1
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Gui R, Jin H. Organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH for biosensing, bioimaging and biotherapeutics applications. Talanta 2024; 275:126171. [PMID: 38703479 DOI: 10.1016/j.talanta.2024.126171] [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: 01/31/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
In recent years, organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH (DFR-MPs-pH) have been attracting much interest in fundamental application research fields. More and more scientific publications have reported the exploration of various DFR-MPs-pH systems that have unique dual-fluorescence ratiometry as the signal output, in-built and signal self-calibration functions to improve precise detection of targets. DFR-MPs-pH systems possess high-performance applications in biosensing, bioimaging and biomedicine fields. This review has comprehensively summarized recent advances of DFR-MPs-pH for the first time. First of all, the compositions and types of DFR-MPs-pH are introduced by summarizing different organic fluorophores-based molecule systems. Then, construction strategies are analyzed based on specific components, structures, properties and functions of DFR-MPs-pH. Afterward, biosensing and bioimaging applications are discussed in detail, primarily referring to pH sensing and imaging detection at the levels of living cells and small animals. Finally, biomedicine applications are fully summarized, majorly involving bio-toxicity evaluation, bio-distribution, biomedical diagnosis and therapeutics. Meanwhile, the current status, challenges and perspectives are rationally commented after detailed discussions of representative and state-of-the-art studies. Overall, this present review is comprehensive, in-time and in-depth, and can facilitate the following further exploration of new and versatile DFR-MPs-pH systems toward rational design, facile preparation, superior properties, adjustable functions and highly efficient applications in promising fields.
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Affiliation(s)
- Rijun Gui
- College of Chemistry and Chemical Engineering, Intellectual Property Research Institute, Qingdao University, Shandong, 266071, PR China.
| | - Hui Jin
- College of Chemistry and Chemical Engineering, Intellectual Property Research Institute, Qingdao University, Shandong, 266071, PR China
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2
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Benyamin MS, Perisin MP, Hellman CA, Schwalm ND, Jahnke JP, Sund CJ. Modeling control and transduction of electrochemical gradients in acid-stressed bacteria. iScience 2023; 26:107140. [PMID: 37404371 PMCID: PMC10316662 DOI: 10.1016/j.isci.2023.107140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Transmembrane electrochemical gradients drive solute uptake and constitute a substantial fraction of the cellular energy pool in bacteria. These gradients act not only as "homeostatic contributors," but also play a dynamic and keystone role in several bacterial functions, including sensing, stress response, and metabolism. At the system level, multiple gradients interact with ion transporters and bacterial behavior in a complex, rapid, and emergent manner; consequently, experiments alone cannot untangle their interdependencies. Electrochemical gradient modeling provides a general framework to understand these interactions and their underlying mechanisms. We quantify the generation, maintenance, and interactions of electrical, proton, and potassium potential gradients under lactic acid-stress and lactic acid fermentation. Further, we elucidate a gradient-mediated mechanism for intracellular pH sensing and stress response. We demonstrate that this gradient model can yield insights on the energetic limitations of membrane transport, and can predict bacterial behavior across changing environments.
