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Hoque NJ, Rivera S, Young PG, Weinert EE, Liu Y. Heme pocket hydrogen bonding residue interactions within the Pectobacterium Diguanylate cyclase-containing globin coupled sensor: A resonance Raman study. J Inorg Biochem 2024; 260:112686. [PMID: 39106644 DOI: 10.1016/j.jinorgbio.2024.112686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
Abstract
Heme-based sensor proteins are used by organisms to control signaling and physiological effects in response to their gaseous environment. Globin-coupled sensors (GCS) are oxygen-sensing proteins that are widely distributed in bacteria. These proteins consist of a heme globin domain linked by a middle domain to various output domains, including diguanylate cyclase domains, which are responsible for synthesizing c-di-GMP, a bacterial second messenger crucial for regulating biofilm formation. To understand the roles of heme pocket residues in controlling activity of the diguanylate cyclase domain, variants of the Pectobacterium carotovorum GCS (PccGCS) were characterized by enzyme kinetics and resonance Raman (rR) spectroscopy. Results of these studies have identified roles for hydrogen bonding and heme edge residues in modulating heme pocket conformation and flexibility. Better understanding of the ligand-dependent GCS signaling mechanism and the residues involved may allow for future development of methods to control O2-dependent c-di-GMP production.
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Affiliation(s)
- Nushrat J Hoque
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Shannon Rivera
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Paul G Young
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Emily E Weinert
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Yilin Liu
- Department of Chemistry, University of Akron, Akron, OH 44325, USA.
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2
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Potter JR, Rivera S, Young PG, Patterson DC, Namitz KE, Yennawar N, Kincaid JR, Liu Y, Weinert EE. Heme pocket modulates protein conformation and diguanylate cyclase activity of a tetrameric globin coupled sensor. J Inorg Biochem 2024; 258:112638. [PMID: 38878680 DOI: 10.1016/j.jinorgbio.2024.112638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 07/01/2024]
Abstract
Bacteria use the second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) to control biofilm formation and other key phenotypes in response to environmental signals. Changes in oxygen levels can alter c-di-GMP signaling through a family of proteins termed globin coupled sensors (GCS) that contain diguanylate cyclase domains. Previous studies have found that GCS diguanylate cyclase activity is controlled by ligand binding to the heme within the globin domain, with oxygen binding resulting in the greatest increase in catalytic activity. Herein, we present evidence that heme-edge residues control O2-dependent signaling in PccGCS, a GCS protein from Pectobacterium carotovorum, by modulating heme distortion. Using enzyme kinetics, resonance Raman spectroscopy, small angle X-ray scattering, and multi-wavelength analytical ultracentrifugation, we have developed an integrated model of the full-length PccGCS tetramer and have identified conformational changes associated with ligand binding, heme conformation, and cyclase activity. Taken together, these studies provide new insights into the mechanism by which O2 binding modulates activity of diguanylate cyclase-containing GCS proteins.
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Affiliation(s)
- Jacob R Potter
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Shannon Rivera
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Paul G Young
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Dayna C Patterson
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin E Namitz
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA.
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA; Department of Chemistry, University of Akron, Akron, OH 44325, USA.
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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3
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Schuelke-Sanchez A, Yennawar NH, Weinert EE. Oxygen-selective regulation of cyclic di-GMP synthesis by a globin coupled sensor with a shortened linking domain modulates Shewanella sp. ANA-3 biofilm. J Inorg Biochem 2024; 252:112482. [PMID: 38218138 DOI: 10.1016/j.jinorgbio.2024.112482] [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: 09/28/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Bacteria utilize heme proteins, such as globin coupled sensors (GCSs), to sense and respond to oxygen levels. GCSs are predicted in almost 2000 bacterial species and consist of a globin domain linked by a central domain to a variety of output domains, including diguanylate cyclase domains that synthesize c-di-GMP, a major regulator of biofilm formation. To investigate the effects of middle domain length and heme edge residues on GCS diguanylate cyclase activity and cellular function, a putative diguanylate cyclase-containing GCS from Shewanella sp. ANA-3 (SA3GCS) was characterized. Binding of O2 to the heme resulted in activation of diguanylate cyclase activity, while NO and CO binding had minimal effects on catalysis, demonstrating that SA3GCS exhibits greater ligand selectivity for cyclase activation than many other diguanylate cyclase-containing GCSs. Small angle X-ray scattering analysis of dimeric SA3GCS identified movement of the cyclase domains away from each other, while maintaining the globin dimer interface, as a potential mechanism for regulating cyclase activity. Comparison of the Shewanella ANA-3 wild type and SA3GCS deletion (ΔSA3GCS) strains identified changes in biofilm formation, demonstrating that SA3GCS diguanylate cyclase activity modulates Shewanella phenotypes.
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Affiliation(s)
- Ariel Schuelke-Sanchez
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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4
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Jacob J, Veras I, Calderόn O, Porter-Morgan HA, Tan J, Aguilar HE, Elkins WT, Martinez Castro VP, Fulton V, Yousri WK. Possibly pathogenic bacteria in aerosols and foams as a result of aeration remediation in a polluted urban waterway. Folia Microbiol (Praha) 2024; 69:235-246. [PMID: 37777646 PMCID: PMC10876779 DOI: 10.1007/s12223-023-01096-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Newtown Creek is a tributary of the Hudson River Estuary. It has a legacy of both industrial pollution and sewage pollution and has been designated a Superfund site. To ameliorate the chronically low levels of dissolved oxygen detected in the Creek, the New York City Department of Environmental Protection has been installing aerators. The abundance of various bacteria in the aerosols, foams, and water, at two sites in the Creek, was studied before, during, and after the aeration process. Additionally, aerosols and dispersed foams created by the aeration process were sampled and cultured to determine what unique taxa of bacteria could be grown and identified. Taxa including Actinobacteria and Firmicutes were prevalent in cultures taken from aerosols, whereas Gammaproteobacteria were prevalent in cultures taken from foam. Campylobacteria was found to have a significant presence in both samples taken after the aerators were turned off. These taxa include potentially pathogenic bacteria and are therefore of particular concern.
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Affiliation(s)
- Joby Jacob
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA.
| | - Ingrid Veras
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Olga Calderόn
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Holly A Porter-Morgan
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Joshua Tan
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Harry E Aguilar
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | | | - Veronica P Martinez Castro
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Vania Fulton
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
| | - Wesam K Yousri
- Natural Sciences Department, LaGuardia Community College, City University of New York, Long Island City, NY, USA
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5
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Hoque NJ, Weinert EE. Control of bacterial second messenger signaling and motility by heme-based direct oxygen-sensing proteins. Curr Opin Microbiol 2023; 76:102396. [PMID: 37864983 DOI: 10.1016/j.mib.2023.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
Bacteria sense and respond to their environment, allowing them to maximize their survival and growth under changing conditions, such as oxygen levels. Direct oxygen-sensing proteins allow bacteria to rapidly sense concentration changes and adapt by regulating signaling pathways and/or cellular machinery. Recent work has identified roles for direct oxygen-sensing proteins in controlling second messenger levels and motility machinery, as well as effects on biofilm formation, virulence, and motility. In this review, we discuss recent progress in understanding O2-dependent regulation of cyclic di-GMP signaling and motility and highlight the emerging importance in controlling bacterial physiology and behavior.
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Affiliation(s)
- Nushrat J Hoque
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
| | - Emily E Weinert
- Department of Chemistry, Penn State University, University Park, PA 16802, USA; Department of Biochemistry & Molecular Biology, Penn State University, University Park, PA 16802, USA.
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Chen S, Ding Y. A bibliography study of Shewanella oneidensis biofilm. FEMS Microbiol Ecol 2023; 99:fiad124. [PMID: 37796898 PMCID: PMC10630087 DOI: 10.1093/femsec/fiad124] [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: 07/17/2023] [Revised: 08/28/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
This study employs a bibliography study method to evaluate 472 papers focused on Shewanella oneidensis biofilms. Biofilms, which are formed when microorganisms adhere to surfaces or interfaces, play a crucial role in various natural, engineered, and medical settings. Within biofilms, microorganisms are enclosed in extracellular polymeric substances (EPS), creating a stable working environment. This characteristic enhances the practicality of biofilm-based systems in natural bioreactors, as they are less susceptible to temperature and pH fluctuations compared to enzyme-based bioprocesses. Shewanella oneidensis, a nonpathogenic bacterium with the ability to transfer electrons, serves as an example of a species isolated from its environment that exhibits extensive biofilm applications. These applications, such as heavy metal removal, offer potential benefits for environmental engineering and human health. This paper presents a comprehensive examination and review of the biology and engineering aspects of Shewanella biofilms, providing valuable insights into their functionality.
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Affiliation(s)
- Shan Chen
- Department of Applied Social Sciences, The Hong Kong Polytechnic University, 11 Yuk Choi Rd, Hung Hom, Hong Kong, China
| | - Yuanzhao Ding
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY, United Kingdom
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7
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Wray AC, Gorman-Lewis D. Bioenergetics of aerobic and anaerobic growth of Shewanella putrefaciens CN32. Front Microbiol 2023; 14:1234598. [PMID: 37601367 PMCID: PMC10433392 DOI: 10.3389/fmicb.2023.1234598] [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: 06/04/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Shewanella putrefaciens is a model dissimilatory iron-reducing bacterium that can use Fe(III) and O2 as terminal electron acceptors. Consequently, it has the ability to influence both aerobic and anaerobic groundwater systems, making it an ideal microorganism for improving our understanding of facultative anaerobes with iron-based metabolism. In this work, we examine the bioenergetics of O2 and Fe(III) reduction coupled to lactate oxidation in Shewanella putrefaciens CN32. Bioenergetics were measured directly via isothermal calorimetry and by changes to the chemically defined growth medium. We performed these measurements from 25 to 36°C. Modeling metabolism with macrochemical equations allowed us to define a theoretical growth stoichiometry for the catabolic reaction of 1.00 O2:lactate and 1.33 Fe(III):lactate that was consistent with the observed ratios of O2:lactate (1.20 ± 0.23) and Fe(III):lactate (1.46 ± 0.15) consumption. Aerobic growth showed minimal variation with temperature and minimal variation in thermodynamic potentials of incubation. Fe(III)-based growth showed a strong temperature dependence. The Gibbs energy and enthalpy of incubation was minimized at ≥30°C. Energy partitioning modeling of Fe(III)-based calorimetric incubation data predicted that energy consumption for non-growth associate maintenance increases substantially above 30°C. This prediction agrees with the data at 33 and 35°C. These results suggest that the effects of temperature on Shewanella putrefaciens CN32 are metabolism dependent. Gibbs energy of incubation above 30°C was 3-5 times more exergonic with Fe(III)-based growth than with aerobic growth. We compared data gathered in this study with predictions of microbial growth based on standard-state conditions and based on the thermodynamic efficiency of microbial growth. Quantifying the growth requirements of Shewanella putrefaciens CN32 has advanced our understanding of the thermodynamic constraints of this dissimilatory iron-reducing bacterium.
