1
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Majdi C, Meffre P, Benfodda Z. Recent advances in the development of bacterial response regulators inhibitors as antibacterial and/or antibiotic adjuvant agent: A new approach to combat bacterial resistance. Bioorg Chem 2024; 150:107606. [PMID: 38968903 DOI: 10.1016/j.bioorg.2024.107606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
The number of new antibacterial agents currently being discovered is insufficient to combat bacterial resistance. It is extremely challenging to find new antibiotics and to introduce them to the pharmaceutical market. Therefore, special attention must be given to find new strategies to combat bacterial resistance and prevent bacteria from developing resistance. Two-component system is a transduction system and the most prevalent mechanism employed by bacteria to respond to environmental changes. This signaling system consists of a membrane sensor histidine kinase that perceives environmental stimuli and a response regulator which acts as a transcription factor. The approach consisting of developing response regulators inhibitors with antibacterial activity or antibiotic adjuvant activity is a novel approach that has never been previously reviewed. In this review we report for the first time, the importance of targeting response regulators and summarizing all existing studies carried out from 2008 until now on response regulators inhibitors as antibacterial agents or / and antibiotic adjuvants. Moreover, we describe the antibacterial activity and/or antibiotic adjuvants activity against the studied bacterial strains and the mechanism of different response regulator inhibitors when it's possible.
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2
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Singh MK, Kenney LJ. Visualizing the invisible: novel approaches to visualizing bacterial proteins and host-pathogen interactions. Front Bioeng Biotechnol 2024; 12:1334503. [PMID: 38415188 PMCID: PMC10898356 DOI: 10.3389/fbioe.2024.1334503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
Host-pathogen interactions play a critical role in infectious diseases, and understanding the underlying mechanisms is vital for developing effective therapeutic strategies. The visualization and characterization of bacterial proteins within host cells is key to unraveling the dynamics of these interactions. Various protein labeling strategies have emerged as powerful tools for studying host-pathogen interactions, enabling the tracking, localization, and functional analysis of bacterial proteins in real-time. However, the labeling and localization of Salmonella secreted type III secretion system (T3SS) effectors in host cells poses technical challenges. Conventional methods disrupt effector stoichiometry and often result in non-specific staining. Bulky fluorescent protein fusions interfere with effector secretion, while other tagging systems such as 4Cys-FLaSH/Split-GFP suffer from low labeling specificity and a poor signal-to-noise ratio. Recent advances in state-of-the-art techniques have augmented the existing toolkit for monitoring the translocation and dynamics of bacterial effectors. This comprehensive review delves into the bacterial protein labeling strategies and their application in imaging host-pathogen interactions. Lastly, we explore the obstacles faced and potential pathways forward in the realm of protein labeling strategies for visualizing interactions between hosts and pathogens.
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Affiliation(s)
- Moirangthem Kiran Singh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
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3
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Lucidi M, Capecchi G, Visaggio D, Gasperi T, Parisi M, Cincotti G, Rampioni G, Visca P, Kolmakov K. Expanding the microbiologist toolbox via new far-red-emitting dyes suitable for bacterial imaging. Microbiol Spectr 2024; 12:e0369023. [PMID: 38095476 PMCID: PMC10782969 DOI: 10.1128/spectrum.03690-23] [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: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE By harnessing the versatility of fluorescence microscopy and super-resolution imaging, bacteriologists explore critical aspects of bacterial physiology and resolve bacterial structures sized beyond the light diffraction limit. These techniques are based on fluorophores with profitable photochemical and tagging properties. The paucity of available far-red (FR)-emitting dyes for bacterial imaging strongly limits the multicolor choice of bacteriologists, hindering the possibility of labeling multiple structures in a single experiment. The set of FR fluorophores characterized in this study expands the palette of dyes useful for microbiologists, as they can be used for bacterial LIVE/DEAD staining and for tagging the membranes of viable Escherichia coli and Bacillus subtilis cells. The absence of toxicity makes these dyes suitable for live-cell imaging and allows monitoring of bacterial membrane biogenesis. Moreover, a newly synthesized FR-fluorophore can be employed for imaging bacterial membranes with stimulated emission depletion microscopy, a super-resolution technique capable of increasing the resolving power of conventional microscopes.
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Affiliation(s)
- Massimiliano Lucidi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | | | - Daniela Visaggio
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Rome, Italy
| | - Miranda Parisi
- Department of Engineering, University Roma Tre, Rome, Italy
| | | | - Giordano Rampioni
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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4
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Lee Upton S, Tay JW, Schwartz DK, Sousa MC. Similarly slow diffusion of BAM and SecYEG complexes in live E. coli cells observed with 3D spt-PALM. Biophys J 2023; 122:4382-4394. [PMID: 37853695 PMCID: PMC10698321 DOI: 10.1016/j.bpj.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023] Open
Abstract
The β-barrel assembly machinery (BAM) complex is responsible for inserting outer membrane proteins (OMPs) into the Escherichia coli outer membrane. The SecYEG translocon inserts inner membrane proteins into the inner membrane and translocates both soluble proteins and nascent OMPs into the periplasm. Recent reports describe Sec possibly playing a direct role in OMP biogenesis through interactions with the soluble polypeptide transport-associated (POTRA) domains of BamA (the central OMP component of BAM). Here we probe the diffusion behavior of these protein complexes using photoactivatable super-resolution localization microscopy and single-particle tracking in live E. coli cells of BAM and SecYEG components BamA and SecE and compare them to other outer and inner membrane proteins. To accurately measure trajectories on the highly curved cell surface, three-dimensional tracking was performed using double-helix point-spread function microscopy. All proteins tested exhibit two diffusive modes characterized by "slow" and "fast" diffusion coefficients. We implement a diffusion coefficient analysis as a function of the measurement lag time to separate positional uncertainty from true mobility. The resulting true diffusion coefficients of the slow and fast modes showed a complete immobility of full-length BamA constructs in the time frame of the experiment, whereas the OMP OmpLA displayed a slow diffusion consistent with the high viscosity of the outer membrane. The periplasmic POTRA domains of BamA were found to anchor BAM to other cellular structures and render it immobile. However, deletion of individual distal POTRA domains resulted in increased mobility, suggesting that these domains are required for the full set of cellular interactions. SecE diffusion was much slower than that of the inner membrane protein PgpB and was more like OMPs and BamA. Strikingly, SecE diffused faster upon POTRA domain deletion. These results are consistent with the existence of a BAM-SecYEG trans-periplasmic assembly in live E. coli cells.