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Affiliation(s)
- Marcus S. Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Matthew P. Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Caleb A. Hellman
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Nathan D. Schwalm
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Justin P. Jahnke
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Christian J. Sund
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
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3
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Fernández-Silva A, Juárez-Vázquez AL, González-Segura L, Juárez-Díaz JA, Muñoz-Clares RA. The uncharacterized Pseudomonas aeruginosa PA4189 is a novel and efficient aminoacetaldehyde dehydrogenase. Biochem J 2023; 480:259-281. [PMID: 36727473 DOI: 10.1042/bcj20220567] [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: 11/24/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/03/2023]
Abstract
Neither the Pseudomonas aeruginosa aldehyde dehydrogenase encoded by the PA4189 gene nor its ortholog proteins have been biochemically or structurally characterized and their physiological function is unknown. We cloned the PA4189 gene, obtained the PA4189 recombinant protein, and studied its structure-function relationships. PA4189 is an NAD+-dependent aminoaldehyde dehydrogenase highly efficient with protonated aminoacetaldehyde and 3-aminopropionaldehyde, which are much more preferred to the non-protonated species as indicated by pH studies. Based on the higher activity with aminoacetaldehyde than with 3-aminopropionaldehyde, we propose that aminoacetaldehyde might be the PA4189 physiological substrate. Even though at the physiological pH of P. aeruginosa cells the non-protonated aminoacetaldehyde species will be predominant, and despite the competition of these species with the protonated ones, PA4189 would very efficiently oxidize ACTAL in vivo, producing glycine. To our knowledge, PA4189 is the first reported enzyme that might metabolize ACTAL, which is considered a dead-end metabolite because its consuming reactions are unknown. The PA4189 crystal structure reported here suggested that the charge and size of the active-site residue Glu457, which narrows the aldehyde-entrance tunnel, greatly define the specificity for small positively charged aldehydes, as confirmed by the kinetics of the E457G and E457Q variants. Glu457 and the residues that determine Glu457 conformation inside the active site are conserved in the PA4189 orthologs, which we only found in proteobacteria species. Also is conserved the PA4189 genomic neighborhood, which suggests that PA4189 participates in an uncharacterized metabolic pathway. Our results open the door to future efforts to characterize this pathway.
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Affiliation(s)
- Arline Fernández-Silva
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Ana L Juárez-Vázquez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Lilian González-Segura
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Javier Andrés Juárez-Díaz
- Departamento de Biología Comparada, Facultad de Ciencias, Ciudad Universitaria, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Rosario A Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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4
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Harshaw NS, Meyer MD, Stella NA, Lehner KM, Kowalski RP, Shanks RMQ. The Short-chain Fatty Acid Propionic Acid Activates the Rcs Stress Response System Partially through Inhibition of d-Alanine Racemase. mSphere 2023; 8:e0043922. [PMID: 36645277 PMCID: PMC9942566 DOI: 10.1128/msphere.00439-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/16/2022] [Indexed: 01/17/2023] Open
Abstract
The Enterobacterial Rcs stress response system reacts to envelope stresses through a complex two-component phosphorelay system to regulate a variety of environmental response genes, such as capsular polysaccharide and flagella biosynthesis genes. However, beyond Escherichia coli, the stresses that activate Rcs are not well-understood. In this study, we used a Rcs system-dependent luminescent transcriptional reporter to screen a library of over 240 antimicrobial compounds for those that activated the Rcs system in Serratia marcescens, a Yersiniaceae family bacterium. Using an isogenic rcsB mutant to establish specificity, both new and expected activators were identified, including the short-chain fatty acid propionic acid, which is found at millimolar levels in the human gut. Propionic acid did not reduce the bacterial intracellular pH, as was hypothesized for its antibacterial mechanism. Instead, data suggest that the Rcs-activation by propionic acid is due, in part, to an inactivation of alanine racemase. This enzyme is responsible for the biosynthesis of d-alanine, which is an amino-acid that is required for the generation of bacterial cell walls. Consistent with what was observed in S. marcescens, in E. coli, alanine racemase mutants demonstrated elevated expression of the Rcs-reporter in a d-alanine-dependent and RcsB-dependent manner. These results suggest that host gut short-chain fatty acids can influence bacterial behavior via the activation of the Rcs stress response system. IMPORTANCE The Rcs bacterial stress response system responds to envelope stresses by globally altering gene expression to profoundly impact host-pathogen interactions, virulence, and antibiotic tolerance. In this study, a luminescent Rcs-reporter plasmid was used to screen a library of compounds for activators of Rcs. Among the strongest inducers was the short-chain fatty acid propionic acid, which is found at high concentrations in the human gut. This study suggests that gut short-chain fatty acids can affect both bacterial virulence and antibiotic tolerance via the induction of the Rcs system.