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Affiliation(s)
- Addien C. Wray
- Earth and Space Sciences, University of Washington, Seattle, WA, United States
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8
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Xiong R, Yan J, Mei J, Ye J, Xie J. The enhanced expression of genes encoding diguanylate cyclases under cold stress contributes to the adhesion and biofilm formation of Shewanella putrefaciens WS13. Front Nutr 2022; 9:1076932. [DOI: 10.3389/fnut.2022.1076932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022] Open
Abstract
Shewanella putrefaciens is a special spoilage bacterium of seafood during cold storage, which is easy to form biofilm and bring serious hazard to the seafood quality. Life cycle of biofilm starts after bacterial adhesion, which is essential for the formation and development of biofilm. As a ubiquitous second messenger in bacteria, c-di-GMP regulates the conversion between bacterial planktonic state and biofilm state. In this study, the adhesion and biofilm formation of S. putrefaciens WS13 under 4°C were compared to those under 30°C. Atom force microscope and scanning electron microscope were used to study the bacterial adhesion. Biofilm was analyzed by Fourier transform infrared spectroscopy, Bradford assay and phenol-sulfuric acid method. High-performance liquid chromatographic-tandem mass spectrometric and quantitative real-time PCR were applied to study c-di-GMP level and genes encoding diguanylate cyclases in cells, respectively. Results showed that the swarming mobility of S. putrefaciens WS13 was weaker under 4°C, however, the adhesive force under 4°C was 4–5 times higher than that under 30°C. Biofilm biomass, extracellular polysaccharides and extracellular proteins were 2.5 times, 3 times, and 1.6 times more than those under 30°C, respectively, but biofilm composition formed under both temperatures were similar. c-di-GMP level in S. putrefaciens WS13 under 30°C was no more than half of that in the corresponding growth stage under 4°C. Quantitative real-time PCR analysis also showed that the expression of genes encoding diguanylate cyclases were significantly enhanced under 4°C than that under 30°C. S. putrefaciens WS13 adapted to the cold stress by enhancing the expression of genes encoding diguanylate cyclases to promote bacterial adhesion and biofilm formation. This study provides a theoretical foundation for the research on the cold adaptation mechanism of specific spoilage bacteria of seafood based on c-di-GMP, and also provides a new idea to control seafood quality from the perspective of microbial molecular biology.
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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: 7] [Impact Index Per Article: 3.5] [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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Yi Z, Xie J. Genomic Analysis of Two Representative Strains of Shewanella putrefaciens Isolated from Bigeye Tuna: Biofilm and Spoilage-Associated Behavior. Foods 2022; 11:foods11091261. [PMID: 35563985 PMCID: PMC9100107 DOI: 10.3390/foods11091261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Shewanella putrefaciens can cause the spoilage of seafood and shorten its shelf life. In this study, both strains of S. putrefaciens (YZ08 and YZ-J) isolated from spoiled bigeye tuna were subjected to in-depth phenotypic and genotypic characterization to better understand their roles in seafood spoilage. The complete genome sequences of strains YZ08 and YZ-J were reported. Unique genes of the two S. putrefaciens strains were identified by pan-genomic analysis. In vitro experiments revealed that YZ08 and YZ-J could adapt to various environmental stresses, including cold-shock temperature, pH, NaCl, and nutrient stresses. YZ08 was better at adapting to NaCl stress, and its genome possessed more NaCl stress-related genes compared with the YZ-J strain. YZ-J was a higher biofilm and exopolysaccharide producer than YZ08 at 4 and 30 °C, while YZ08 showed greater motility and enhanced capacity for biogenic amine metabolism, trimethylamine metabolism, and sulfur metabolism compared with YZ-J at both temperatures. That YZ08 produced low biofilm and exopolysaccharide contents and displayed high motility may be associated with the presence of more a greater number of genes encoding chemotaxis-related proteins (cheX) and low expression of the bpfA operon. This study provided novel molecular targets for the development of new antiseptic antisepsis strategies.
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Affiliation(s)
- Zhengkai Yi
- College of Food Science & Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai 201306, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering, Shanghai 201306, China
| | - Jing Xie
- College of Food Science & Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai 201306, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai 201306, China
- Correspondence: ; Tel.: +86-02161900391
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Mendez-Romero O, Ricardez-García C, Castañeda-Tamez P, Chiquete-Félix N, Uribe-Carvajal S. Thriving in Oxygen While Preventing ROS Overproduction: No Two Systems Are Created Equal. Front Physiol 2022; 13:874321. [PMID: 35444563 PMCID: PMC9013945 DOI: 10.3389/fphys.2022.874321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
From 2.5 to 2.0 billion years ago, atmospheric oxygen concentration [O2] rose thousands of times, leading to the first mass extinction. Reactive Oxygen Species (ROS) produced by the non-catalyzed partial reduction of O2 were highly toxic eliminating many species. Survivors developed different strategies to cope with ROS toxicity. At the same time, using O2 as the final acceptor in respiratory chains increased ATP production manifold. Thus, both O2 and ROS were strong drivers of evolution, as species optimized aerobic metabolism while developing ROS-neutralizing mechanisms. The first line of defense is preventing ROS overproduction and two mechanisms were developed in parallel: 1) Physiological uncoupling systems (PUS), which increase the rate of electron fluxes in respiratory systems. 2) Avoidance of excess [O2]. However, it seems that as avoidance efficiency improved, PUSs became less efficient. PUS includes branched respiratory chains and proton sinks, which may be proton specific, the mitochondrial uncoupling proteins (UCPs) or unspecific, the mitochondrial permeability transition pore (PTP). High [O2] avoidance also involved different strategies: 1) Cell association, as in biofilms or in multi-cellularity allowed gas-permeable organisms (oxyconformers) from bacterial to arthropods to exclude O2. 2) Motility, to migrate from hypoxic niches. 3) Oxyregulator organisms: as early as in fish, and O2-impermeable epithelium excluded all gases and only exact amounts entered through specialized respiratory systems. Here we follow the parallel evolution of PUS and O2-avoidance, PUS became less critical and lost efficiency. In regard, to proton sinks, there is fewer evidence on their evolution, although UCPs have indeed drifted in function while in some species it is not clear whether PTPs exist.
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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. mSystems 2022; 7:e0151821. [PMID: 35311563 PMCID: PMC9040814 DOI: 10.1128/msystems.01518-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shewanella spp. play important ecological and biogeochemical roles, due in part to their versatile metabolism and swift integration of stimuli. While Shewanella spp. are primarily considered environmental microbes, Shewanella algae is increasingly recognized as an occasional human pathogen. S. algae shares the broad metabolic and respiratory repertoire of Shewanella spp. and thrives in similar ecological niches. In S. algae, nitrate and dimethyl sulfoxide (DMSO) respiration promote biofilm formation strain specifically, with potential implication of taxis and cyclic diguanosine monophosphate (c-di-GMP) signaling. Signal transduction systems in S. algae have not been investigated. To fill these knowledge gaps, we provide here an inventory of the c-di-GMP turnover proteome and chemosensory networks of the type strain S. algae CECT 5071 and compare them with those of 41 whole-genome-sequenced clinical and environmental S. algae isolates. Besides comparative analysis of genetic content and identification of laterally transferred genes, the occurrence and topology of c-di-GMP turnover proteins and chemoreceptors were analyzed. We found S. algae strains to encode 61 to 67 c-di-GMP turnover proteins and 28 to 31 chemoreceptors, placing S. algae near the top in terms of these signaling capacities per Mbp of genome. Most c-di-GMP turnover proteins were predicted to be catalytically active; we describe in them six novel N-terminal sensory domains that appear to control their catalytic activity. Overall, our work defines the c-di-GMP and chemosensory signal transduction pathways in S. algae, contributing to a better understanding of its ecophysiology and establishing S. algae as an auspicious model for the analysis of metabolic and signaling pathways within the genus Shewanella. IMPORTANCEShewanella spp. are widespread aquatic bacteria that include the well-studied freshwater model strain Shewanella oneidensis MR-1. In contrast, the physiology of the marine and occasionally pathogenic species Shewanella algae is poorly understood. Chemosensory and c-di-GMP signal transduction systems integrate environmental stimuli to modulate gene expression, including the switch from a planktonic to sessile lifestyle and pathogenicity. Here, we systematically dissect the c-di-GMP proteome and chemosensory pathways of the type strain S. algae CECT 5071 and 41 additional S. algae isolates. We provide insights into the activity and function of these proteins, including a description of six novel sensory domains. Our work will enable future analyses of the complex, intertwined c-di-GMP metabolism and chemotaxis networks of S. algae and their ecophysiological role.
