1
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Scribani Rossi C, Eckartt K, Scarchilli E, Angeli S, Price-Whelan A, Di Matteo A, Chevreuil M, Raynal B, Arcovito A, Giacon N, Fiorentino F, Rotili D, Mai A, Espinosa-Urgel M, Cutruzzolà F, Dietrich LEP, Paone A, Paiardini A, Rinaldo S. Molecular insights into RmcA-mediated c-di-GMP consumption: Linking redox potential to biofilm morphogenesis in Pseudomonas aeruginosa. Microbiol Res 2023; 277:127498. [PMID: 37776579 DOI: 10.1016/j.micres.2023.127498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
The ability of many bacteria to form biofilms contributes to their resilience and makes infections more difficult to treat. Biofilm growth leads to the formation of internal oxygen gradients, creating hypoxic subzones where cellular reducing power accumulates, and metabolic activities can be limited. The pathogen Pseudomonas aeruginosa counteracts the redox imbalance in the hypoxic biofilm subzones by producing redox-active electron shuttles (phenazines) and by secreting extracellular matrix, leading to an increased surface area-to-volume ratio, which favors gas exchange. Matrix production is regulated by the second messenger bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP) in response to different environmental cues. RmcA (Redox modulator of c-di-GMP) from P. aeruginosa is a multidomain phosphodiesterase (PDE) that modulates c-di-GMP levels in response to phenazine availability. RmcA can also sense the fermentable carbon source arginine via a periplasmic domain, which is linked via a transmembrane domain to four cytoplasmic Per-Arnt-Sim (PAS) domains followed by a diguanylate cyclase (DGC) and a PDE domain. The biochemical characterization of the cytoplasmic portion of RmcA reported in this work shows that the PAS domain adjacent to the catalytic domain tunes RmcA PDE activity in a redox-dependent manner, by differentially controlling protein conformation in response to FAD or FADH2. This redox-dependent mechanism likely links the redox state of phenazines (via FAD/FADH2 ratio) to matrix production as indicated by a hyperwrinkling phenotype in a macrocolony biofilm assay. This study provides insights into the role of RmcA in transducing cellular redox information into a structural response of the biofilm at the population level. Conditions of resource (i.e. oxygen and nutrient) limitation arise during chronic infection, affecting the cellular redox state and promoting antibiotic tolerance. An understanding of the molecular linkages between condition sensing and biofilm structure is therefore of crucial importance from both biological and engineering standpoints.
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Affiliation(s)
- Chiara Scribani Rossi
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Kelly Eckartt
- Department of Biological Sciences, Columbia University, New York, USA
| | - Elisabetta Scarchilli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Simone Angeli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | | | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, I-00185 Rome, Italy
| | - Maelenn Chevreuil
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
| | - Noah Giacon
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection. Estación Experimental del Zaidin, CSIC, Granada, Spain
| | - Francesca Cutruzzolà
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, USA
| | - Alessio Paone
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Alessandro Paiardini
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
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2
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Hoque NJ, Weinert EE. Control of bacterial second messenger signaling and motility by heme-based direct oxygen-sensing proteins. Curr Opin Microbiol 2023; 76:102396. [PMID: 37864983 DOI: 10.1016/j.mib.2023.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
Bacteria sense and respond to their environment, allowing them to maximize their survival and growth under changing conditions, such as oxygen levels. Direct oxygen-sensing proteins allow bacteria to rapidly sense concentration changes and adapt by regulating signaling pathways and/or cellular machinery. Recent work has identified roles for direct oxygen-sensing proteins in controlling second messenger levels and motility machinery, as well as effects on biofilm formation, virulence, and motility. In this review, we discuss recent progress in understanding O2-dependent regulation of cyclic di-GMP signaling and motility and highlight the emerging importance in controlling bacterial physiology and behavior.
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Affiliation(s)
- Nushrat J Hoque
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
| | - Emily E Weinert
- Department of Chemistry, Penn State University, University Park, PA 16802, USA; Department of Biochemistry & Molecular Biology, Penn State University, University Park, PA 16802, USA.