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Affiliation(s)
- Stephen Lee Upton
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Jian Wei Tay
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Daniel Keith Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado
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5
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Hasan MK, Scott NE, Hays MP, Hardwidge PR, El Qaidi S. Salmonella T3SS effector SseK1 arginine-glycosylates the two-component response regulator OmpR to alter bile salt resistance. Sci Rep 2023; 13:9018. [PMID: 37270573 DOI: 10.1038/s41598-023-36057-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/28/2023] [Indexed: 06/05/2023] Open
Abstract
Type III secretion system (T3SS) effector proteins are primarily recognized for binding host proteins to subvert host immune response during infection. Besides their known host target proteins, several T3SS effectors also interact with endogenous bacterial proteins. Here we demonstrate that the Salmonella T3SS effector glycosyltransferase SseK1 glycosylates the bacterial two-component response regulator OmpR on two arginine residues, R15 and R122. Arg-glycosylation of OmpR results in reduced expression of ompF, a major outer membrane porin gene. Glycosylated OmpR has reduced affinity to the ompF promoter region, as compared to the unglycosylated form of OmpR. Additionally, the Salmonella ΔsseK1 mutant strain had higher bile salt resistance and increased capacity to form biofilms, as compared to WT Salmonella, thus linking OmpR glycosylation to several important aspects of bacterial physiology.
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Affiliation(s)
- Md Kamrul Hasan
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne Within the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
| | - Michael P Hays
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
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6
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Singh MK, Kenney LJ. Super-resolution imaging of bacterial pathogens and visualization of their secreted effectors. FEMS Microbiol Rev 2021; 45:5911101. [PMID: 32970796 DOI: 10.1093/femsre/fuaa050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Recent advances in super-resolution imaging techniques, together with new fluorescent probes have enhanced our understanding of bacterial pathogenesis and their interplay within the host. In this review, we provide an overview of what these techniques have taught us about the bacterial lifestyle, the nucleoid organization, its complex protein secretion systems, as well as the secreted virulence factors.
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Affiliation(s)
- Moirangthem Kiran Singh
- Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Linda J Kenney
- Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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7
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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8
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Mayr S, Hauser F, Puthukodan S, Axmann M, Göhring J, Jacak J. Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model. PLoS Comput Biol 2020; 16:e1007902. [PMID: 32603371 PMCID: PMC7384682 DOI: 10.1371/journal.pcbi.1007902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/27/2020] [Accepted: 04/22/2020] [Indexed: 11/19/2022] Open
Abstract
We present the software platform 2CALM that allows for a comparative analysis of 3D localisation microscopy data representing protein distributions in two biological samples. The in-depth statistical analysis reveals differences between samples at the nanoscopic level using parameters such as cluster-density and -curvature. An automatic classification system combines multiplex and multi-level statistical approaches into one comprehensive parameter for similarity testing of the compared samples. We demonstrated the biological importance of 2CALM, comparing the protein distributions of CD41 and CD62p on activated platelets in a 3D artificial clot. Additionally, using 2CALM, we quantified the impact of the inflammatory cytokine interleukin-1β on platelet activation in clots. The platform is applicable to any other cell type and biological system and can provide new insights into biological and medical applications.
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Affiliation(s)
- Sandra Mayr
- University of Applied Sciences Upper Austria, Linz, Austria
| | - Fabian Hauser
- University of Applied Sciences Upper Austria, Linz, Austria
| | | | - Markus Axmann
- University of Applied Sciences Upper Austria, Linz, Austria
| | - Janett Göhring
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Jaroslaw Jacak
- University of Applied Sciences Upper Austria, Linz, Austria
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9
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Ma Y, Li L, Awasthi MK, Tian H, Lu M, Megharaj M, Pan Y, He W. Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations. Appl Microbiol Biotechnol 2020; 104:5873-5887. [PMID: 32415321 DOI: 10.1007/s00253-020-10672-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 01/02/2023]
Abstract
Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.