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An H, Tian T, Wang Z, Jin R, Zhou J. Role of extracellular polymeric substances in the immobilization of hexavalent chromium by Shewanella putrefaciens CN32 unsaturated biofilms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151184. [PMID: 34699809 DOI: 10.1016/j.scitotenv.2021.151184] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/05/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Microbial remediation provides a promising avenue for the management and restoration of heavy metal-contaminated soils. Microorganisms in soils usually exist within unsaturated biofilms, however, their response to heavy metals is still limited compared to saturated biofilms. This work investigated the Cr(VI) immobilization by Shewanella putrefaciens CN32 unsaturated biofilms, and explored the underlying mechanisms of Cr(VI) complexation. Results reveal a dose-dependent toxicity of Cr(VI) to the growth of the unsaturated biofilms. During the early growth stage, the Cr(VI) addition stimulated more extracellular polymeric substances (EPS) production. In the meantime, the EPS were demonstrated to be the primary components for Cr(VI) immobilization, which accounted for more than 60% of the total adsorbed Cr(VI). The Fourier transform infrared spectra and X-ray photoelectron spectra corroborated that the binding sites for immobilizing Cr(VI) were hydroxyl, carboxyl, phosphoryl and amino functional groups of the proteins and polysaccharides in EPS. However, for the starved unsaturated biofilms, EPS were depleted and the EPS-bound Cr(VI) were released, which caused approximately 60% of the adsorbed Cr(VI) onto cell components and further aggravated the Cr(VI) stress to cells. This work extends our understanding about the Cr(VI) immobilization by unsaturated biofilms, and provides useful information for remediation of heavy metal-contaminated soils.
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Affiliation(s)
- Hui An
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environment Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Tian Tian
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environment Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ziting Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environment Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ruofei Jin
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environment Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environment Science and Technology, Dalian University of Technology, Dalian 116024, China
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Xie R, Zhang T, Weng H, Chai GL. Progress, Advantages, and Challenges of Topological Material Catalysts. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202100106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Ruikuan Xie
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P. R. China
- University of Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Tan Zhang
- University of Chinese Academy of Sciences Beijing 100190 P. R. China
- Beijing National Research Center for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Hongming Weng
- University of Chinese Academy of Sciences Beijing 100190 P. R. China
- Beijing National Research Center for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Guo-Liang Chai
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P. R. China
- University of Chinese Academy of Sciences Beijing 100190 P. R. China
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15
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Zhao M, Xia T, Xing J, Yin L, Li X, Pan J, Liu J, Sun L, Wang M, Li T, Mao J, Han Q, Xue W, Cai H, Wang K, Xu X, Li T, He K, Wang N, Li A, Zhou T, Zhang X, Li W, Li T. The stress granule protein G3BP1 promotes pre-condensation of cGAS to allow rapid responses to DNA. EMBO Rep 2022; 23:e53166. [PMID: 34779554 PMCID: PMC8728604 DOI: 10.15252/embr.202153166] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 01/07/2023] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) functions as a key sensor for microbial invasion and cellular damage by detecting emerging cytosolic DNA. Here, we report that GTPase-activating protein-(SH3 domain)-binding protein 1 (G3BP1) primes cGAS for its prompt activation by engaging cGAS in a primary liquid-phase condensation state. Using high-resolution microscopy, we show that in resting cells, cGAS exhibits particle-like morphological characteristics, which are markedly weakened when G3BP1 is deleted. Upon DNA challenge, the pre-condensed cGAS undergoes liquid-liquid phase separation (LLPS) more efficiently. Importantly, G3BP1 deficiency or its inhibition dramatically diminishes DNA-induced LLPS and the subsequent activation of cGAS. Interestingly, RNA, previously reported to form condensates with cGAS, does not activate cGAS. Accordingly, we find that DNA - but not RNA - treatment leads to the dissociation of G3BP1 from cGAS. Taken together, our study shows that the primary condensation state of cGAS is critical for its rapid response to DNA.
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Affiliation(s)
- Ming Zhao
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Tian Xia
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Jia‐Qing Xing
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Le‐Hua Yin
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Xiao‐Wei Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Jie Pan
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Jia‐Yu Liu
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Li‐Ming Sun
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Miao Wang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Tingting Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Jie Mao
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Qiu‐Ying Han
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Wen Xue
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Hong Cai
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Kai Wang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Xin Xu
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Teng Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Kun He
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Na Wang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Ai‐Ling Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Tao Zhou
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Xue‐Min Zhang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
- School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Wei‐Hua Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Tao Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
- School of Basic Medical SciencesFudan UniversityShanghaiChina
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16
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YgfY Contributes to Stress Tolerance in Shewanella oneidensis Neither as an Antitoxin Nor as a Flavinylation Factor of Succinate Dehydrogenase. Microorganisms 2021; 9:microorganisms9112316. [PMID: 34835442 PMCID: PMC8621075 DOI: 10.3390/microorganisms9112316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
YgfY(SdhE/CptB) is highly conserved while has controversial functions in bacteria. It works as an antitoxin and composes a type IV toxin-antitoxin system with YgfX(CptA) typically in Escherichia coli, while functions as an flavinylation factor of succinate dehydrogenase and fumarate reductase typically in Serratia sp. In this study, we report the contribution of YgfY in Shewanella oneidensis MR-1 to tolerance of low temperature and nitrite. YgfY deficiency causes several growth defects of S. oneidensis MR-1 at low temperature, while YgfX do not cause a growth defect or morphological change of S. oneidensis MR1-1 and E. coli. YgfY do not interact with FtsZ and MreB nor with YgfX examined by bacterial two-hybrid assay. YgfY effect on growth under low temperature is not attributed to succinate dehydrogenase (SDH) because a mutant without SDH grows comparably with the wild-type strain in the presence of succinate. The ygfY mutant shows impaired tolerance to nitrite. Transcription of nitrite reductase and most ribosome proteins is significantly decreased in the ygfY mutant, which is consistent with the phenotypes detected above. Effects of YgfY on growth and nitrite tolerance are closely related to the RGXXE motif in YgfY. In summary, this study demonstrates pleiotropic impacts of YgfY in S. oneidensis MR-1, and sheds a light on the physiological versatility of YgfY in bacteria.
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17
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Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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18
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Patterson DC, Ruiz MP, Yoon H, Walker JA, Armache JP, Yennawar NH, Weinert EE. Differential ligand-selective control of opposing enzymatic activities within a bifunctional c-di-GMP enzyme. Proc Natl Acad Sci U S A 2021; 118:e2100657118. [PMID: 34475207 PMCID: PMC8433548 DOI: 10.1073/pnas.2100657118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/02/2021] [Indexed: 01/23/2023] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a second messenger that modulates bacterial cellular processes, including biofilm formation. While proteins containing both c-di-GMP synthesizing (GGDEF) and c-di-GMP hydrolyzing (EAL) domains are widely predicted in bacterial genomes, it is poorly understood how domains with opposing enzymatic activity are regulated within a single polypeptide. Herein, we report the characterization of a globin-coupled sensor protein (GCS) from Paenibacillus dendritiformis (DcpG) with bifunctional c-di-GMP enzymatic activity. DcpG contains a regulatory sensor globin domain linked to diguanylate cyclase (GGDEF) and phosphodiesterase (EAL) domains that are differentially regulated by gas binding to the heme; GGDEF domain activity is activated by the Fe(II)-NO state of the globin domain, while EAL domain activity is activated by the Fe(II)-O2 state. The in vitro activity of DcpG is mimicked in vivo by the biofilm formation of P. dendritiformis in response to gaseous environment, with nitric oxide conditions leading to the greatest amount of biofilm formation. The ability of DcpG to differentially control GGDEF and EAL domain activity in response to ligand binding is likely due to the unusual properties of the globin domain, including rapid ligand dissociation rates and high midpoint potentials. Using structural information from small-angle X-ray scattering and negative stain electron microscopy studies, we developed a structural model of DcpG, providing information about the regulatory mechanism. These studies provide information about full-length GCS protein architecture and insight into the mechanism by which a single regulatory domain can selectively control output domains with opposing enzymatic activities.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Myrrh Perez Ruiz
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Hyerin Yoon
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | | | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802;
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
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19
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Haque MM, Mosharaf MK, Haque MA, Tanvir MZH, Alam MK. Biofilm Formation, Production of Matrix Compounds and Biosorption of Copper, Nickel and Lead by Different Bacterial Strains. Front Microbiol 2021; 12:615113. [PMID: 34177820 PMCID: PMC8222582 DOI: 10.3389/fmicb.2021.615113] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/06/2021] [Indexed: 12/01/2022] Open
Abstract
Bacterial biofilms play a key role in metal biosorption from wastewater. Recently, Enterobacter asburiae ENSD102, Enterobacter ludwigii ENSH201, Vitreoscilla sp. ENSG301, Acinetobacter lwoffii ENSG302, and Bacillus thuringiensis ENSW401 were shown to form air–liquid (AL) and solid–air–liquid (SAL) biofilms in a static condition at 28 and 37°C, respectively. However, how environmental and nutritional conditions affect biofilm formation; production of curli and cellulose; and biosorption of copper (Cu), nickel (Ni), and lead (Pb) by these bacteria have not been studied yet. In this study, E. asburiae ENSD102, E. ludwigii ENSH201, and B. thuringiensis ENSW401 developed the SAL biofilms at pH 8, while E. asburiae ENSD102 and Vitreoscilla sp. ENSG301 constructed the SAL biofilms at pH 4. However, all these strains produced AL biofilms at pH 7. In high osmolarity and ½-strength media, all these bacteria built fragile AL biofilms, while none of these strains generated the biofilms in anaerobic conditions. Congo red binding results showed that both environmental cues and bacterial strains played a vital role in curli and cellulose production. Calcofluor binding and spectrophotometric results revealed that all these bacterial strains produced significantly lesser amounts of cellulose at 37°C, pH 8, and in high osmotic conditions as compared to the regular media, at 28°C, and pH 7. Metal biosorption was drastically reduced in these bacteria at 37°C than at 28°C. Only Vitreoscilla sp. ENSG301 and B. thuringiensis ENSW401 completely removed (100%) Cu and Ni at an initial concentration of 12.5 mg l–1, while all these bacteria totally removed (100%) Pb at concentrations of 12.5 and 25 mg l–1 at pH 7 and 28°C. At an initial concentration of 100 mg l–1, the removal of Cu (92.5 to 97.8%) and Pb (89.3 to 98.3%) was the highest at pH 6, while it was higher (84.7 to 93.9%) for Ni at pH 7. Fourier transform infrared spectroscopy results showed metal-unloaded biomass biofilms contained amino, hydroxyl, carboxyl, carbonyl, and phosphate groups. The peak positions of these groups were shifted responding to Cu, Ni, and Pb, suggesting biosorption of metals. Thus, these bacterial strains could be utilized to remove Cu, Ni, and Pb from aquatic environment.