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3
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Yaeger LN, French S, Brown ED, Côté JP, Burrows LL. Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics. PLoS Genet 2023; 19:e1011013. [PMID: 37917668 PMCID: PMC10645362 DOI: 10.1371/journal.pgen.1011013] [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: 07/22/2023] [Revised: 11/14/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Exposure of Escherichia coli to sub-inhibitory antibiotics stimulates biofilm formation through poorly characterized mechanisms. Using a high-throughput Congo Red binding assay to report on biofilm matrix production, we screened ~4000 E. coli K12 deletion mutants for deficiencies in this biofilm stimulation response. We screened using three different antibiotics to identify core components of the biofilm stimulation response. Mutants lacking acnA, nuoE, or lpdA failed to respond to sub-MIC cefixime and novobiocin, implicating central metabolism and aerobic respiration in biofilm stimulation. These genes are members of the ArcA/B regulon-controlled by a respiration-sensitive two-component system. Mutants of arcA and arcB had a 'pre-activated' phenotype, where biofilm formation was already high relative to wild type in vehicle control conditions, and failed to increase further with the addition of sub-MIC cefixime. Using a tetrazolium dye and an in vivo NADH sensor, we showed spatial co-localization of increased metabolic activity with sub-lethal concentrations of the bactericidal antibiotics cefixime and novobiocin. Supporting a role for respiratory stress, the biofilm stimulation response to cefixime and novobiocin was inhibited when nitrate was provided as an alternative electron acceptor. Deletion of a gene encoding part of the machinery for respiring nitrate abolished its ameliorating effects, and nitrate respiration increased during growth with sub-MIC cefixime. Finally, in probing the generalizability of biofilm stimulation, we found that the stimulation response to translation inhibitors, unlike other antibiotic classes, was minimally affected by nitrate supplementation, suggesting that targeting the ribosome stimulates biofilm formation in distinct ways. By characterizing the biofilm stimulation response to sub-MIC antibiotics at a systems level, we identified multiple avenues for design of therapeutics that impair bacterial stress management.
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Affiliation(s)
- Luke N. Yaeger
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jean Philippe Côté
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Lori L. Burrows
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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4
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Hengge R, Pruteanu M, Stülke J, Tschowri N, Turgay K. Recent advances and perspectives in nucleotide second messenger signaling in bacteria. MICROLIFE 2023; 4:uqad015. [PMID: 37223732 PMCID: PMC10118264 DOI: 10.1093/femsml/uqad015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological versatility, the mechanistic diversity of second messenger synthesis, degradation, and action as well as the high level of integration of second messenger pathways and networks in prokaryotes has only recently become apparent. In these networks, specific second messengers play conserved general roles. Thus, (p)ppGpp coordinates growth and survival in response to nutrient availability and various stresses, while c-di-GMP is the nucleotide signaling molecule to orchestrate bacterial adhesion and multicellularity. c-di-AMP links osmotic balance and metabolism and that it does so even in Archaea may suggest a very early evolutionary origin of second messenger signaling. Many of the enzymes that make or break second messengers show complex sensory domain architectures, which allow multisignal integration. The multiplicity of c-di-GMP-related enzymes in many species has led to the discovery that bacterial cells are even able to use the same freely diffusible second messenger in local signaling pathways that can act in parallel without cross-talking. On the other hand, signaling pathways operating with different nucleotides can intersect in elaborate signaling networks. Apart from the small number of common signaling nucleotides that bacteria use for controlling their cellular "business," diverse nucleotides were recently found to play very specific roles in phage defense. Furthermore, these systems represent the phylogenetic ancestors of cyclic nucleotide-activated immune signaling in eukaryotes.
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Affiliation(s)
- Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
| | | | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
| | - Kürşad Turgay
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
- Max Planck Unit for the Science of Pathogens, 10115 Berlin, Germany
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5
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Wu D, Zhang Z, Li X, Han J, Hu Q, Yu Y, Mao Z. Cucurbit[10]uril-based supramolecular radicals: Powerful arms to kill facultative anaerobic bacteria. J Control Release 2023; 354:626-634. [PMID: 36681280 DOI: 10.1016/j.jconrel.2023.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/23/2023]
Abstract
Two water-soluble supramolecular complexes (CB[10]⊃PSA and CB[10]⊃TPE-cyc) are constructed based on the host-guest interaction between cucurbit[10]uril (CB[10]) and perylene diimide derivative (PSA) or tetracationic cyclophane (TPE-cyc). Attributing to the matched redox potential, both supramolecular complexes can be specifically reduced into corresponding supramolecular radical cations or anions by facultative anaerobic E. coli. Benefiting from the strong near-infrared (NIR) absorption, CB[10]⊃PSA radical anions and CB[10]⊃TPE-cyc radical cations act as efficient NIR photosensitizers and perform an excellent antimicrobial activity (close to 100%) via PTT. In addition, the biocompatibility of TPE-cyc is notably improved under the protection of CB[10], guaranteeing its biosafety for in vivo application. CB[10]⊃PSA radical anions and CB[10]⊃TPE-cyc radical cations are in situ generated in the E. coli-infected abscess of mice and effectively inhibit the bacterial infection without obvious system toxicity. It is anticipated that this supramolecular strategy may pave a new way for the selective bacteria inhibition to regulate the balance of different bacterial flora.