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Affiliation(s)
- Nathaniel S. Harshaw
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mitchell D. Meyer
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nicholas A. Stella
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kara M. Lehner
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Regis P. Kowalski
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert M. Q. Shanks
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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5
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Nieweglowska ES, Brilot AF, Méndez-Moran M, Kokontis C, Baek M, Li J, Cheng Y, Baker D, Bondy-Denomy J, Agard DA. The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nat Commun 2023; 14:927. [PMID: 36807264 PMCID: PMC9938867 DOI: 10.1038/s41467-023-36526-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 02/03/2023] [Indexed: 02/20/2023] Open
Abstract
To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the phage nucleus while other phage and host proteins are excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that nucleus fragments isolated from ϕPA3 infected Pseudomonas aeruginosa form a 2-dimensional lattice, having p2 or p4 symmetry. We further demonstrate that recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into similar 2D sheets with p2 and p4 symmetry. We resolve the dominant p2 symmetric state to 3.9 Å by cryo-EM. Our structure reveals a two-domain core, organized into quasi-symmetric tetramers. Flexible loops and termini mediate adaptable inter-tetramer contacts that drive subunit assembly into a lattice and enable the adoption of different symmetric states. While the interfaces between subunits are mostly well packed, two are open, forming channels that likely have functional implications for the transport of proteins, mRNA, and small molecules.
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Affiliation(s)
- Eliza S Nieweglowska
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Axel F Brilot
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
- Sauer Structural Biology Laboratory, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, USA
| | - Melissa Méndez-Moran
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Claire Kokontis
- Department of Microbiology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Minkyung Baek
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Junrui Li
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA
| | - Yifan Cheng
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David A Agard
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA.
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6
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Wu N, Zhang Y, Zhang S, Yuan Y, Liu S, Xu T, Cui P, Zhang W, Zhang Y. Polynucleotide Phosphorylase Mediates a New Mechanism of Persister Formation in Escherichia coli. Microbiol Spectr 2023; 11:e0154622. [PMID: 36475972 PMCID: PMC9927094 DOI: 10.1128/spectrum.01546-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Despite the identification of many genes and pathways involved in the persistence phenomenon in bacteria, the mechanisms of persistence are not well understood. Here, using Escherichia coli, we identified polynucleotide phosphorylase (PNPase) as a key regulator of persister formation. We constructed the pnp knockout strain (Δpnp) and its complemented strain and exposed them to antibiotics and stress conditions. The results showed that, compared with the wild-type strain W3110, the Δpnp strain had significant defects in persistence to antibiotics and stresses, and the persistence phenotype was restored upon complementation with the pnp gene. Transcriptome sequencing (RNA-seq) analysis revealed that 242 (166 upregulated and 76 downregulated) genes were differentially expressed in the Δpnp strain compared with the W3110 strain. KEGG analysis of the upregulated genes showed that these genes were mostly mapped to metabolism and virulence pathways, of which most are positively regulated by the global regulator cyclic AMP receptor protein (CRP). Correspondingly, the transcription level of the crp gene in the Δpnp strain increased 3.22-fold in the early stationary phase. We further explored the indicators of cellular metabolism of the Δpnp strain, the phenotype of the pnp and crp double-deletion mutant, and the transcriptional activity of the crp gene. Our results indicate that PNPase controls cellular metabolism by negatively regulating the crp operon via targeting the 5'-untranslated region of the crp transcript. This study reveals a persister mechanism and provides novel targets for the development of drugs against persisters for more effective treatment. IMPORTANCE Persisters pose significant challenges for a more effective treatment of persistent infections. An improved understanding of mechanisms of persistence will provide therapeutic targets important for the development of better treatments. Since recent studies with the key tuberculosis persister drug pyrazinamide have implicated polynucleotide phosphorylase (PNPase) as a drug target, in this study, we addressed the possibility that PNPase might be involved in persistence in Escherichia coli. Our study demonstrates PNPase indeed being involved in persistence, provides a mechanism by which PNPase controls persister formation, and suggests a new therapeutic target for treating persistent bacterial infections.
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Affiliation(s)
- Nan Wu
- Department of Clinical Laboratory, Shanghai Stomatological Hospital, Shanghai, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yumeng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shanshan Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Youhua Yuan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shuang Liu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Tao Xu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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7
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Martínez-García E, Fraile S, Algar E, Aparicio T, Velázquez E, Calles B, Tas H, Blázquez B, Martín B, Prieto C, Sánchez-Sampedro L, Nørholm MH, Volke D, Wirth N, Dvořák P, Alejaldre L, Grozinger L, Crowther M, Goñi-Moreno A, Nikel P, Nogales J, de Lorenzo V. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Res 2023; 51:D1558-D1567. [PMID: 36420904 PMCID: PMC9825617 DOI: 10.1093/nar/gkac1059] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/27/2022] Open
Abstract
The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.