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Affiliation(s)
- Md Manjurul Haque
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md Khaled Mosharaf
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md Amdadul Haque
- Department of Agro-Processing, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md Zahid Hasan Tanvir
- Department of Environmental Science, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md Khairul Alam
- Soil Science Division, Bangladesh Agricultural Research Institute, Gazipur, Bangladesh
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20
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Martín-Rodríguez AJ, Reyes-Darias JA, Martín-Mora D, González JM, Krell T, Römling U. Reduction of alternative electron acceptors drives biofilm formation in Shewanella algae. NPJ Biofilms Microbiomes 2021; 7:9. [PMID: 33504806 PMCID: PMC7840931 DOI: 10.1038/s41522-020-00177-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/11/2020] [Indexed: 01/30/2023] Open
Abstract
Shewanella spp. possess a broad respiratory versatility, which contributes to the occupation of hypoxic and anoxic environmental or host-associated niches. Here, we observe a strain-specific induction of biofilm formation in response to supplementation with the anaerobic electron acceptors dimethyl sulfoxide (DMSO) and nitrate in a panel of Shewanella algae isolates. The respiration-driven biofilm response is not observed in DMSO and nitrate reductase deletion mutants of the type strain S. algae CECT 5071, and can be restored upon complementation with the corresponding reductase operon(s) but not by an operon containing a catalytically inactive nitrate reductase. The distinct transcriptional changes, proportional to the effect of these compounds on biofilm formation, include cyclic di-GMP (c-di-GMP) turnover genes. In support, ectopic expression of the c-di-GMP phosphodiesterase YhjH of Salmonella Typhimurium but not its catalytically inactive variant decreased biofilm formation. The respiration-dependent biofilm response of S. algae may permit differential colonization of environmental or host niches.
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Affiliation(s)
| | - José A. Reyes-Darias
- grid.418877.50000 0000 9313 223XDepartment of Environmental Protection, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - David Martín-Mora
- grid.418877.50000 0000 9313 223XDepartment of Environmental Protection, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - José M. González
- grid.10041.340000000121060879Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Tino Krell
- grid.418877.50000 0000 9313 223XDepartment of Environmental Protection, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Ute Römling
- grid.465198.7Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
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21
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Zhang C, Wang C, Zhao S, Xiu Z. Role of c-di-GMP in improving stress resistance of alginate-chitosan microencapsulated Bacillus subtilis cells in simulated digestive fluids. Biotechnol Lett 2021; 43:677-690. [PMID: 33385252 DOI: 10.1007/s10529-020-03055-0] [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: 11/05/2020] [Accepted: 12/10/2020] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Probiotics (Bacillus subtilis 04178) were entrapped in alginate-chitosan microcapsules by high-voltage electrostatic process. The encapsulation pattern was established as entrapped low density cells with culture (ELDCwc). The performance of ELDCwc cells was investigated against stress environments of simulated digestive fluids. RESULTS After incubation in simulated gastric (pH 2.5) and intestinal fluids (4% bile salt) for 2 h, the survival rate of ELDCwc cells (18.19% and 27.54%) was significantly higher than that of the free cells (0.0000009% and 0.0005%). The reason why B. subtilis embedded in microcapsules can resist the stress environments was that the mass production of extracellular proteins and polysaccharides prompted B. subtilis to form cell aggregates. The production of extracellular proteins and polysaccharides were regulated by the concentration of c-di-GMP and the expression of ydaJKLMN operon, abbA, sinI, slrA, slrB, abrR and sinR. CONCLUSIONS c-di-GMP is important for the production of extracellular polymer substance to enhance probiotic viability in stress environments.
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Affiliation(s)
- Chaolei Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian, 116024, China
| | - Chao Wang
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing, 100084, China
| | - Shan Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Science, 116023, Dalian, China
| | - Zhilong Xiu
- School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian, 116024, China.
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22
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Regulation of c-di-GMP in Biofilm Formation of Klebsiella pneumoniae in Response to Antibiotics and Probiotic Supernatant in a Chemostat System. Curr Microbiol 2020; 78:133-143. [PMID: 33104852 DOI: 10.1007/s00284-020-02258-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/15/2020] [Indexed: 12/29/2022]
Abstract
The resistance of bacteria to antibiotics is a major public health issue. Klebsiella pneumoniae is a type exemplification of multi-resistant enterobacteria. Its high biofilm forming capacity is a major factor in the recurrent infection of the intestinal tract. In this study, the intrinsic mechanism of secondary growth of K. pneumoniae in response to antibiotics and the inhibition effect of probiotic supernatant on biofilm formation after antibiotic treatment were investigated in a polyester nonwoven chemostat bioreactor. The experimental results showed that the c-di-GMP content in the cells increased after treatment with levofloxacin, leading to the formation of a thick biofilm due to an increase in the production of extracellular polymer substance (EPS) and type 3 fimbriae. Biofilm prevents the mass transfer of levofloxacin and protects K. pneumoniae cells from being killed by levofloxacin. Under suitable conditions, K. pneumoniae cells on the biofilm enter into the suspension for secondary growth. Moreover, the inhibition of probiotic supernatant on the biofilm formation was mainly due to the reduced expression of yfiN and mrkJ genes, and the decreased concentration of c-di-GMP in cells, as well as the less secretion of EPS. At the same time, the decrease in the concentration of c-di-GMP also reduced the expression of the mrkABCDF gene and prevented the synthesis of the type 3 fimbriae. The results would help to understand the mechanism of antibiotic resistance of pathogenic bacteria and to provide evidence to address this problem through the use of probiotics.
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23
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Mukherjee M, Zaiden N, Teng A, Hu Y, Cao B. Shewanella biofilm development and engineering for environmental and bioenergy applications. Curr Opin Chem Biol 2020; 59:84-92. [PMID: 32750675 DOI: 10.1016/j.cbpa.2020.05.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 12/31/2022]
Abstract
The genus Shewanella comprises about 70 species of Gram-negative, facultative anaerobic bacteria inhabiting various environments, which have shown great potential in various biotechnological applications ranging from environmental bioremediation, metal(loid) recovery and material synthesis to bioenergy generation. Most environmental and energy applications of Shewanella involve the biofilm mode of growth on surfaces of solid minerals or electrodes. In this article, we first provide an overview of Shewanella biofilm biology with the focus on biofilm dynamics, biofilm matrix, and key signalling systems involved in Shewanella biofilm development. Then we review strategies recently exploited to engineer Shewanella biofilms to improve biofilm-mediated bioprocesses.
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Affiliation(s)
- Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore
| | - Norazean Zaiden
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 637335, Singapore
| | - Aloysius Teng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 637335, Singapore
| | - Yidan Hu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, 637335, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore.
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24
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Hydrogen production driven by formate oxidation in Shewanella oneidensis MR-1. Appl Microbiol Biotechnol 2020; 104:5579-5591. [DOI: 10.1007/s00253-020-10608-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/29/2020] [Accepted: 04/05/2020] [Indexed: 10/24/2022]
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25
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Cheng L, Min D, Liu DF, Zhu TT, Wang KL, Yu HQ. Deteriorated biofilm-forming capacity and electroactivity of Shewanella oneidnsis MR-1 induced by insertion sequence (IS) elements. Biosens Bioelectron 2020; 156:112136. [PMID: 32174561 DOI: 10.1016/j.bios.2020.112136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/17/2022]
Abstract
Shewanella oneidensis MR-1, a model species of exoelectrogenic bacteria (EEB), has been widely applied in bioelectrochemical systems. Biofilms of EEB grown on electrodes are essential in governing the current output and power density of bioelectrochemical systems. The MR-1 genome is exceptionally dynamic due to the existence of a large number of insertion sequence (IS) elements. However, to date, the impacts of IS elements on the biofilm-forming capacity of EEB and performance of bioelectrochemical systems remain unrevealed. Herein, we isolated a non-motile mutant (NMM) with biofilm-deficient phenotype from MR-1. We found that the insertion of an ISSod2 element into the flrA (encoding the master regulator for flagella synthesis and assembly) of MR-1 resulted in the non-motile and biofilm-deficient phenotypes in NMM cells. Notably, such a variant was readily confused with the wild-type strain because there were no obvious differences in growth rates and colonial morphologies between the two strains. However, the reduced biofilm formation on the electrodes and the deteriorated performances of bioelectrochemical systems and Cr(VI) immobilization for the strain NMM were observed. Given the wide distribution of IS elements in EEB, appropriate cultivation and preservation conditions should be adopted to reduce the likelihood that IS elements-mediated mutation occurs in EEB. These findings reveal the negative impacts of IS elements on the biofilm-forming capacity of EEB and performance of bioelectrochemical systems and suggest that great attention should be given to the actual physiological states of EEB before their applications.
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Affiliation(s)
- Lei Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China.
| | - Ting-Ting Zhu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Kai-Li Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China.