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Affiliation(s)
- Yinghui Ma
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xi'an, 710043, Shaanxi, PR China.,College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Lijun Li
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xi'an, 710043, Shaanxi, PR China.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Haixia Tian
- College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Meihuan Lu
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xi'an, 710043, Shaanxi, PR China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| | - Yalei Pan
- Shaanxi Collaborative Innovation Center of Chinese Medicine Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, 712046, PR China
| | - Wenxiang He
- College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
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10
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Kenney LJ, Anand GS. EnvZ/OmpR Two-Component Signaling: An Archetype System That Can Function Noncanonically. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0001-2019. [PMID: 32003321 PMCID: PMC7192543 DOI: 10.1128/ecosalplus.esp-0001-2019] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Indexed: 01/09/2023]
Abstract
Two-component regulatory systems represent the major paradigm for signal transduction in prokaryotes. The simplest systems are composed of a sensor kinase and a response regulator. The sensor is often a membrane protein that senses a change in environmental conditions and is autophosphorylated by ATP on a histidine residue. The phosphoryl group is transferred onto an aspartate of the response regulator, which activates the regulator and alters its output, usually resulting in a change in gene expression. In this review, we present a historical view of the archetype EnvZ/OmpR two-component signaling system, and then we provide a new view of signaling based on our recent experiments. EnvZ responds to cytoplasmic signals that arise from changes in the extracellular milieu, and OmpR acts canonically (requiring phosphorylation) to regulate the porin genes and noncanonically (without phosphorylation) to activate the acid stress response. Herein, we describe how insights gleaned from stimulus recognition and response in EnvZ are relevant to nearly all sensor kinases and response regulators.
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Affiliation(s)
- Linda J Kenney
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Mechanobiology Institute, T-Lab, National University of Singapore, Singapore
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore
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11
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Rosales-Hurtado M, Meffre P, Szurmant H, Benfodda Z. Synthesis of histidine kinase inhibitors and their biological properties. Med Res Rev 2019; 40:1440-1495. [PMID: 31802520 DOI: 10.1002/med.21651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 11/11/2022]
Abstract
Infections caused by multidrug-resistant bacteria represent a significant and ever-increasing cause of morbidity and mortality. There is thus an urgent need to develop efficient and well-tolerated antibacterials targeting unique cellular processes. Numerous studies have led to the identification of new biological targets to fight bacterial resistance. Two-component signal transduction systems are widely employed by bacteria to translate external and cellular signals into a cellular response. They are ubiquitous in bacteria, absent in the animal kingdom and are integrated into various virulence pathways. Several chemical series, including isothiazolidones, imidazolium salts, benzoxazines, salicylanilides, thiophenes, thiazolidiones, benzimidazoles, and other derivatives deduced by different approaches have been reported in the literature to have histidine kinase (HK) inhibitory activity. In this review, we report on the design and the synthesis of these HKs inhibitors and their potential to serve as antibacterial agents.
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Affiliation(s)
| | | | - Hendrik Szurmant
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, California
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12
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Dietz MS, Heilemann M. Optical super-resolution microscopy unravels the molecular composition of functional protein complexes. NANOSCALE 2019; 11:17981-17991. [PMID: 31573593 DOI: 10.1039/c9nr06364a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Optical super-resolution microscopy has revolutionized our understanding of cell biology. Next to visualizing cellular structures with near-molecular spatial resolution, an additional benefit is the molecular characterization of biomolecular complexes directly in an intact cell. Single-molecule localization microscopy, as one technology out of the toolbox of super-resolution methods, generates images by detecting the position of single fluorophore labels and is particularly suited for molecular quantification. We review imaging and analysis methods employing single-molecule localization microscopy and extract molecule numbers.
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Affiliation(s)
- Marina S Dietz
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany.
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13
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Karmakar K, Nair AV, Chandrasekharan G, Garai P, Nath U, Nataraj KN, N B P, Chakravortty D. Rhizospheric life of Salmonella requires flagella-driven motility and EPS-mediated attachment to organic matter and enables cross-kingdom invasion. FEMS Microbiol Ecol 2019; 95:fiz107. [PMID: 31271416 DOI: 10.1093/femsec/fiz107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/03/2019] [Indexed: 09/19/2023] Open
Abstract
Salmonella is an established pathogen of the members of the kingdom Animalia. Reports indicate that the association of Salmonella with fresh, edible plant products occurs at the pre-harvest state, i.e. in the field. In this study, we follow the interaction of Salmonella Typhimurium with the model plant Arabidopsis thaliana to understand the process of migration in soil. Plant factors like root exudates serve as chemo-attractants. Our ex situ experiments allowed us to track Salmonella from its free-living state to the endophytic state. We found that genes encoding two-component systems and proteins producing extracellular polymeric substances are essential for Salmonella to adhere to the soil and roots. To understand the trans-kingdom flow of Salmonella, we fed the contaminated plants to mice and observed that it invades and colonizes liver and spleen. To complete the disease cycle, we re-established the infection in plant by mixing the potting mixture with the fecal matter collected from the diseased animals. Our experiments revealed a cross-kingdom invasion by the pathogen via passage through a murine intermediate, a mechanism for its persistence in the soil and invasion in a non-canonical host. These results form a basis to break the life-cycle of Salmonella before it reaches its animal host and thus reduce Salmonella contamination of food products.