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Affiliation(s)
- Esteban Martínez-García
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Sofía Fraile
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Algar
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Tomás Aparicio
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Velázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Huseyin Tas
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Blas Blázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | | | | | | | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pavel Dvořák
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500 Czech Republic
| | - Lorea Alejaldre
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Lewis Grozinger
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Matthew Crowther
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Angel Goñi-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Juan Nogales
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
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8
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Calero P, Gurdo N, Nikel PI. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ Microbiol 2022; 24:5082-5104. [PMID: 35726888 PMCID: PMC9796867 DOI: 10.1111/1462-2920.16110] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
The presence of mineral fluoride (F- ) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F- salts on the metabolism and physiology of environmental bacteria remained underexplored thus far. In this work, we studied and characterized tolerance mechanisms deployed by the model soil bacterium Pseudomonas putida KT2440 against NaF. By adopting systems-level omic approaches, including functional genomics and metabolomics, we gauged the impact of this anion at different regulatory levels under conditions that impair bacterial growth. Several genes involved in halide tolerance were isolated in a genome-wide Tn-Seq screening-among which crcB, encoding an F- -specific exporter, was shown to play the predominant role in detoxification. High-resolution metabolomics, combined with the assessment of intracellular and extracellular pH values and quantitative physiology experiments, underscored the key nodes in central carbon metabolism affected by the presence of F- . Taken together, our results indicate that P. putida undergoes a general, multi-level stress response when challenged with NaF that significantly differs from that caused by other saline stressors. While microbial stress responses to saline and oxidative challenges have been extensively studied and described in the literature, very little is known about the impact of fluoride (F- ) on bacterial physiology and metabolism. This state of affairs contrasts with the fact that F- is more abundant than other halides in the Earth crust (e.g. in some soils, the F- concentration can reach up to 1 mg gsoil -1 ). Understanding the global effects of NaF treatment on bacterial physiology is not only relevant to unveil distinct mechanisms of detoxification but it could also guide microbial engineering approaches for the target incorporation of fluorine into value-added organofluorine molecules. In this regard, the soil bacterium P. putida constitutes an ideal model to explore such scenarios, since this species is particularly known for its high level of stress resistance against a variety of physicochemical perturbations.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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9
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Huang J, Jiang Q, Yang M, Dykes GF, Weetman SL, Xin W, He HL, Liu LN. Probing the Internal pH and Permeability of a Carboxysome Shell. Biomacromolecules 2022; 23:4339-4348. [PMID: 36054822 PMCID: PMC9554877 DOI: 10.1021/acs.biomac.2c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The carboxysome is a protein-based nanoscale organelle
in cyanobacteria
and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)
and carbonic anhydrase (CA) within a polyhedral protein shell. The
intrinsic self-assembly and architectural features of carboxysomes
and the semipermeability of the protein shell provide the foundation
for the accumulation of CO2 within carboxysomes and enhanced
carboxylation. Here, we develop an approach to determine the interior
pH conditions and inorganic carbon accumulation within an α-carboxysome
shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell
permeability. By incorporating a pH reporter, pHluorin2, within empty
α-carboxysome shells produced in Escherichia
coli, we probe the interior pH of the protein shells
with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells
than the cytoplasmic pH and buffer pH, as well as the modulation of
the interior pH in response to changes in external environments, indicating
the shell permeability to bicarbonate ions and protons. We further
determine the saturated HCO3– concentration
of 15 mM within α-carboxysome shells and show the CA-mediated
increase in the interior CO2 level. Uncovering the interior
physiochemical microenvironment of carboxysomes is crucial for understanding
the mechanisms underlying carboxysomal shell permeability and enhancement
of Rubisco carboxylation within carboxysomes. Such fundamental knowledge
may inform reprogramming carboxysomes to improve metabolism and recruit
foreign enzymes for enhanced catalytical performance.