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26
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Lengalova A, Fojtikova-Proskova V, Vavra J, Martínek V, Stranava M, Shimizu T, Martinkova M. Kinetic analysis of a globin-coupled diguanylate cyclase, YddV: Effects of heme iron redox state, axial ligands, and heme distal mutations on catalysis. J Inorg Biochem 2019; 201:110833. [PMID: 31520879 DOI: 10.1016/j.jinorgbio.2019.110833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022]
Abstract
Heme-based oxygen sensors allow bacteria to regulate their activity based on local oxygen levels. YddV, a globin-coupled oxygen sensor with diguanylate cyclase activity from Escherichia coli, regulates cyclic-di-GMP synthesis based on oxygen availability. Stable and active samples of the full-length YddV protein were prepared by attaching it to maltose binding protein (MBP). To better understand the full-length protein's structure, the interactions between its domains were examined by performing a kinetic analysis. The diguanylate cyclase reaction catalyzed by YddV-MBP exhibited Michaelis-Menten kinetics. Its pH optimum was 8.5-9.0, and catalysis required either Mg2+ or Mn2+; other divalent metal ions gave no activity. The most active form of YddV-MBP had a 5-coordinate Fe(III) heme complex; its kinetic parameters were KmGTP 84 ± 21 μM and kcat 1.2 min-1. YddV-MBP with heme Fe(II), heme Fe(II)-O2, and heme Fe(II)-CO complexes had kcat values of 0.3 min-1, 0.95 min-1, and 0.3 min-1, respectively, suggesting that catalysis is regulated by the heme iron's redox state and axial ligand binding. The kcat values for heme Fe(III) complexes of L65G, L65Q, and Y43A YddV-MBP mutants bearing heme distal amino acid replacements were 0.15 min-1, 0.26 min-1 and 0.54 min-1, respectively, implying that heme distal residues play key regulatory roles by mediating signal transduction between the sensing and functional domains. Ultracentrifugation and size exclusion chromatography experiments showed that YddV-MBP is primarily dimeric in solution, with a sedimentation coefficient around 8. The inactive heme-free H93A mutant is primarily octameric, suggesting that catalytically active dimer formation requires heme binding.
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Affiliation(s)
- Alzbeta Lengalova
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Veronika Fojtikova-Proskova
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Jakub Vavra
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Václav Martínek
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic
| | - Marketa Martinkova
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, Czech Republic.
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López-Baena FJ, Vinardell JM, Medina C. Regulation of Protein Secretion Systems Mediated by Cyclic Diguanylate in Plant-Interacting Bacteria. Front Microbiol 2019; 10:1289. [PMID: 31263457 PMCID: PMC6584795 DOI: 10.3389/fmicb.2019.01289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
The ubiquitous second messenger cyclic diguanylate (c-di-GMP) is involved in the regulation of different processes in bacteria. In phytopathogens, intracellular fluctuations in the concentration of this molecule contribute to the lifestyle switching from a motile and virulent stage to a sessile and biofilm-forming phase. Among the virulence mechanisms used by bacterial pathogens, different specific type secretion systems (TSSs) and the effector proteins that they translocate are included. Some of these TSS are conceived to suppress host immune responses during bacterial colonization. The modulation of the expression of secretion systems components and/or effector proteins can be influenced by c-di-GMP levels at transcriptional, translational, or post-translational levels and can take place directly by binding to specific or global regulators, or via transducer proteins. Different genera of plant-interacting bacteria have been analyzed to shed some light in the implications of c-di-GMP in the regulation of host plant colonization through protein secretion systems. Expression of (1) adhesins secreted by Type 1 secretion systems to bind the host plant in Pectobacterium (formerly Erwinia) and some beneficial Pseudomonas strains; (2) catalytic exoproteins delivered by Type 2 secretion systems to break plant cell wall in Dickeya; (3) effectors secreted by Type 3 secretion systems to suppress plant immunity in Xanthomonas; or (4) the activity of Type 6 secretion systems to export an ATPase in Pseudomonas, are finely tuned by c-di-GMP levels. In this minireview, we summarize the knowledge available about the implications of c-di-GMP in the regulation of protein secretion in different plant-interacting bacteria. Topic: Secretion systems and effector proteins of phytopathogenic and beneficial bacteria regulated by NSM.
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Affiliation(s)
| | - Jose María Vinardell
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Carlos Medina
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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Rajeswari R, Islavath N, Raghavender M, Giribabu L. Recent Progress and Emerging Applications of Rare Earth Doped Phosphor Materials for Dye‐Sensitized and Perovskite Solar Cells: A Review. CHEM REC 2019; 20:65-88. [DOI: 10.1002/tcr.201900008] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/03/2019] [Accepted: 05/15/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Ramireddy Rajeswari
- Polymer and Functional Materials DivisionCSIR-Indian Institute of Chemical Technology (IICT) Tarnaka, Hyderabad 500007 Telangana India
| | - Nanaji Islavath
- Polymer and Functional Materials DivisionCSIR-Indian Institute of Chemical Technology (IICT) Tarnaka, Hyderabad 500007 Telangana India
| | - M. Raghavender
- Department of PhysicsYogi Vemana University Kadapa 516003 A.P., India
| | - Lingamallu Giribabu
- Polymer and Functional Materials DivisionCSIR-Indian Institute of Chemical Technology (IICT) Tarnaka, Hyderabad 500007 Telangana India
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Kuang S, Yuan Y, Wu Z, Peng R. Expression, purification and characterization of diguanylate cyclase from Rhodococcus ruber. Protein Expr Purif 2019; 163:105441. [PMID: 31195084 DOI: 10.1016/j.pep.2019.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Abstract
Diguanylate cyclases (DGCs) were responsible for the synthesis of second messenger cyclic di-guanosine monophosphate (c-di-GMP), which were involved in various physiological activities of bacterial species. Here, a full-length DGC from Rhodococcus ruber SD3 fused with glutathione-S-transferase (GST) was expressed in E. coli and purified by glutathione agarose resin. The apparent molecular mass of one subunit of the purified diguanylate cyclase with GST tag (GST-DGC) was estimated to be 71.9 kDa by SDS-PAGE, which was approximately in accordance with the theoretical value of 73.0 kDa. The sequence of GST-DGC was confirmed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The blue native PAGE indicated that GST-DGC formed octamer. The optimum pH and temperature for GST-DGC activity were 8.0 and 47 °C, respectively. The fusion protein exhibited high thermostability, and 94% of activity was retained when the protein was incubated at 87 °C for 1 h. Moreover, the fusion protein showed pH stability. The Km, Vmax and Kcat values for GST-DGC enzyme were 9.8 μM, 0.7 μM/min and 1.3 S-1. Some ions such as Zn2+, Mn2+, Fe2+, Ni2+ and Co2+ had inhibitory effects on the activity of the protein, while other ions such as Mg2+, K+ and Na+ slightly activated the protein. The fusion protein also showed rather high stability in the presence of toluene, cyclohexane and n-hexane.
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Affiliation(s)
- Sufang Kuang
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Yuan Yuan
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Zhonghao Wu
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China
| | - Ren Peng
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, People's Republic of China.
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Dai J, Huang YJ, He X, Zhao M, Wang X, Liu ZS, Xue W, Cai H, Zhan XY, Huang SY, He K, Wang H, Wang N, Sang Z, Li T, Han QY, Mao J, Diao X, Song N, Chen Y, Li WH, Man JH, Li AL, Zhou T, Liu ZG, Zhang XM, Li T. Acetylation Blocks cGAS Activity and Inhibits Self-DNA-Induced Autoimmunity. Cell 2019; 176:1447-1460.e14. [PMID: 30799039 DOI: 10.1016/j.cell.2019.01.016] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 11/27/2018] [Accepted: 01/04/2019] [Indexed: 12/30/2022]
Abstract
The presence of DNA in the cytoplasm is normally a sign of microbial infections and is quickly detected by cyclic GMP-AMP synthase (cGAS) to elicit anti-infection immune responses. However, chronic activation of cGAS by self-DNA leads to severe autoimmune diseases for which no effective treatment is available yet. Here we report that acetylation inhibits cGAS activation and that the enforced acetylation of cGAS by aspirin robustly suppresses self-DNA-induced autoimmunity. We find that cGAS acetylation on either Lys384, Lys394, or Lys414 contributes to keeping cGAS inactive. cGAS is deacetylated in response to DNA challenges. Importantly, we show that aspirin can directly acetylate cGAS and efficiently inhibit cGAS-mediated immune responses. Finally, we demonstrate that aspirin can effectively suppress self-DNA-induced autoimmunity in Aicardi-Goutières syndrome (AGS) patient cells and in an AGS mouse model. Thus, our study reveals that acetylation contributes to cGAS activity regulation and provides a potential therapy for treating DNA-mediated autoimmune diseases.
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Affiliation(s)
- Jiang Dai
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China; State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Yi-Jiao Huang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Xinhua He
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Ming Zhao
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Xinzheng Wang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Zhao-Shan Liu
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Wen Xue
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Hong Cai
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Xiao-Yan Zhan
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Shao-Yi Huang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China; State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Kun He
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Hongxia Wang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Na Wang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Zhihong Sang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Tingting Li
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Qiu-Ying Han
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Jie Mao
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Xinwei Diao
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China; Department of Pathology, Xinqiao Hospital, 3(rd) Military Medical University, Chongqing 400037, China
| | - Nan Song
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Yuan Chen
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Wei-Hua Li
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Jiang-Hong Man
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Ai-Ling Li
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Tao Zhou
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China
| | - Zheng-Gang Liu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Xue-Min Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China; State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China; Cancer Research Institute of Jilin University, the First Hospital of Jilin University, Changchun, Jilin Province 130021, China.
| | - Tao Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China; State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing 100850, China.