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Affiliation(s)
- Kapudeep Karmakar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Abhilash Vijay Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Giridhar Chandrasekharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Department of Microbiology, St. Joseph's College Autonomous, Bangalore, India
| | - Preeti Garai
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Utpal Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Karaba N Nataraj
- Department of Crop Physiology, University of Agricultural Science, Bangalore, India
| | - Prakash N B
- Department of Soil Science and Agricultural Chemistry, University of Agricultural Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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14
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Visualizing the inner life of microbes: practices of multi-color single-molecule localization microscopy in microbiology. Biochem Soc Trans 2019; 47:1041-1065. [PMID: 31296734 DOI: 10.1042/bst20180399] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 12/28/2022]
Abstract
In this review, we discuss multi-color single-molecule imaging and tracking strategies for studying microbial cell biology. We first summarize and compare the methods in a detailed literature review of published studies conducted in bacteria and fungi. We then introduce a guideline on which factors and parameters should be evaluated when designing a new experiment, from fluorophore and labeling choices to imaging routines and data analysis. Finally, we give some insight into some of the recent and promising applications and developments of these techniques and discuss the outlook for this field.
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15
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Smit JH, Li Y, Warszawik EM, Herrmann A, Cordes T. ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data. PLoS One 2019; 14:e0217524. [PMID: 31216308 PMCID: PMC6583990 DOI: 10.1371/journal.pone.0217524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
Single-molecule fluorescence microscopy studies of bacteria provide unique insights into the mechanisms of cellular processes and protein machineries in ways that are unrivalled by any other technique. With the cost of microscopes dropping and the availability of fully automated microscopes, the volume of microscopy data produced has increased tremendously. These developments have moved the bottleneck of throughput from image acquisition and sample preparation to data analysis. Furthermore, requirements for analysis procedures have become more stringent given the demand of various journals to make data and analysis procedures available. To address these issues we have developed a new data analysis package for analysis of fluorescence microscopy data from rod-like cells. Our software ColiCoords structures microscopy data at the single-cell level and implements a coordinate system describing each cell. This allows for the transformation of Cartesian coordinates from transmission light and fluorescence images and single-molecule localization microscopy (SMLM) data to cellular coordinates. Using this transformation, many cells can be combined to increase the statistical power of fluorescence microscopy datasets of any kind. ColiCoords is open source, implemented in the programming language Python, and is extensively documented. This allows for modifications for specific needs or to inspect and publish data analysis procedures. By providing a format that allows for easy sharing of code and associated data, we intend to promote open and reproducible research. The source code and documentation can be found via the project’s GitHub page.
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Affiliation(s)
- Jochem H. Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- * E-mail: (JHS); (TC)
| | - Yichen Li
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Eliza M. Warszawik
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andreas Herrmann
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
- * E-mail: (JHS); (TC)
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16
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Liew ATF, Foo YH, Gao Y, Zangoui P, Singh MK, Gulvady R, Kenney LJ. Single cell, super-resolution imaging reveals an acid pH-dependent conformational switch in SsrB regulates SPI-2. eLife 2019; 8:e45311. [PMID: 31033442 PMCID: PMC6557628 DOI: 10.7554/elife.45311] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/28/2019] [Indexed: 12/29/2022] Open
Abstract
After Salmonella is phagocytosed, it resides in an acidic vacuole. Its cytoplasm acidifies to pH 5.6; acidification activates pathogenicity island 2 (SPI-2). SPI-2 encodes a type three secretion system whose effectors modify the vacuole, driving endosomal tubulation. Using super-resolution imaging in single bacterial cells, we show that low pH induces expression of the SPI-2 SsrA/B signaling system. Single particle tracking, atomic force microscopy, and single molecule unzipping assays identified pH-dependent stimulation of DNA binding by SsrB. A so-called phosphomimetic form (D56E) was unable to bind to DNA in live cells. Acid-dependent DNA binding was not intrinsic to regulators, as PhoP and OmpR binding was not pH-sensitive. The low level of SPI-2 injectisomes observed in single cells is not due to fluctuating SsrB levels. This work highlights the surprising role that acid pH plays in virulence and intracellular lifestyles of Salmonella; modifying acid survival pathways represents a target for inhibiting Salmonella.
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Affiliation(s)
- Andrew Tze Fui Liew
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yunfeng Gao
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Parisa Zangoui
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | | | - Ranjit Gulvady
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Linda J Kenney
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
- Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonUnited States
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17
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Lebedev N, Stroud RM, Yates MD, Tender LM. Spatially Resolved Chemical Analysis of Geobacter sulfurreducens Cell Surface. ACS NANO 2019; 13:4834-4842. [PMID: 30943001 DOI: 10.1021/acsnano.9b02032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Geobacter sulfurreducens is of interest for the highest efficiency of power generation and extremely long extracellular electron transfer (EET) between the bacterium and electrodes. Despite more than 15 years of intensive molecular biological research, there is still no clear answer which molecules are responsible for these processes. In the present work, we look at the problem from another (atomic) perspective and identify the location and shape of the compounds that are known to be conductive, particularly those containing Fe atoms. By using highly sophisticated energy dispersive X-ray spectroscopy combined with high-angle annular dark-field transmission electron microscopy enabling detection, identification, and localization of chemical compounds on the surface at nearly atomic spatial resolution, we analyze Fe spatial distribution within the G. sulfurreducens community. We discover the presence of small Fe-containing particles on the surface of the bacterium cells. The size of the particles (diameter 5.6 nm) is highly reproducible and comparable with the size of a single protein. The particles cover about 2% of the cell surface, which is similar to that expected for molecular conductors responsible for electron transfer through the bacterium cell wall. We find that G. sulfurreducens filaments ("bacterial molecular wires") also contain Fe atoms in their bundles. We observe that the bacterium enable changing the distance between the Fe-containing bundles in the filaments from separated to attached (the latter is needed for the efficient electron transfer between the Fe-containing particles), depending on the bacterium metabolic activity and attachment to extracellular substrates. These results are consistent with the recently published research about the role of Fe atoms in protein molecular conductance ( Phys. Chem. Chem. Phys. , 2018 , 20 , 14072 - 14081 ) and show what type of Fe-containing particles are involved in the bacterial extracellular communication. They can be used for the design and construction of artificial biomolecular wires and bioinorganic interfaces.