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Affiliation(s)
- Jiafeng Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,School of Life Sciences, Central South University, Changsha 410017, China
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Samantha L Weetman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271000, China
| | - Hai-Lun He
- School of Life Sciences, Central South University, Changsha 410017, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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10
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Lin WH, Jacobs-Wagner C. Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli. Curr Biol 2022; 32:3911-3924.e4. [PMID: 35961315 DOI: 10.1016/j.cub.2022.07.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/21/2022] [Accepted: 07/14/2022] [Indexed: 10/15/2022]
Abstract
Adenosine triphosphate (ATP) is an abundant and essential metabolite that cells consume and regenerate in large amounts to support growth. Although numerous studies have inferred the intracellular concentration of ATP in bacterial cultures, what happens in individual bacterial cells under stable growth conditions is less clear. Here, we use the QUEEN-2m biosensor to quantify ATP dynamics in single Escherichia coli cells in relation to their growth rate, metabolism, cell cycle, and cell lineage. We find that ATP dynamics are more complex than expected from population studies and are associated with growth-rate variability. Under stable nutrient-rich condition, cells can display large fluctuations in ATP level that are partially coordinated with the cell cycle. Abrogation of aerobic acetate fermentation (overflow metabolism) through genetic deletion considerably reduces both the amplitude of ATP level fluctuations and the cell-cycle trend. Similarly, growth in media in which acetate fermentation is lower or absent results in the reduction of ATP level fluctuation and cell-cycle trend. This suggests that overflow metabolism exhibits temporal dynamics, which contributes to fluctuating ATP levels during growth. Remarkably, at the single-cell level, growth rate negatively correlates with the amplitude of ATP fluctuation for each tested condition, linking ATP dynamics to growth-rate heterogeneity in clonal populations. Our work highlights the importance of single-cell analysis in studying metabolism and its implication to phenotypic diversity and cell growth.
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Affiliation(s)
- Wei-Hsiang Lin
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA; Chemistry, Engineering, Medicine for Human Health Institute, Stanford University, Palo Alto, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA; Chemistry, Engineering, Medicine for Human Health Institute, Stanford University, Palo Alto, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA.
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11
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Byun H, Park J, Fabia BU, Bingwa J, Nguyen MH, Lee H, Ahn JH. Generalized Approach towards Secretion-Based Protein Production via Neutralization of Secretion-Preventing Cationic Substrate Residues. Int J Mol Sci 2022; 23:ijms23126700. [PMID: 35743142 PMCID: PMC9223453 DOI: 10.3390/ijms23126700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 02/04/2023] Open
Abstract
Many heterologous proteins can be secreted by bacterial ATP-binding cassette (ABC) transporters, provided that they are fused with the C-terminal signal sequence, but some proteins are not secretable even though they carry the right signal sequence. The invention of a method to secrete these non-secretable proteins would be valuable both for understanding the secretory physiology of ABC transporters and for industrial applications. Herein, we postulate that cationic “supercharged” regions within the target substrate protein block the secretion by ABC transporters. We also suggest that the secretion of such substrate proteins can be rescued by neutralizing those cationic supercharged regions via structure-preserving point mutageneses. Surface-protruding, non-structural cationic amino acids within the cationic supercharged regions were replaced by anionic or neutral hydrophilic amino acids, reducing the cationic charge density. The examples of rescued secretions we provide include the spike protein of SARS-CoV-2, glutathione-S-transferase, streptavidin, lipase, tyrosinase, cutinase, growth factors, etc. In summary, our study provides a method to predict the secretability and a tool to rescue the secretion by correcting the secretion-blocking regions, making a significant step in understanding the physiological properties of ABC transporter-dependent protein secretion and laying the foundation for the development of a secretion-based protein-producing platform.
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Affiliation(s)
- Hyunjong Byun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea;
| | - Jiyeon Park
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, Korea; (J.P.); (B.U.F.); (J.B.); (M.H.N.)
| | - Benedict U. Fabia
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, Korea; (J.P.); (B.U.F.); (J.B.); (M.H.N.)
| | - Joshua Bingwa
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, Korea; (J.P.); (B.U.F.); (J.B.); (M.H.N.)
| | - Mihn Hieu Nguyen
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, Korea; (J.P.); (B.U.F.); (J.B.); (M.H.N.)
| | - Haeshin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Correspondence: (H.L.); (J.H.A.); Tel.: +82-10-8974-5141 (H.L.); +82-10-8826-6109 (J.H.A.)
| | - Jung Hoon Ahn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea;
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, Korea; (J.P.); (B.U.F.); (J.B.); (M.H.N.)