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31
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Liu C, Sun D, Zhu J, Liu W. Two-Component Signal Transduction Systems: A Major Strategy for Connecting Input Stimuli to Biofilm Formation. Front Microbiol 2019; 9:3279. [PMID: 30687268 PMCID: PMC6335343 DOI: 10.3389/fmicb.2018.03279] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/17/2018] [Indexed: 11/29/2022] Open
Abstract
Biofilms are multicellular communities of microbes that are encased within an extracellular matrix. Environmental factors induce bacteria to form biofilm. Bacteria have several regulatory mechanisms in response to environmental changes, and the two-component signal transduction system (TCS) is a major strategy in connecting changes in input signals to changes in cellular physiological output. The TCS employs multiple mechanisms such as cross-regulation, to integrate and coordinate various input stimuli to control biofilm formation. In this mini-review, we demonstrate the roles of TCS on biofilm formation, illustrating these input signals and modulation modes, which may be utilized by future investigations in elucidating the regulatory signals and underlying the mechanisms of biofilm formation.
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Affiliation(s)
- Cong Liu
- School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Di Sun
- School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Weijie Liu
- School of Life Science, Jiangsu Normal University, Xuzhou, China
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Liu W, You Y, Sun D, Wang S, Zhu J, Liu C. Decolorization and detoxification of water-insoluble Sudan dye by Shewanella putrefaciens CN32 co-cultured with Bacillus circulans BWL1061. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 166:11-17. [PMID: 30240930 DOI: 10.1016/j.ecoenv.2018.09.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/08/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Effluents loaded with various synthetic dyes are considered as a huge burden to the surrounding ecosystems. Sudan dyes are relatively difficult to decolorize due to its water-insolubility. In the present study, the strain Shewanella putrefaciens CN32 was firstly applied to decolorize Sudan dyes under the anaerobic condition, and the physicochemical parameters on the decolorization were optimized. The results demonstrated that the suitable decolorization condition was temperature 26 °C, initial pH 7.0-8.0 and NaCl concentrations 0-20 g/L. Electron competitive acceptors including nitrite, nitrate, dimethyl sulphoxide and oxygen could cause the significant inhibition to the decolorization of Sudan dyes. Biosurfactant rhamnolipid played a positive role in enhancing the decolorization of Sudan I. The co-culture of S. putrefaciens CN32 and Bacillus circulans BWL1061 is reported for the first time to accelerate the decolorization through improving the synergistic effect of enzymatic degradation and biological reductive effect. The highest decolorization of 90.23% to Sudan I was achieved within 108 h, suggesting that co-culture technique has a good potential in the treatment of dyeing wastewater. Furthermore, the microbial toxicity tests indicated that the toxicity of Sudan I to Escherichia coli BL21 and Bacillus subtilis 168 was obviously decreased after the decolorization.
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Affiliation(s)
- Weijie Liu
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Yanting You
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Di Sun
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Shiwei Wang
- School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, China
| | - Jingrong Zhu
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Cong Liu
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China.
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G3BP1 promotes DNA binding and activation of cGAS. Nat Immunol 2018; 20:18-28. [PMID: 30510222 DOI: 10.1038/s41590-018-0262-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/17/2018] [Indexed: 01/05/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is a key sensor responsible for cytosolic DNA detection. Here we report that GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) is critical for DNA sensing and efficient activation of cGAS. G3BP1 enhanced DNA binding of cGAS by promoting the formation of large cGAS complexes. G3BP1 deficiency led to inefficient DNA binding by cGAS and inhibited cGAS-dependent interferon (IFN) production. The G3BP1 inhibitor epigallocatechin gallate (EGCG) disrupted existing G3BP1-cGAS complexes and inhibited DNA-triggered cGAS activation, thereby blocking DNA-induced IFN production both in vivo and in vitro. EGCG administration blunted self DNA-induced autoinflammatory responses in an Aicardi-Goutières syndrome (AGS) mouse model and reduced IFN-stimulated gene expression in cells from a patient with AGS. Thus, our study reveals that G3BP1 physically interacts with and primes cGAS for efficient activation. Furthermore, EGCG-mediated inhibition of G3BP1 provides a potential treatment for cGAS-related autoimmune diseases.
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Rivera S, Young PG, Hoffer ED, Vansuch GE, Metzler CL, Dunham CM, Weinert EE. Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. Inorg Chem 2018; 57:14386-14395. [PMID: 30378421 DOI: 10.1021/acs.inorgchem.8b02584] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to respond to external stimuli, bacteria have evolved sensor proteins linking external signals to intracellular outputs that can then regulate downstream pathways and phenotypes. Globin coupled sensor proteins (GCSs) serve to link environmental O2 levels to cellular processes by coupling a heme-containing sensor globin domain to a catalytic output domain. However, the mechanism by which O2 binding activates these proteins is currently unknown. To provide insights into the signaling mechanism, two distinct dimeric complexes of the isolated globin domain of the GCS from Bordetella pertussis ( BpeGlobin) were solved via X-ray crystallography in which differences in ligand-bound states were observed. Both monomers of one dimer contain Fe(II)-O2 states, while the other dimer consists of the Fe(III)-H2O and Fe(II)-O2 states. These data provide the first molecular insights into the heme pocket conformation of the active Fe(II)-O2 form of these enzymes. In addition, heme distortion modes and heme-protein interactions were found to correlate with the ligation state of the globin, suggesting that these conformational changes play a role in O2-dependent signaling. Fourier transform infrared spectroscopy (FTIR) of the full-length GCS from B. pertussis ( BpeGReg) and the closely related GCS from Pectobacterium carotovorum ssp. carotovorum ( PccGCS) confirmed the importance of an ordered water within the heme pocket and two distal residues (Tyr43 and Ser68) as hydrogen-bond donors. Taken together, this work provides mechanistic insights into BpeGReg O2 sensing and the signaling mechanisms of diguanylate cyclase-containing GCS proteins.
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Affiliation(s)
- Shannon Rivera
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Paul G Young
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Eric D Hoffer
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Gregory E Vansuch
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Carmen L Metzler
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Christine M Dunham
- Department of Biochemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Emily E Weinert
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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Type 1 Does the Two-Step: Type 1 Secretion Substrates with a Functional Periplasmic Intermediate. J Bacteriol 2018; 200:JB.00168-18. [PMID: 29866808 DOI: 10.1128/jb.00168-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacteria have evolved several secretion strategies for polling and responding to environmental flux and insult. Of these, the type 1 secretion system (T1SS) is known to secrete an array of biologically diverse proteins-from small, <10-kDa bacteriocins to gigantic adhesins with a mass >1 MDa. For the last several decades, T1SSs have been characterized as a one-step translocation strategy whereby the secreted substrate is transported directly into the extracellular environment from the cytoplasm with no periplasmic intermediate. Recent phylogenetic, biochemical, and genetic evidences point to a distinct subgroup of T1SS machinery linked with a bacterial transglutaminase-like cysteine proteinase (BTLCP), which uses a two-step secretion mechanism. BTLCP-linked T1SSs transport a class of repeats-in-toxin (RTX) adhesins that are critical for biofilm formation. The prototype of this RTX adhesin group, LapA of Pseudomonas fluorescens Pf0-1, uses a novel N-terminal retention module to anchor the adhesin at the cell surface as a secretion intermediate threaded through the outer membrane-localized TolC-like protein LapE. This secretion intermediate is posttranslationally cleaved by the BTLCP family LapG protein to release LapA from its cognate T1SS pore. Thus, the secretion of LapA and related RTX adhesins into the extracellular environment appears to be a T1SS-mediated two-step process that involves a periplasmic intermediate. In this review, we contrast the T1SS machinery and substrates of the BLTCP-linked two-step secretion process with those of the classical one-step T1SS to better understand the newly recognized and expanded role of this secretion machinery.
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Liu ZS, Zhang ZY, Cai H, Zhao M, Mao J, Dai J, Xia T, Zhang XM, Li T. RINCK-mediated monoubiquitination of cGAS promotes antiviral innate immune responses. Cell Biosci 2018; 8:35. [PMID: 29760876 PMCID: PMC5944131 DOI: 10.1186/s13578-018-0233-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/04/2018] [Indexed: 12/19/2022] Open
Abstract
Background As an important danger signal, the presence of DNA in cytoplasm triggers potent immune responses. Cyclic GMP-AMP synthase (cGAS) is a recently characterized key sensor for cytoplasmic DNA. The engagement of cGAS with DNA leads to the synthesis of a second messenger, cyclic GMP-AMP (cGAMP), which binds and activates the downstream adaptor protein STING to promote type I interferon production. Although cGAS has been shown to play a pivotal role in innate immunity, the exact regulation of cGAS activation is not fully understood. Results We report that an E3 ubiquitin ligase, RING finger protein that interacts with C kinase (RINCK, also known as tripartite motif protein 41, TRIM41), is critical for cGAS activation by mediating the monoubiquitination of cGAS. Using CRISPR/Cas9, we generated RINCK-deletion cells and showed that the deficiency of RINCK resulted in dampened interferon production in response to cytosolic DNA. Consistently, the RINCK-deletion cells also exhibited insufficient interferon production upon herpes simplex virus 1, a DNA virus, infection. As a result, the viral load in RINCK-deficient cells was significantly higher than that in wild-type cells. We also found that RINCK deficiency inhibited the up-stream signaling of DNA-triggered interferon production pathway, which was reflected by the phosphorylation of the TANK-binding kinase 1 and the interferon regulatory factor 3. Interestingly, we found that RINCK binds to cGAS and promotes the monoubiquitination of cGAS, thereby positively regulating the cGAS-mediated cGAMP synthesis. Conclusions Our study reveals that monoubiquitination is an important regulation for cGAS activation and uncovers a critical role of RINCK in the cGAS-mediated innate immunity.
