Bange G, Knauer SK, Graumann PL, Thormann KM. GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP. NPJ Biofilms Microbiomes 2022; 8:35. [PMID: 35501424 PMCID: PMC9061725 DOI: 10.1038/s41522-022-00297-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractIn bacteria, the monopolar localization of enzymes and protein complexes can result in a bimodal distribution of enzyme activity between the dividing cells and heterogeneity of cellular behaviors. In Shewanella putrefaciens, the multidomain hybrid diguanylate cyclase/phosphodiesterase PdeB, which degrades the secondary messenger c-di-GMP, is located at the flagellated cell pole. Here, we show that direct interaction between the inactive diguanylate cyclase (GGDEF) domain of PdeB and the FimV domain of the polar landmark protein HubP is crucial for full function of PdeB as a phosphodiesterase. Thus, the GGDEF domain serves as a spatially controlled on-switch that effectively restricts PdeBs activity to the flagellated cell pole. PdeB regulates abundance and activity of at least two crucial surface-interaction factors, the BpfA surface-adhesion protein and the MSHA type IV pilus. The heterogeneity in c-di-GMP concentrations, generated by differences in abundance and timing of polar appearance of PdeB, orchestrates the population behavior with respect to cell-surface interaction and environmental spreading.
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Poulin MB, Kuperman LL. Regulation of Biofilm Exopolysaccharide Production by Cyclic Di-Guanosine Monophosphate. Front Microbiol 2021; 12:730980. [PMID: 34566936 PMCID: PMC8461298 DOI: 10.3389/fmicb.2021.730980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022] Open
Abstract
Many bacterial species in nature possess the ability to transition into a sessile lifestyle and aggregate into cohesive colonies, known as biofilms. Within a biofilm, bacterial cells are encapsulated within an extracellular polymeric substance (EPS) comprised of polysaccharides, proteins, nucleic acids, lipids, and other small molecules. The transition from planktonic growth to the biofilm lifecycle provides numerous benefits to bacteria, such as facilitating adherence to abiotic surfaces, evasion of a host immune system, and resistance to common antibiotics. As a result, biofilm-forming bacteria contribute to 65% of infections in humans, and substantially increase the energy and time required for treatment and recovery. Several biofilm specific exopolysaccharides, including cellulose, alginate, Pel polysaccharide, and poly-N-acetylglucosamine (PNAG), have been shown to play an important role in bacterial biofilm formation and their production is strongly correlated with pathogenicity and virulence. In many bacteria the biosynthetic machineries required for assembly of these exopolysaccharides are regulated by common signaling molecules, with the second messenger cyclic di-guanosine monophosphate (c-di-GMP) playing an especially important role in the post-translational activation of exopolysaccharide biosynthesis. Research on treatments of antibiotic-resistant and biofilm-forming bacteria through direct targeting of c-di-GMP signaling has shown promise, including peptide-based treatments that sequester intracellular c-di-GMP. In this review, we will examine the direct role c-di-GMP plays in the biosynthesis and export of biofilm exopolysaccharides with a focus on the mechanism of post-translational activation of these pathways, as well as describe novel approaches to inhibit biofilm formation through direct targeting of c-di-GMP.
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Affiliation(s)
- Myles B Poulin
- Department of Chemistry and Biochemistry, University of Maryland, College Park, College Park, MD, United States
| | - Laura L Kuperman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, College Park, MD, United States
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Hengge R. High-Specificity Local and Global c-di-GMP Signaling. Trends Microbiol 2021; 29:993-1003. [PMID: 33640237 DOI: 10.1016/j.tim.2021.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 11/26/2022]
Abstract
The striking multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins in many bacteria has brought second messenger signaling back onto the agenda of contemporary microbiology. How can several signaling pathways act in parallel in a specific manner if all of them use the same diffusible second messenger present at a certain global cellular concentration? Recent research has now shown that bacteria achieve this by flexibly combining modes of local and global c-di-GMP signaling in complex signaling networks. Three criteria have to be met to define local c-di-GMP signaling: specific knockout phenotypes, direct interactions between proteins involved, and actual cellular c-di-GMP levels remaining below the Kd of effectors. Adaptive changes in signaling network architecture can further enhance signaling flexibility.
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Affiliation(s)
- Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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