- Correspondence: (H.L.); (J.H.A.); Tel.: +82-10-8974-5141 (H.L.); +82-10-8826-6109 (J.H.A.)
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12
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Dual Effect: High NADH Levels Contribute to Efflux-Mediated Antibiotic Resistance but Drive Lethality Mediated by Reactive Oxygen Species. mBio 2022; 13:e0243421. [PMID: 35038918 PMCID: PMC8764520 DOI: 10.1128/mbio.02434-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In light of the antibiotic crisis, emerging strategies to sensitize bacteria to available antibiotics should be explored. Several studies on the mechanisms of killing suggest that bactericidal antibiotic activity is enforced through the generation of reactive oxygen species (ROS-lethality hypothesis). Here, we artificially manipulated the redox homeostasis of the model opportunistic pathogen Pseudomonas aeruginosa using specific enzymes that catalyze either the formation or oxidation of NADH. Increased NADH levels led to the activation of antibiotic efflux pumps and high levels of antibiotic resistance. However, higher NADH levels also resulted in increased intracellular ROS and amplified antibiotic killing. Our results demonstrate that growth inhibition and killing activity are mediated via different mechanisms. Furthermore, the profound changes in bioenergetics produced low-virulence phenotypes characterized by reduced interbacterial signaling controlled pathogenicity traits. Our results pave the way for a more effective infection resolution and add an antivirulence strategy to maximize chances to combat devastating P. aeruginosa infections while reducing the overall use of antibiotics. IMPORTANCE The emergence of antibiotic resistance has become one of the major threats to public health. A better understanding of antimicrobial killing mechanisms promises to uncover new ways to resensitize bacteria to commonly used antibiotics. In this context, there is increasing evidence that the metabolic status of the cell plays a fundamental role in reactive oxygen species (ROS)-mediated cell death. In this work, we artificially manipulated the redox balance in Pseudomonas aeruginosa by the expression of two orthologous enzymes. We found that the increase of intracellular NADH concentrations leads to higher antibiotic resistance but also generates a burst in the production of ROS that amplified antimicrobial killing. Our work suggests that the combination of bactericidal antibiotics with agents that disturb the cellular redox homeostasis could significantly enhance antibiotic killing via sensitization of pathogens to currently available antibiotics.
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13
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Biosynthesis of the Pseudomonas aeruginosa common polysaccharide antigen by D-Rhamnosyltransferases WbpX and WbpY. Glycoconj J 2022; 39:393-411. [PMID: 35166992 PMCID: PMC8853325 DOI: 10.1007/s10719-022-10040-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 12/28/2022]
Abstract
The Gram-negative bacterium Pseudomonas aeruginosa simultaneously expresses two O-antigenic glycoforms. While the O-specific antigen (OSA) is variable in composition, the common polysaccharide antigen (CPA) is highly conserved and is composed of a homopolymer of D-rhamnose (D-Rha) in trisaccharide repeating units [D-Rhaα1-2-D-Rhaα1-3-D-Rhaɑ1-3]n. We have previously reported that α3-D-Rha-transferase WbpZ transfers a D-Rha residue from GDP-D-Rha to D-GlcNAcα-O-PO3-PO3-(CH2)11-O-phenyl. Genes encoding two more D-Rha-transferases are found in the O antigen gene cluster (wbpX and wbpY). In this study we showed that WbpX and WbpY recombinantly expressed in E. coli differ in their donor and acceptor specificities and have properties of GT-B folded enzymes of the GT4 glycosyltransferase family. NMR spectroscopic analysis of the WbpY reaction product showed that WbpY transferred one D-Rha residue in α1-3 linkage to synthetic D-Rhaα1-3-D-GlcNAcα-O-PO3-PO3-(CH2)11-O-phenyl acceptor. WbpX synthesized several products that contained D-Rha in both α1-2 and α1-3 linkages. Mass spectrometry indicated that the mixture of WbpX and WbpY efficiently catalyzed the synthesis of D-Rha oligomers in a non-processive mechanism. Since O antigens are virulence factors, these findings open the door to advancing technology for antibacterial drug discovery and vaccine development.