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Affiliation(s)
- Zhao-Shan Liu
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China
| | - Zi-Yu Zhang
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China
| | - Hong Cai
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China
| | - Ming Zhao
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China
| | - Jie Mao
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China
| | - Jiang Dai
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China.,2State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850 China
| | - Tian Xia
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China
| | - Xue-Min Zhang
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China.,2State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850 China
| | - Tao Li
- 1State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, 27 Tai-Ping Rd., Beijing, 100850 China
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Effect of anode polarization on biofilm formation and electron transfer in Shewanella oneidensis /graphite felt microbial fuel cells. Bioelectrochemistry 2018; 120:1-9. [DOI: 10.1016/j.bioelechem.2017.10.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 10/30/2017] [Accepted: 10/30/2017] [Indexed: 11/20/2022]
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38
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An N-Terminal Retention Module Anchors the Giant Adhesin LapA of Pseudomonas fluorescens at the Cell Surface: a Novel Subfamily of Type I Secretion Systems. J Bacteriol 2018; 200:JB.00734-17. [PMID: 29437852 DOI: 10.1128/jb.00734-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/31/2018] [Indexed: 11/20/2022] Open
Abstract
LapA of Pseudomonas fluorescens Pf0-1 belongs to a diverse family of cell surface-associated bacterial adhesins that are secreted via the type I secretion system (T1SS). We previously reported that the periplasmic protease LapG cleaves the N terminus of LapA at a canonical dialanine motif to release the adhesin from the cell surface under conditions unfavorable to biofilm formation, thus decreasing biofilm formation. Here, we characterize LapA as the first type I secreted substrate that does not follow the "one-step" rule of T1SS. Rather, a novel N-terminal element, called the retention module (RM), localizes LapA at the cell surface as a secretion intermediate. Our genetic, biochemical, and molecular modeling analyses support a model wherein LapA is tethered to the cell surface through its T1SS outer membrane TolC-like pore, LapE, until LapG cleaves LapA in the periplasm. We further demonstrate that this unusual retention strategy is likely conserved among LapA-like proteins, and it reveals a new subclass of T1SS ABC transporters involved in transporting this group of surface-associated LapA-like adhesins. These studies demonstrate a novel cell surface retention strategy used throughout the Proteobacteria and highlight a previously unappreciated flexibility of function for T1SS.IMPORTANCE Bacteria have evolved multiple secretion strategies to interact with their environment. For many bacteria, the secretion of cell surface-associated adhesins is key for initiating contact with a preferred substratum to facilitate biofilm formation. Our work demonstrates that P. fluorescens uses a previously unrecognized secretion strategy to retain the giant adhesin LapA at its cell surface. Further, we identify likely LapA-like adhesins in various pathogenic and commensal proteobacteria and provide phylogenetic evidence that these adhesins are secreted by a new subclass of T1SS ABC transporters.
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Burns JL, Jariwala PB, Rivera S, Fontaine BM, Briggs L, Weinert EE. Oxygen-Dependent Globin Coupled Sensor Signaling Modulates Motility and Virulence of the Plant Pathogen Pectobacterium carotovorum. ACS Chem Biol 2017; 12:2070-2077. [PMID: 28612602 DOI: 10.1021/acschembio.7b00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial pathogens utilize numerous signals to identify the presence of their host and coordinate changes in gene expression that allow for infection. Within plant pathogens, these signals typically include small molecules and/or proteins from their plant hosts and bacterial quorum sensing molecules to ensure sufficient bacterial cell density for successful infection. In addition, bacteria use environmental signals to identify conditions when the host defenses are weakened and potentially to signal entry into an appropriate host/niche for infection. A globin coupled sensor protein (GCS), termed PccGCS, within the soft rot bacterium Pectobacterium carotovorum ssp. carotovorum WPP14 has been identified as an O2 sensor and demonstrated to alter virulence factor excretion and control motility, with deletion of PccGCS resulting in decreased rotting of a potato host. Using small molecules that modulate bacterial growth and quorum sensing, PccGCS signaling also has been shown to modulate quorum sensing pathways, resulting in the PccGCS deletion strain being more sensitive to plant-derived phenolic acids, which can function as quorum sensing inhibitors, and exhibiting increased N-acylhomoserine lactone (AHL) production. These findings highlight a role for GCS proteins in controlling key O2-dependent phenotypes of pathogenic bacteria and suggest that modulating GCS signaling to limit P. carotovorum motility may provide a means to decrease rotting of plant hosts.
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Affiliation(s)
- Justin L. Burns
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Parth B. Jariwala
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Shannon Rivera
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Laura Briggs
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515
Dickey Drive, Atlanta, Georgia 30322, United States
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40
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Wan X, Saito JA, Newhouse JS, Hou S, Alam M. The importance of conserved amino acids in heme-based globin-coupled diguanylate cyclases. PLoS One 2017; 12:e0182782. [PMID: 28792538 PMCID: PMC5549716 DOI: 10.1371/journal.pone.0182782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/24/2017] [Indexed: 02/05/2023] Open
Abstract
Globin-coupled diguanylate cyclases contain globin, middle, and diguanylate cyclase domains that sense O2 to synthesize c-di-GMP and regulate bacterial motility, biofilm formation, and virulence. However, relatively few studies have extensively examined the roles of individual residues and domains of globin-coupled diguanylate cyclases, which can shed light on their signaling mechanisms and provide drug targets. Here, we report the critical residues of two globin-coupled diguanylate cyclases, EcGReg from Escherichia coli and BpeGReg from Bordetella pertussis, and show that their diguanylate cyclase activity requires an intact globin domain. In the distal heme pocket of the globin domain, residues Phe42, Tyr43, Ala68 (EcGReg)/Ser68 (BpeGReg), and Met69 are required to maintain full diguanylate cyclase activity. The highly conserved amino acids His223/His225 and Lys224/Lys226 in the middle domain of EcGReg/BpeGReg are essential to diguanylate cyclase activity. We also identified sixteen important residues (Leu300, Arg306, Asp333, Phe337, Lys338, Asn341, Asp342, Asp350, Leu353, Asp368, Arg372, Gly374, Gly375, Asp376, Glu377, and Phe378) in the active site and inhibitory site of the diguanylate cyclase domain of EcGReg. Moreover, BpeGReg266 (residues 1–266) and BpeGReg296 (residues 1–296), which only contain the globin and middle domains, can inhibit bacterial motility. Our findings suggest that the distal residues of the globin domain affect diguanylate cyclase activity and that BpeGReg may interact with other c-di-GMP-metabolizing proteins to form mixed signaling teams.
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Affiliation(s)
- Xuehua Wan
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
- * E-mail:
| | - Jennifer A. Saito
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - James S. Newhouse
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Maqsudul Alam
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
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Abstract
The discovery of the globin-coupled sensor (GCS) family of haem proteins has provided new insights into signalling proteins and pathways by which organisms sense and respond to changing oxygen levels. GCS proteins consist of a sensor globin domain linked to a variety of output domains, suggesting roles in controlling numerous cellular pathways, and behaviours in response to changing oxygen concentration. Members of this family of proteins have been identified in the genomes of numerous organisms and characterization of GCS with output domains, including methyl accepting chemotaxis proteins, kinases, and diguanylate cyclases, have yielded an understanding of the mechanism by which oxygen controls activity of GCS protein output domains, as well as downstream proteins and pathways regulated by GCS signalling. Future studies will expand our understanding of these proteins both in vitro and in vivo, likely demonstrating broad roles for GCS in controlling oxygen-dependent microbial physiology and phenotypes.
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Sodium Lactate Negatively Regulates Shewanella putrefaciens CN32 Biofilm Formation via a Three-Component Regulatory System (LrbS-LrbA-LrbR). Appl Environ Microbiol 2017; 83:AEM.00712-17. [PMID: 28500045 DOI: 10.1128/aem.00712-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/09/2017] [Indexed: 11/20/2022] Open
Abstract
The capability of biofilm formation has a major impact on the industrial and biotechnological applications of Shewanella putrefaciens CN32. However, the detailed regulatory mechanisms underlying biofilm formation in this strain remain largely unknown. In the present report, we describe a three-component regulatory system which negatively regulates the biofilm formation of S. putrefaciens CN32. This system consists of a histidine kinase LrbS (Sputcn32_0303) and two cognate response regulators, including a transcription factor, LrbA (Sputcn32_0304), and a phosphodiesterase, LrbR (Sputcn32_0305). LrbS responds to the signal of the carbon source sodium lactate and subsequently activates LrbA. The activated LrbA then promotes the expression of lrbR, the gene for the other response regulator. The bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) phosphodiesterase LrbR, containing an EAL domain, decreases the concentration of intracellular c-di-GMP, thereby negatively regulating biofilm formation. In summary, the carbon source sodium lactate acts as a signal molecule that regulates biofilm formation via a three-component regulatory system (LrbS-LrbA-LrbR) in S. putrefaciens CN32.IMPORTANCE Biofilm formation is a significant capability used by some bacteria to survive in adverse environments. Numerous environmental factors can affect biofilm formation through different signal transduction pathways. Carbon sources are critical nutrients for bacterial growth, and their concentrations and types significantly influence the biomass and structure of biofilms. However, knowledge about the underlying mechanism of biofilm formation regulation by carbon source is still limited. This work elucidates a modulation pattern of biofilm formation negatively regulated by sodium lactate as a carbon source via a three-component regulatory system in S. putrefaciens CN32, which may serve as a good example for studying how the carbon sources impact biofilm development in other bacteria.