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Affiliation(s)
- Nikolai Lebedev
- Center for Bio/Molecular Science and Engineering , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
| | - Rhonda M Stroud
- Materials Science and Technology Division , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
| | - Matthew D Yates
- Center for Bio/Molecular Science and Engineering , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
| | - Leonard Martin Tender
- Center for Bio/Molecular Science and Engineering , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
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18
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Baldering TN, Dietz MS, Gatterdam K, Karathanasis C, Wieneke R, Tampé R, Heilemann M. Synthetic and genetic dimers as quantification ruler for single-molecule counting with PALM. Mol Biol Cell 2019; 30:1369-1376. [PMID: 30969885 PMCID: PMC6724688 DOI: 10.1091/mbc.e18-10-0661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
How membrane proteins oligomerize determines their function. Superresolution microscopy can report on protein clustering and extract quantitative molecular information. Here, we evaluate the blinking kinetics of four photoactivatable fluorescent proteins for quantitative single-molecule microscopy. We identified mEos3.2 and mMaple3 to be suitable for molecular quantification through blinking histogram analysis. We designed synthetic and genetic dimers of mEos3.2 as well as fusion proteins of monomeric and dimeric membrane proteins as reference structures, and we demonstrate their versatile use for quantitative superresolution imaging in vitro and in situ. We further found that the blinking behavior of mEos3.2 and mMaple3 is modified by a reducing agent, offering the possibility to adjust blinking parameters according to experimental needs.
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Affiliation(s)
- Tim N Baldering
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Marina S Dietz
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Karl Gatterdam
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Christos Karathanasis
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Ralph Wieneke
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Mike Heilemann
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
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19
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Cai Q, Wang G, Li Z, Zhang L, Fu Y, Yang X, Lin W, Lin X. SWATH based quantitative proteomics analysis reveals Hfq2 play an important role on pleiotropic physiological functions in Aeromonas hydrophila. J Proteomics 2019; 195:1-10. [DOI: 10.1016/j.jprot.2018.12.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/15/2018] [Accepted: 12/26/2018] [Indexed: 12/14/2022]
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20
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Kenney LJ. The role of acid stress in Salmonella pathogenesis. Curr Opin Microbiol 2019; 47:45-51. [DOI: 10.1016/j.mib.2018.11.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/10/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022]
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21
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Chakraborty S, Kenney LJ. A New Role of OmpR in Acid and Osmotic Stress in Salmonella and E. coli. Front Microbiol 2018; 9:2656. [PMID: 30524381 PMCID: PMC6262077 DOI: 10.3389/fmicb.2018.02656] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/17/2018] [Indexed: 12/24/2022] Open
Abstract
Bacteria survive and respond to diverse environmental conditions and during infection inside the host by systematic regulation of stress response genes. E. coli and S. Typhimurium can undergo large changes in intracellular osmolality (up to 1.8 Osmol/kg) and can tolerate cytoplasmic acidification to at least pHi 5.6. Recent analyses of single cells challenged a long held view that bacteria respond to extracellular acid stress by rapid acidification followed by a rapid recovery. It is now appreciated that both S. Typhimurium and E. coli maintain an acidic cytoplasm through the actions of the outer membrane protein regulator OmpR via its regulation of distinct signaling pathways. However, a comprehensive comparison of OmpR regulons between S. Typhimurium and E. coli is lacking. In this study, we examined the expression profiles of wild-type and ompR null strains of the intracellular pathogen S. Typhimurium and a commensal E. coli in response to acid and osmotic stress. Herein, we classify distinct OmpR regulons and also identify shared OmpR regulatory pathways between S. Typhimurium and E. coli in response to acid and osmotic stress. Our study establishes OmpR as a key regulator of bacterial virulence, growth and metabolism, in addition to its role in regulating outer membrane proteins.
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Affiliation(s)
- Smarajit Chakraborty
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Linda J. Kenney
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
- Departments of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, United States
- Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
- Jesse Brown Veterans Administration Medical Center, Chicago, IL, United States
- *Correspondence: Linda J. Kenney,
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22
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Stockmar I, Feddersen H, Cramer K, Gruber S, Jung K, Bramkamp M, Shin JY. Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy. Sci Rep 2018; 8:10137. [PMID: 29973667 PMCID: PMC6031688 DOI: 10.1038/s41598-018-28472-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/19/2018] [Indexed: 11/08/2022] Open
Abstract
mNeonGreen fluorescent protein is capable of photo-switching, hence in principle applicable for super-resolution imaging. However, difficult-to-control blinking kinetics that lead to simultaneous emission of multiple nearby mNeonGreen molecules impedes its use for PALM. Here, we determined the on- and off- switching rate and the influence of illumination power on the simultaneous emission. Increasing illumination power reduces the probability of simultaneous emission, but not enough to generate high quality PALM images. Therefore, we introduce a simple data post-processing step that uses temporal and spatial information of molecule localizations to further reduce artifacts arising from simultaneous emission of nearby emitters. We also systematically evaluated various sample preparation steps to establish an optimized protocol to preserve cellular morphology and fluorescence signal. In summary, we propose a workflow for super-resolution imaging with mNeonGreen based on optimization of sample preparation, data acquisition and simple post-acquisition data processing. Application of our protocol enabled us to resolve the expected double band of bacterial cell division protein DivIVA, and to visualize that the chromosome organization protein ParB organized into sub-clusters instead of the typically observed diffraction-limited foci. We expect that our workflow allows a broad use of mNeonGreen for super-resolution microscopy, which is so far difficult to achieve.