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14
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Nam Y, Goo E, Kang Y, Hwang I. Membrane Depolarization and Apoptosis-Like Cell Death in an Alkaline Environment in the Rice Pathogen Burkholderia glumae. Front Microbiol 2021; 12:755596. [PMID: 34712216 PMCID: PMC8546246 DOI: 10.3389/fmicb.2021.755596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
The rice pathogen Burkholderia glumae uses amino acids as a principal carbon source and thus produces ammonia in amino acid-rich culture medium such as Luria-Bertani (LB) broth. To counteract ammonia-mediated environmental alkaline toxicity, the bacterium produces a public good, oxalate, in a quorum sensing (QS)-dependent manner. QS mutants of B. glumae experience alkaline toxicity and may undergo cell death at the stationary phase when grown in LB medium. Here, we show that the cell-death processes of QS mutants due to alkaline environmental conditions are similar to the apoptosis-like cell death reported in other bacteria. Staining QS mutants with bis-(1,3-dibutylbarbituric acid)-trimethine oxonol revealed membrane depolarization. CellROX™ staining showed excessive generation of reactive oxygen species (ROS) in QS mutants. The expression of genes encoding HNH endonuclease (BGLU_1G15690), oligoribonuclease (BGLU_1G09120), ribonuclease E (BGLU_1G09400), and Hu-beta (BGLU_1G13530) was significantly elevated in QS mutants compared to that in wild-type BGR1, consistent with the degradation of cellular materials as observed under transmission electron microscopy (TEM). A homeostatic neutral pH was not attainable by QS mutants grown in LB broth or by wild-type BGR1 grown in an artificially amended alkaline environment. At an artificially adjusted alkaline pH, wild-type BGR1 underwent apoptosis-like cell death similar to that observed in QS mutants. These results show that environmental alkaline stress interferes with homeostatic neutral cellular pH, induces membrane depolarization, and causes apoptosis-like cell death in B. glumae.
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Affiliation(s)
- Yewon Nam
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yongsung Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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15
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16
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Iwadate Y, Ramezanifard R, Golubeva YA, Fenlon LA, Slauch JM. PaeA (YtfL) protects from cadaverine and putrescine stress in Salmonella Typhimurium and E. coli. Mol Microbiol 2021; 115:1379-1394. [PMID: 33481283 PMCID: PMC10923242 DOI: 10.1111/mmi.14686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Salmonella and E. coli synthesize, import, and export cadaverine, putrescine, and spermidine to maintain physiological levels and provide pH homeostasis. Both low and high intracellular levels of polyamines confer pleiotropic phenotypes or lethality. Here, we demonstrate that the previously uncharacterized inner membrane protein PaeA (YtfL) is required for reducing cytoplasmic cadaverine and putrescine concentrations. We identified paeA as a gene involved in stationary phase survival when cells were initially grown in acidic medium, in which they produce cadaverine. The paeA mutant is also sensitive to putrescine, but not to spermidine or spermine. Sensitivity to external cadaverine in stationary phase is only observed at pH > 8, suggesting that the polyamines need to be deprotonated to passively diffuse into the cell cytoplasm. In the absence of PaeA, intracellular polyamine levels increase and the cells lose viability. Degradation or modification of the polyamines is not relevant. Ectopic expression of the known cadaverine exporter, CadB, in stationary phase partially suppresses the paeA phenotype, and overexpression of PaeA in exponential phase partially complements a cadB mutant grown in acidic medium. These data support the hypothesis that PaeA is a cadaverine/putrescine exporter, reducing potentially toxic levels under certain stress conditions.