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Affiliation(s)
- Dan Wu
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhankui Zhang
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xinyue Li
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jin Han
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China..
| | - Qinglian Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China..
| | - Yuan Yu
- Zhejiang Provincial Key Laboratory of Fiber Materials and Manufacturing Technology, Zhejiang Sci-Tech University, Hangzhou 310018, PR China..
| | - Zhengwei Mao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, PR China..
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6
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Martín-Rodríguez AJ. Respiration-induced biofilm formation as a driver for bacterial niche colonization. Trends Microbiol 2023; 31:120-134. [PMID: 36075785 DOI: 10.1016/j.tim.2022.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.
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7
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Liang Q, Zhang Y, Zhang H, Wu S, Gong W, Perrett S. Reversible Redox-Dependent Conformational Switch of the C-Terminal α-Helical Lid of Human Hsp70 Observed by In-Cell NMR. ACS Chem Biol 2023; 18:176-183. [PMID: 36524733 DOI: 10.1021/acschembio.2c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glutathionylation of human stress-inducible Hsp70 (hHsp70) under oxidative stress conditions has been suggested to act as an on/off switch of hHsp70 chaperone activity and thus transfer redox signals to hHsp70 clients through a change in conformation. The mechanism of this switch involves unfolding of the C-terminal α-helical lid, SBDα, upon glutathionylation, which then binds to and blocks the hHsp70 substrate-binding site. This process is reversible and redox-regulated and has been demonstrated for purified protein in solution. Here, we found that this redox-regulated reversible process also occurs in the cellular environment. Using Escherichia coli as a model system, in-cell NMR data clearly indicate that hHsp70 SBDα undergoes a conformational transition from ordered to disordered after diamide stimulation. The disordered SBDα could spontaneously recover back to the helix bundle conformation over time. This oxidative-stress induced process also occurred in cell lysate, with a similar unfolding rate as in cells, but the refolding rate was significantly slower in cell lysate. Increased temperature accelerates this process. Under heat stress alone, unfolding of the SBDα could not be detected in cells. Our in-cell NMR results provide direct support for the molecular switch model of hHsp70 redox regulation and also demonstrate the power of in-cell NMR for real-time study of protein structures during biological processes in living cells.
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Affiliation(s)
- Qihui Liang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yiying Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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8
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HslO ameliorates arrested ΔrecA polA cell growth and reduces DNA damage and oxidative stress responses. Sci Rep 2022; 12:22182. [PMID: 36564489 PMCID: PMC9789031 DOI: 10.1038/s41598-022-26703-z] [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: 07/04/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Chromosome damage combined with defective recombinase activity has been widely considered to render cells inviable, owing to deficient double-strand break repair. However, temperature-sensitive recAts polA cells grow well upon induction of DNA damage and supplementation with catalase at restrictive temperatures. These treatments reduce intracellular reactive oxygen species (ROS) levels, which suggests that recAts polA cells are susceptible to ROS, but not chronic chromosome damage. Therefore, we investigated whether polA cells can tolerate a complete lack of recombinase function. We introduced a ΔrecA allele in polA cells in the presence or absence of the hslO-encoding redox molecular chaperon Hsp33 expression plasmid. Induction of the hslO gene with IPTG resulted in increased cell viability in ΔrecA polA cells with the hslO expression plasmid. ΔrecA polA cells in the absence of the hslO expression plasmid showed rich medium sensitivity with increasing ROS levels. Adding catalase to the culture medium considerably rescued growth arrest and decreased ROS. These results suggest that hslO expression manages oxidative stress to an acceptable level in cells with oxidative damage and rescues cell growth. Overall, ROS may regulate several processes, from damage response to cell division, via ROS-sensitive cell metabolism.