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Affiliation(s)
- Iris Stockmar
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Max Plank Institute for Biochemistry, Martinsried, Germany
| | - Helge Feddersen
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kimberly Cramer
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Max Plank Institute for Biochemistry, Martinsried, Germany
| | - Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
| | - Jae Yen Shin
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
- Max Plank Institute for Biochemistry, Martinsried, Germany.
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23
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Zhang DF, Ye JZ, Dai HH, Lin XM, Li H, Peng XX. Identification of ethanol tolerant outer membrane proteome reveals OmpC-dependent mechanism in a manner of EnvZ/OmpR regulation in Escherichia coli. J Proteomics 2018. [PMID: 29518576 DOI: 10.1016/j.jprot.2018.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ethanol is an efficient disinfectant, but long-term and wide usage of ethanol leads to microbial tolerance. Bacteria with the tolerance are widely identified. However, mechanisms of the tolerance are not elucidated. To explore the mechanisms of outer membrane (OM) proteins underlying ethanol tolerance in bacteria, functional proteomic methodologies were utilized to characterize OM proteins of E. coli suddenly exposed to 3.125% ethanol. Of eleven proteins altered significantly, seven were OM proteins, in which LamB, FadL and OmpC were up-regulated, and OmpT, OmpF, Tsx and OmpA were down-regulated. The alterations were validated using Western blot. Then, functional characterization of the altered abundance of OM proteins was investigated in gene-deleted and gene-complemented mutants cultured in 1.56-6.25% ethanol. Higher inhibiting rate was detected in ΔompC than ΔlamB and ΔompA, but no difference was found between Δtsx, ΔompF, ΔfadL or ΔompT and control. Furthermore, EnvZ/OmpR two-component signal transduction system, which regulates OmpC and OmpF expression, was determined to participate in the tolerance. Finally, our results show that absence of envZ, ompR or ompC and ompA led to elevated and reduced intracellular ethanol, respectively. These findings indicate EnvZ-dependent phosphotransfer signaling pathway of the OmpR-mediated expression of OmpC plays a crucial role in ethanol tolerance. BIOLOGICAL SIGNIFICANCE Ethanol tolerance is an adaptation strategy of bacteria. In the present study, we used the proteomic approaches involving 2-DE and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) to determined outer membrane (OM) protein changes in E. coli K-12 after 2 h of 1/2 MIC of ethanol exposure. Under ethanol stress, seven differential OM proteins were found, which were validated by Western blot. Functions of these seven OM proteins were compared using their genetically modified strains. Furthermore, the role of EnvZ/OmpR two-component signal transduction system was identified in ethanol tolerance of E. coli. Finally, Loss of ompC, envZ or ompR increases intracellular ethanol, while absence of ompA reduces reversal effect. This is the first report of OM proteomics in E. coli exposed to ethanol. Our findings reveal an unknown OmpC-dependent mechanism of ethanol tolerance in a manner of EnvZ/OmpR regulation.
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Affiliation(s)
- Dan-Feng Zhang
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, People's Republic of China
| | - Jin-Zhou Ye
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China
| | - Hong-Hou Dai
- Clinical Laboratory, Affiliated Hospital of Jinggangshan University, 343000, People's Republic of China
| | - Xiang-Min Lin
- Agroecological Institute, Fujian Agricultural and Forestry University, Fuzhou 350002, People's Republic of China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China.
| | - Xuan-Xian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China.
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24
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Lugger J, Mulder DJ, Sijbesma R, Schenning A. Nanoporous Polymers Based on Liquid Crystals. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E104. [PMID: 29324669 PMCID: PMC5793602 DOI: 10.3390/ma11010104] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 12/15/2022]
Abstract
In the present review, we discuss recent advances in the field of nanoporous networks based on polymerisable liquid crystals. The field has matured in the last decade, yielding polymers having 1D, 2D, and 3D channels with pore sizes on the nanometer scale. Next to the current progress, some of the future challenges are presented, with the integration of nanoporous membranes in functional devices considered as the biggest challenge.