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Affiliation(s)
- Yumi Iwadate
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Rouhallah Ramezanifard
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Yekaterina A. Golubeva
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Luke A. Fenlon
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
- Current address: Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, Utah 84132
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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17
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Biquet-Bisquert A, Labesse G, Pedaci F, Nord AL. The Dynamic Ion Motive Force Powering the Bacterial Flagellar Motor. Front Microbiol 2021; 12:659464. [PMID: 33927708 PMCID: PMC8076557 DOI: 10.3389/fmicb.2021.659464] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a rotary molecular motor embedded in the cell membrane of numerous bacteria. It turns a flagellum which acts as a propeller, enabling bacterial motility and chemotaxis. The BFM is rotated by stator units, inner membrane protein complexes that stochastically associate to and dissociate from individual motors at a rate which depends on the mechanical and electrochemical environment. Stator units consume the ion motive force (IMF), the electrochemical gradient across the inner membrane that results from cellular respiration, converting the electrochemical energy of translocated ions into mechanical energy, imparted to the rotor. Here, we review some of the main results that form the base of our current understanding of the relationship between the IMF and the functioning of the flagellar motor. We examine a series of studies that establish a linear proportionality between IMF and motor speed, and we discuss more recent evidence that the stator units sense the IMF, altering their rates of dynamic assembly. This, in turn, raises the question of to what degree the classical dependence of motor speed on IMF is due to stator dynamics vs. the rate of ion flow through the stators. Finally, while long assumed to be static and homogeneous, there is mounting evidence that the IMF is dynamic, and that its fluctuations control important phenomena such as cell-to-cell signaling and mechanotransduction. Within the growing toolbox of single cell bacterial electrophysiology, one of the best tools to probe IMF fluctuations may, ironically, be the motor that consumes it. Perfecting our incomplete understanding of how the BFM employs the energy of ion flow will help decipher the dynamical behavior of the bacterial IMF.
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Affiliation(s)
- Anaïs Biquet-Bisquert
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Francesco Pedaci
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Ashley L Nord
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
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18
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Arginine Decarboxylase Is Essential for Pneumococcal Stress Responses. Pathogens 2021; 10:pathogens10030286. [PMID: 33801541 PMCID: PMC7998104 DOI: 10.3390/pathogens10030286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 02/08/2023] Open
Abstract
Polyamines such as putrescine, cadaverine, and spermidine are small cationic molecules that play significant roles in cellular processes, including bacterial stress responses and host–pathogen interactions. Streptococcus pneumoniae is an opportunistic human pathogen, which causes several diseases that account for significant morbidity and mortality worldwide. As it transits through different host niches, S. pneumoniae is exposed to and must adapt to different types of stress in the host microenvironment. We earlier reported that S. pneumoniae TIGR4, which harbors an isogenic deletion of an arginine decarboxylase (ΔspeA), an enzyme that catalyzes the synthesis of agmatine in the polyamine synthesis pathway, has a reduced capsule. Here, we report the impact of arginine decarboxylase deletion on pneumococcal stress responses. Our results show that ΔspeA is more susceptible to oxidative, nitrosative, and acid stress compared to the wild-type strain. Gene expression analysis by qRT-PCR indicates that thiol peroxidase, a scavenger of reactive oxygen species and aguA from the arginine deiminase system, could be important for peroxide stress responses in a polyamine-dependent manner. Our results also show that speA is essential for endogenous hydrogen peroxide and glutathione production in S. pneumoniae. Taken together, our findings demonstrate the critical role of arginine decarboxylase in pneumococcal stress responses that could impact adaptation and survival in the host.
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Draft Genome Sequence of Multidrug-Resistant Pseudomonas protegens Strain 11HC2, Isolated from Marine Plastic Collected from the West Coast of Norway. Microbiol Resour Announc 2021; 10:10/2/e01285-20. [PMID: 33446595 PMCID: PMC7849708 DOI: 10.1128/mra.01285-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of multidrug-resistant Pseudomonas protegens strain 11HC2, isolated from polypropylene collected from the water column near a beach in Øygarden, Norway. The genome sequence is 6,861,219 bp long, with a G+C content of 63.4%. Strain 11HC2 is resistant to cefotaxime, ampicillin, trimethoprim, and chloramphenicol.
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20
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Kim NM, Sinnott RW, Sandoval NR. Transcription factor-based biosensors and inducible systems in non-model bacteria: current progress and future directions. Curr Opin Biotechnol 2020; 64:39-46. [DOI: 10.1016/j.copbio.2019.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 10/25/2022]
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