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Electron-shuttling antibiotics structure bacterial communities by modulating cellular levels of c-di-GMP. Proc Natl Acad Sci U S A 2017; 114:E5236-E5245. [PMID: 28607054 DOI: 10.1073/pnas.1700264114] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Diverse organisms secrete redox-active antibiotics, which can be used as extracellular electron shuttles by resistant microbes. Shuttle-mediated metabolism can support survival when substrates are available not locally but rather at a distance. Such conditions arise in multicellular communities, where the formation of chemical gradients leads to resource limitation for cells at depth. In the pathogenic bacterium Pseudomonas aeruginosa PA14, antibiotics called phenazines act as oxidants to balance the intracellular redox state of cells in anoxic biofilm subzones. PA14 colony biofilms show a profound morphogenic response to phenazines resulting from electron acceptor-dependent inhibition of ECM production. This effect is reminiscent of the developmental responses of some eukaryotic systems to redox control, but for bacterial systems its mechanistic basis has not been well defined. Here, we identify the regulatory protein RmcA and show that it links redox conditions to PA14 colony morphogenesis by modulating levels of bis-(3',5')-cyclic-dimeric-guanosine (c-di-GMP), a second messenger that stimulates matrix production, in response to phenazine availability. RmcA contains four Per-Arnt-Sim (PAS) domains and domains with the potential to catalyze the synthesis and degradation of c-di-GMP. Our results suggest that phenazine production modulates RmcA activity such that the protein degrades c-di-GMP and thereby inhibits matrix production during oxidizing conditions. RmcA thus forms a mechanistic link between cellular redox sensing and community morphogenesis analogous to the functions performed by PAS-domain-containing regulatory proteins found in complex eukaryotes.
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FlrA Represses Transcription of the Biofilm-Associated bpfA Operon in Shewanella putrefaciens. Appl Environ Microbiol 2017; 83:AEM.02410-16. [PMID: 27986717 DOI: 10.1128/aem.02410-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/11/2016] [Indexed: 12/30/2022] Open
Abstract
Manipulation of biofilm formation in Shewanella is beneficial for application to industrial and environmental biotechnology. BpfA is an adhesin largely responsible for biofilm formation in many Shewanella species. However, the mechanism underlying BpfA production and the resulting biofilm remains vaguely understood. We previously described the finding that BpfA expression is enhanced by DosD, an oxygen-stimulated diguanylate cyclase, under aerobic growth. In the present work, we identify FlrA as a critical transcription regulator of the bpfA operon in Shewanella putrefaciens CN32 by transposon mutagenesis. FlrA acted as a repressor of the operon promoter by binding to two boxes overlapping the -10 and -35 sites recognized by σ70 DosD regulation of the expression of the bpfA operon was mediated by FlrA, and cyclic diguanylic acid (c-di-GMP) abolished FlrA binding to the operon promoter. We also demonstrate that FlhG, an accessory protein for flagellum synthesis, antagonized FlrA repression of the expression of the bpfA operon. Collectively, this work demonstrates that FlrA acts as a central mediator in the signaling pathway from c-di-GMP to BpfA-associated biofilm formation in S. putrefaciens CN32. IMPORTANCE Motility and biofilm are mutually exclusive lifestyles, shifts between which are under the strict regulation of bacteria attempting to adapt to the fluctuation of diverse environmental conditions. The FlrA protein in many bacteria is known to control motility as a master regulator of flagellum synthesis. This work elucidates its effect on biofilm formation by controlling the expression of the adhesin BpfA in S. putrefaciens CN32 in response to c-di-GMP. Therefore, FlrA plays a dual role in controlling motility and biofilm formation in S. putrefaciens CN32. The cooccurrence of flrA, bpfA, and the FlrA box in the promoter region of the bpfA operon in diverse Shewanella strains suggests that bpfA is a common mechanism that controls biofilm formation in this bacterial species.
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45
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Burns JL, Rivera S, Deer DD, Joynt SC, Dvorak D, Weinert EE. Oxygen and Bis(3',5')-cyclic Dimeric Guanosine Monophosphate Binding Control Oligomerization State Equilibria of Diguanylate Cyclase-Containing Globin Coupled Sensors. Biochemistry 2016; 55:6642-6651. [PMID: 27933792 DOI: 10.1021/acs.biochem.6b00526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria sense their environment to alter phenotypes, including biofilm formation, to survive changing conditions. Heme proteins play important roles in sensing the bacterial gaseous environment and controlling the switch between motile and sessile (biofilm) states. Globin coupled sensors (GCS), a family of heme proteins consisting of a globin domain linked by a central domain to an output domain, are often found with diguanylate cyclase output domains that synthesize c-di-GMP, a major regulator of biofilm formation. Characterization of diguanylate cyclase-containing GCS proteins from Bordetella pertussis and Pectobacterium carotovorum demonstrated that cyclase activity is controlled by ligand binding to the heme within the globin domain. Both O2 binding to the heme within the globin domain and c-di-GMP binding to a product-binding inhibitory site (I-site) within the cyclase domain control oligomerization states of the enzymes. Changes in oligomerization state caused by c-di-GMP binding to the I-site also affect O2 kinetics within the globin domain, suggesting that shifting the oligomer equilibrium leads to broad rearrangements throughout the protein. In addition, mutations within the I-site that eliminate product inhibition result in changes to the accessible oligomerization states and decreased catalytic activity. These studies provide insight into the mechanism by which ligand binding to the heme and I-site controls activity of GCS proteins and suggests a role for oligomerization-dependent activity in vivo.
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Affiliation(s)
- Justin L Burns
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Shannon Rivera
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - D Douglas Deer
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Shawnna C Joynt
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - David Dvorak
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
| | - Emily E Weinert
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30307, United States
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46
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Huo YC, Li WW, Chen CB, Li CX, Zeng R, Lau TC, Huang TY. Biogenic FeS accelerates reductive dechlorination of carbon tetrachloride by Shewanella putrefaciens CN32. Enzyme Microb Technol 2016; 95:236-241. [PMID: 27866621 DOI: 10.1016/j.enzmictec.2016.09.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 11/28/2022]
Abstract
Dissimilatory metal reducing bacteria (DMRB) widely exist in the subsurface environment and are involved in various contaminant degradation and element geochemical cycling processes. Recent studies suggest that DMRB can biosynthesize metal nanoparticles during metal reduction, but it is unclear yet how such biogenic nanomaterials would affect their decontamination behaviors. In this study, we found that the dechlorination rates of carbon tetrachloride (CT) by Shewanella putrefaciens CN32 was significantly increased by 8 times with the formation of biogenic ferrous sulfide (FeS) nanoparticles. The pasteurized biogenic FeS enabled 5 times faster dechlorination than abiotic FeS that had larger sizes and irregular structure, confirming a significant contribution of the biogenic FeS to CT bioreduction resulting from its good dispersion and relatively high dechlorination activity. This study highlights a potentially important role of biosynthesized nanoparticles in environmental bioremediation.
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Affiliation(s)
- Ying-Chao Huo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China; Advanced Laboratory for Environmental Research & Technology (ALERT), USTC-CityU, Suzhou 215123, China; Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Wen-Wei Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China; Advanced Laboratory for Environmental Research & Technology (ALERT), USTC-CityU, Suzhou 215123, China.
| | - Chang-Bin Chen
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China; Advanced Laboratory for Environmental Research & Technology (ALERT), USTC-CityU, Suzhou 215123, China
| | - Chen-Xuan Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China; Advanced Laboratory for Environmental Research & Technology (ALERT), USTC-CityU, Suzhou 215123, China
| | - Raymond Zeng
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China; Advanced Laboratory for Environmental Research & Technology (ALERT), USTC-CityU, Suzhou 215123, China
| | - Tai-Chu Lau
- Advanced Laboratory for Environmental Research & Technology (ALERT), USTC-CityU, Suzhou 215123, China; Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Tian-Yin Huang
- School of Environment, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215011, China
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Rivera S, Burns JL, Vansuch GE, Chica B, Weinert EE. Globin domain interactions control heme pocket conformation and oligomerization of globin coupled sensors. J Inorg Biochem 2016; 164:70-76. [PMID: 27614715 DOI: 10.1016/j.jinorgbio.2016.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/24/2022]
Abstract
Globin coupled sensors (GCS) are O2-sensing proteins used by bacteria to monitor the surrounding gaseous environment. To investigate the biphasic O2 dissociation kinetics observed for full-length GCS proteins, isolated globin domains from Pectobacterium carotovorum ssp. carotovorum (PccGlobin), and Bordetella pertussis (BpeGlobin), have been characterized. PccGlobin is found to be dimeric, while BpeGlobin is monomeric, indicating key differences in the globin domain dimer interface. Through characterization of wild type globin domains and globin variants with mutations at the dimer interface and within the distal pocket, dimerization of the globin domain is demonstrated to correlate with biphasic dissociation kinetics. Furthermore, a distal pocket tyrosine is identified as the primary hydrogen bond donor, while a secondary hydrogen bond donor within the distal heme pocket is involved in conformation(s) that lead to the second O2 dissociation rate. These findings highlight the role of the globin dimer interface in controlling properties of both the heme pocket and full-length GCS proteins.
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Affiliation(s)
- Shannon Rivera
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Justin L Burns
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Gregory E Vansuch
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Bryant Chica
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Emily E Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA.
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48
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Oh E, Kim JC, Jeon B. Stimulation of biofilm formation by oxidative stress in Campylobacter jejuni under aerobic conditions. Virulence 2016; 7:846-51. [PMID: 27268722 DOI: 10.1080/21505594.2016.1197471] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Euna Oh
- a School of Public Health, University of Alberta , Edmonton , AB , Canada
| | - Jong-Chul Kim
- a School of Public Health, University of Alberta , Edmonton , AB , Canada
| | - Byeonghwa Jeon
- a School of Public Health, University of Alberta , Edmonton , AB , Canada
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49
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Abstract
During the first step of biofilm formation, initial attachment is dictated by physicochemical and electrostatic interactions between the surface and the bacterial envelope. Depending on the nature of these interactions, attachment can be transient or permanent. To achieve irreversible attachment, bacterial cells have developed a series of surface adhesins promoting specific or nonspecific adhesion under various environmental conditions. This article reviews the recent advances in our understanding of the secretion, assembly, and regulation of the bacterial adhesins during biofilm formation, with a particular emphasis on the fimbrial, nonfimbrial, and discrete polysaccharide adhesins in Gram-negative bacteria.
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50
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Experimental evaluation of the metabolic reversibility of ANME-2d between anaerobic methane oxidation and methanogenesis. Appl Microbiol Biotechnol 2016; 100:6481-6490. [DOI: 10.1007/s00253-016-7475-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 01/26/2023]
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