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Affiliation(s)
- Jody Lugger
- Laboratory of Supramolecular Polymer Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Dirk Jan Mulder
- Laboratory of Stimuli-Responsive Functional Materials and Devices, Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Dutch Polymer Institute, P.O. Box 902, 5600 AZ Eindhoven, The Netherlands.
| | - Rint Sijbesma
- Laboratory of Supramolecular Polymer Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Albert Schenning
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
- Laboratory of Stimuli-Responsive Functional Materials and Devices, Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
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25
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Chakraborty S, Winardhi RS, Morgan LK, Yan J, Kenney LJ. Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells. Nat Commun 2017; 8:1587. [PMID: 29138484 PMCID: PMC5686162 DOI: 10.1038/s41467-017-02030-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022] Open
Abstract
Unlike eukaryotes, bacteria undergo large changes in osmolality and cytoplasmic pH. It has been described that during acid stress, bacteria internal pH promptly acidifies, followed by recovery. Here, using pH imaging in single living cells, we show that following acid stress, bacteria maintain an acidic cytoplasm and the osmotic stress transcription factor OmpR is required for acidification. The activation of this response is non-canonical, involving a regulatory mechanism requiring the OmpR cognate kinase EnvZ, but not OmpR phosphorylation. Single cell analysis further identifies an intracellular pH threshold ~6.5. Acid stress reduces the internal pH below this threshold, increasing OmpR dimerization and DNA binding. During osmotic stress, the internal pH is above the threshold, triggering distinct OmpR-related pathways. Preventing intracellular acidification of Salmonella renders it avirulent, suggesting that acid stress pathways represent a potential therapeutic target. These results further emphasize the advantages of single cell analysis over studies of population averages.
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Affiliation(s)
- Smarajit Chakraborty
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Ricksen S Winardhi
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, Singapore, 117551, Singapore
| | - Leslie K Morgan
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA.,Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, 60612, USA
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, Singapore, 117551, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, National University of Singapore, T-Lab, 5A Engineering Drive 1, Singapore, 117411, Singapore. .,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA. .,Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, 60612, USA. .,Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
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26
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Spahn C, Glaesmann M, Gao Y, Foo YH, Lampe M, Kenney LJ, Heilemann M. Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells. Methods Mol Biol 2017; 1624:269-289. [PMID: 28842890 DOI: 10.1007/978-1-4939-7098-8_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Despite their small size and the lack of compartmentalization, bacteria exhibit a striking degree of cellular organization, both in time and space. During the last decade, a group of new microscopy techniques emerged, termed super-resolution microscopy or nanoscopy, which facilitate visualizing the organization of proteins in bacteria at the nanoscale. Single-molecule localization microscopy (SMLM) is especially well suited to reveal a wide range of new information regarding protein organization, interaction, and dynamics in single bacterial cells. Recent developments in click chemistry facilitate the visualization of bacterial chromatin with a resolution of ~20 nm, providing valuable information about the ultrastructure of bacterial nucleoids, especially at short generation times. In this chapter, we describe a simple-to-realize protocol that allows determining precise structural information of bacterial nucleoids in fixed cells, using direct stochastic optical reconstruction microscopy (dSTORM). In combination with quantitative photoactivated localization microscopy (PALM), the spatial relationship of proteins with the bacterial chromosome can be studied. The position of a protein of interest with respect to the nucleoids and the cell cylinder can be visualized by super-resolving the membrane using point accumulation for imaging in nanoscale topography (PAINT). The combination of the different SMLM techniques in a sequential workflow maximizes the information that can be extracted from single cells, while maintaining optimal imaging conditions for each technique.
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Affiliation(s)
- Christoph Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Yunfeng Gao
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Otto-Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Linda J Kenney
- Mechanobiology Institute, T-Lab, National University of Singapore, 5A Engineering Drive 1, Singapore, 117411, Singapore.
- University of Illinois, Chicago, Chicago, IL, 60612, USA.
- Jesse Brown VA Medical Center, Chicago, IL, 60612, USA.
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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27
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Xiao J, Dufrêne YF. Optical and force nanoscopy in microbiology. Nat Microbiol 2016; 1:16186. [PMID: 27782138 PMCID: PMC5839876 DOI: 10.1038/nmicrobiol.2016.186] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.
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Affiliation(s)
- Jie Xiao
- Department of Biophysics &Biophysical Chemistry, The Johns Hopkins School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21212, USA
| | - Yves F Dufrêne
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), Belgium
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28
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Parada C, Orruño M, Kaberdin V, Bravo Z, Barcina I, Arana I. Changes in the Vibrio harveyi Cell Envelope Subproteome During Permanence in Cold Seawater. MICROBIAL ECOLOGY 2016; 72:549-558. [PMID: 27324654 DOI: 10.1007/s00248-016-0802-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
Previous work demonstrated that physiological, morphological, and gene expression changes as well as the time-dependent entry into the viable but not culturable (VBNC) state are used by Vibrio species to survive and cope with diverse stress conditions including seasonal temperature downshifts and starvation. To learn more about the nature and specific contribution of membrane proteins to cell adaptation and survival, we analyzed variations in the protein composition of cell envelope and related them to morphological and physiological changes that were taking place during the long-term permanence of Vibrio harveyi in seawater microcosm at 4 °C. We found that after 21 days of permanence, nearly all population (ca. 99 %) of V. harveyi acquired the VBNC phenotype. Although the size of V. harveyi cells gradually decreased during the incubation time, we found that this morphological change was not directly related to their entry into the VBNC state. Our proteomic study revealed that the level of membrane proteins playing key roles in cellular transport, maintenance of cell structure, and in bioenergetics processes remained unchanged along starvation at low temperature, thus suggesting that V. harveyi might need these proteins for the long-term survival and/or for the resuscitation process. On a contrary, the level of two proteins, elongation factor Tu (EF-TU) and bacterioferritin, greatly increased reaching the maximal values by the end of the incubation period. We further discuss the above data with respect to the putative roles likely exerted by membrane proteins during transition to and maintaining of the VBNC state.