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9
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Kaidow A, Ishii N, Suzuki S, Shiina T, Kasahara H. Reactive oxygen species accumulation is synchronised with growth inhibition of temperature-sensitive recAts polA Escherichia coli. Arch Microbiol 2022; 204:396. [PMID: 35705748 PMCID: PMC9200703 DOI: 10.1007/s00203-022-02957-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
When combined with recombinase defects, chromosome breakage and double-strand break repair deficiencies render cells inviable. However, cells are viable when an SOS response occurs in recAts polA cells in Escherichia coli. Here, we aimed to elucidate the underlying mechanisms of this process. Transposon mutagenesis revealed that the hslO gene, a redox chaperone Hsp33 involved in reactive oxidative species (ROS) metabolism, was required for the suppression of recAts polA lethality at a restricted temperature. Recently, it has been reported that lethal treatments trigger ROS accumulation. We also found that recAts polA cells accumulated ROS at the restricted temperature. A catalase addition to the medium alleviates the temperature sensitivity of recAts polA cells and decreases ROS accumulation. These results suggest that the SOS response and hslO manage oxidative insult to an acceptable level in cells with oxidative damage and rescue cell growth. Overall, ROS might regulate several cellular processes.
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Affiliation(s)
- Akihiro Kaidow
- Department of Biology, School of Biology, Tokai University, Sapporo, 005-8601, Japan.
| | - Noriko Ishii
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
| | - Sinngo Suzuki
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Hirokazu Kasahara
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
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10
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Hu H, Wang H, Yang Y, Xu JF, Zhang X. A Bacteria-Responsive Porphyrin for Adaptable Photodynamic/Photothermal Therapy. Angew Chem Int Ed Engl 2022; 61:e202200799. [PMID: 35332634 DOI: 10.1002/anie.202200799] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 12/17/2022]
Abstract
We report a cationic porphyrin 5,10,15,20-tetrakis-(4-N-methylpyridyl)-porphyrin (TMPyP) that can respond to specific bacteria, followed by adaptable photodynamic/photothermal therapy processes. TMPyP could be reduced to phlorin by facultative anaerobes with a strong reducing ability such as E. coli and S. typhimurium in hypoxic environments, possessing strong NIR absorption and remarkable photothermal conversion capacity, thus demonstrating excellent antimicrobial activity (>99 %) by photothermal therapy. While in an aerobic environment with aerobic bacteria, TMPyP functioned as a typical photosensitizer that killed bacteria effectively (>99.9 %) by photodynamic therapy. By forming a host-guest complex with cucurbit[7]uril, the biocompatibility of TMPyP significantly improved. This kind of bacteria-responsive porphyrin shows specificity and adaptivity in antimicrobial treatment and holds potential in non-invasive treatments of bacterial infections.
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Affiliation(s)
- Hao Hu
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hua Wang
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yuchong Yang
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jiang-Fei Xu
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xi Zhang
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
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11
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Katharios-Lanwermeyer S, O’Toole GA. Biofilm Maintenance as an Active Process: Evidence that Biofilms Work Hard to Stay Put. J Bacteriol 2022; 204:e0058721. [PMID: 35311557 PMCID: PMC9017327 DOI: 10.1128/jb.00587-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Biofilm formation represents a critical strategy whereby bacteria can tolerate otherwise damaging environmental stressors and antimicrobial insults. While the mechanisms bacteria use to establish a biofilm and disperse from these communities have been well-studied, we have only a limited understanding of the mechanisms required to maintain these multicellular communities. Indeed, until relatively recently, it was not clear that maintaining a mature biofilm could be considered an active, regulated process with dedicated machinery. Using Pseudomonas aeruginosa as a model system, we review evidence from recent studies that support the model that maintenance of these persistent, surface-attached communities is indeed an active process. Biofilm maintenance mechanisms include transcriptional regulation and second messenger signaling (including the production of extracellular polymeric substances). We also discuss energy-conserving pathways that play a key role in the maintenance of these communities. We hope to highlight the need for further investigation to uncover novel biofilm maintenance pathways and suggest the possibility that such pathways can serve as novel antibiofilm targets.
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Affiliation(s)
| | - G. A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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12
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Hu H, Wang H, Yang Y, Xu J, Zhang X. A Bacteria‐Responsive Porphyrin for Adaptable Photodynamic/Photothermal Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hao Hu
- Key Lab of Organic Optoelectronics & Molecular Engineering Department of Chemistry Tsinghua University Beijing 100084 China
| | - Hua Wang
- Key Lab of Organic Optoelectronics & Molecular Engineering Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yuchong Yang
- Key Lab of Organic Optoelectronics & Molecular Engineering Department of Chemistry Tsinghua University Beijing 100084 China
| | - Jiang‐Fei Xu
- Key Lab of Organic Optoelectronics & Molecular Engineering Department of Chemistry Tsinghua University Beijing 100084 China
| | - Xi Zhang
- Key Lab of Organic Optoelectronics & Molecular Engineering Department of Chemistry Tsinghua University Beijing 100084 China
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13
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Tejedor-Sanz S, Stevens ET, Li S, Finnegan P, Nelson J, Knoesen A, Light SH, Ajo-Franklin CM, Marco ML. Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism. eLife 2022; 11:e70684. [PMID: 35147079 PMCID: PMC8837199 DOI: 10.7554/elife.70684] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD+/NADH ratio, generate more ATP through substrate-level phosphorylation, and accumulate biomass more rapidly. This novel, hybrid metabolism is dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally requires a flavin-binding extracellular lipoprotein (PplA) under laboratory conditions. It confers increased fermentation product yield, metabolic flux, and environmental acidification in laboratory media and during kale juice fermentation. The discovery of a single pathway that simultaneously blends features of fermentation and respiration in a primarily fermentative microorganism expands our knowledge of energy conservation and provides immediate biotechnology applications.