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Affiliation(s)
- Claudia Parada
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Maite Orruño
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Vladimir Kaberdin
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
- Department of Immunology, Microbiology and Parasitology, IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Zaloa Bravo
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Barcina
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Inés Arana
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain.
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Xia K, Zang N, Zhang J, Zhang H, Li Y, Liu Y, Feng W, Liang X. New insights into the mechanisms of acetic acid resistance in Acetobacter pasteurianus using iTRAQ-dependent quantitative proteomic analysis. Int J Food Microbiol 2016; 238:241-251. [PMID: 27681379 DOI: 10.1016/j.ijfoodmicro.2016.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 12/01/2022]
Abstract
Acetobacter pasteurianus is the main starter in rice vinegar manufacturing due to its remarkable abilities to resist and produce acetic acid. Although several mechanisms of acetic acid resistance have been proposed and only a few effector proteins have been identified, a comprehensive depiction of the biological processes involved in acetic acid resistance is needed. In this study, iTRAQ-based quantitative proteomic analysis was adopted to investigate the whole proteome of different acidic titers (3.6, 7.1 and 9.3%, w/v) of Acetobacter pasteurianus Ab3 during the vinegar fermentation process. Consequently, 1386 proteins, including 318 differentially expressed proteins (p<0.05), were identified. Compared to that in the low titer circumstance, cells conducted distinct biological processes under high acetic acid stress, where >150 proteins were differentially expressed. Specifically, proteins involved in amino acid metabolic processes and fatty acid biosynthesis were differentially expressed, which may contribute to the acetic acid resistance of Acetobacter. Transcription factors, two component systems and toxin-antitoxin systems were implicated in the modulatory network at multiple levels. In addition, the identification of proteins involved in redox homeostasis, protein metabolism, and the cell envelope suggested that the whole cellular system is mobilized in response to acid stress. These findings provide a differential proteomic profile of acetic acid resistance in Acetobacter pasteurianus and have potential application to highly acidic rice vinegar manufacturing.
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Affiliation(s)
- Kai Xia
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Ning Zang
- Medical Scientific Research Center, Guangxi Medical University, Nanning 530021, China
| | - Junmei Zhang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Hong Zhang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Yudong Li
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Ye Liu
- Zhejiang Wuweihe Food Co. Ltd., Huzhou 313213, China
| | - Wei Feng
- Zhejiang Wuweihe Food Co. Ltd., Huzhou 313213, China
| | - Xinle Liang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China.
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30
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Hanne J, Zila V, Heilemann M, Müller B, Kräusslich HG. Super-resolved insights into human immunodeficiency virus biology. FEBS Lett 2016; 590:1858-76. [PMID: 27117435 DOI: 10.1002/1873-3468.12186] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 11/06/2022]
Abstract
The recent development of fluorescence microscopy approaches overcoming the diffraction limit of light microscopy opened possibilities for studying small-scale cellular processes. The spatial resolution achieved by these novel techniques, together with the possibility to perform live-cell and multicolor imaging, make them ideally suited for visualization of native viruses and subviral structures within the complex environment of a host cell or organ, thus providing fundamentally new possibilities for investigating virus-cell interactions. Here, we review the use of super-resolution microscopy approaches to study virus-cell interactions, and discuss recent insights into human immunodeficiency virus biology obtained by exploiting these novel techniques.
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Affiliation(s)
- Janina Hanne
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany.,Optical Nanoscopy Division, German Cancer Research Center, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
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31
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Foo YH, Gao Y, Zhang H, Kenney LJ. Cytoplasmic sensing by the inner membrane histidine kinase EnvZ. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:119-29. [PMID: 25937465 DOI: 10.1016/j.pbiomolbio.2015.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 12/22/2022]
Abstract
Two-component regulatory systems drive signal transduction in bacteria. The simplest of these employs a membrane sensor kinase and a cytoplasmic response regulator. Environmental sensing is typically coupled to gene regulation. The histidine kinase EnvZ and its cognate response regulator OmpR regulate expression of outer membrane proteins (porins) in response to osmotic stress. We used hydrogen:deuterium exchange mass spectrometry to identify conformational changes in the cytoplasmic domain of EnvZ (EnvZc) that were associated with osmosensing. The osmosensor localized to a seventeen amino acid region of the four-helix bundle of the cytoplasmic domain and flanked the His(243) autophosphorylation site. High osmolality increased autophosphorylation of His(243), suggesting that these two events were linked. The transmembrane domains were not required for osmosensing, but mutants in the transmembrane domains altered EnvZ activity. A photoactivatable fusion protein composed of EnvZc fused to the fluorophore mEos2 (EnvZc-mEos2) was as capable as EnvZc in supporting OmpR-dependent ompF and ompC transcription. Over-expression of EnvZc reduced activity, indicating that the EnvZ/OmpR system is not robust. Our results support a model in which osmolytes stabilize helix one in the four-helix bundle of EnvZ by increased hydrogen bonding of the peptide backbone, increasing autophosphorylation and downstream signaling. The likelihood that additional histidine kinases use similar cytoplasmic sensing mechanisms is discussed.
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Affiliation(s)
- Yong Hwee Foo
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Yunfeng Gao
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Hongfang Zhang
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, National University of Singapore, Singapore; Jesse Brown Veterans Affairs Medical Center, Chicago, USA; University of Illinois-Chicago, USA.
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