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Affiliation(s)
- Sara Tejedor-Sanz
- Department of BioSciences, Rice UniversityHoustonUnited States
- Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Eric T Stevens
- Department of Food Science & Technology, University of California‐DavisDavisUnited States
| | - Siliang Li
- Department of BioSciences, Rice UniversityHoustonUnited States
| | - Peter Finnegan
- Department of Food Science & Technology, University of California‐DavisDavisUnited States
| | - James Nelson
- Department of Electrical and Computer Engineering, University of California‐DavisDavisUnited States
| | - Andre Knoesen
- Department of Electrical and Computer Engineering, University of California‐DavisDavisUnited States
| | - Samuel H Light
- Department of Microbiology, University of ChicagoChicagoUnited States
| | - Caroline M Ajo-Franklin
- Department of BioSciences, Rice UniversityHoustonUnited States
- Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Maria L Marco
- Department of Food Science & Technology, University of California‐DavisDavisUnited States
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14
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Biondo M, Panuzzo C, Ali SM, Bozzaro S, Osella M, Bracco E, Pergolizzi B. The Dynamics of Aerotaxis in a Simple Eukaryotic Model. Front Cell Dev Biol 2021; 9:720623. [PMID: 34888305 PMCID: PMC8650612 DOI: 10.3389/fcell.2021.720623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/13/2021] [Indexed: 01/09/2023] Open
Abstract
In aerobic organisms, oxygen is essential for efficient energy production, and it acts as the last acceptor of the mitochondrial electron transport chain and as regulator of gene expression. However, excessive oxygen can lead to production of deleterious reactive oxygen species. Therefore, the directed migration of single cells or cell clumps from hypoxic areas toward a region of optimal oxygen concentration, named aerotaxis, can be considered an adaptive mechanism that plays a major role in biological and pathological processes. One relevant example is the development of O2 gradients when tumors grow beyond their vascular supply, leading frequently to metastasis. In higher eukaryotic organisms, aerotaxis has only recently begun to be explored, but genetically amenable model organisms suitable to dissect this process remain an unmet need. In this regard, we sought to assess whether Dictyostelium cells, which are an established model for chemotaxis and other motility processes, could sense oxygen gradients and move directionally in their response. By assessing different physical parameters, our findings indicate that both growing and starving Dictyostelium cells under hypoxic conditions migrate directionally toward regions of higher O2 concentration. This migration is characterized by a specific pattern of cell arrangement. A thickened circular front of high cell density (corona) forms in the cell cluster and persistently moves following the oxygen gradient. Cells in the colony center, where hypoxia is more severe, are less motile and display a rounded shape. Aggregation-competent cells forming streams by chemotaxis, when confined under hypoxic conditions, undergo stream or aggregate fragmentation, giving rise to multiple small loose aggregates that coordinately move toward regions of higher O2 concentration. By testing a panel of mutants defective in chemotactic signaling, and a catalase-deficient strain, we found that the latter and the pkbR1null exhibited altered migration patterns. Our results suggest that in Dictyostelium, like in mammalian cells, an intracellular accumulation of hydrogen peroxide favors the migration toward optimal oxygen concentration. Furthermore, differently from chemotaxis, this oxygen-driven migration is a G protein-independent process.
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Affiliation(s)
- Marta Biondo
- Department of Physics, INFN, University of Turin, Turin, Italy
| | - Cristina Panuzzo
- Department of Clinical and Biological Science, University of Turin, Turin, Italy
| | - Shahzad M Ali
- Department of Clinical and Biological Science, University of Turin, Turin, Italy
| | - Salvatore Bozzaro
- Department of Clinical and Biological Science, University of Turin, Turin, Italy
| | - Matteo Osella
- Department of Physics, INFN, University of Turin, Turin, Italy
| | - Enrico Bracco
- Department of Oncology, University of Turin, Turin, Italy
| | - Barbara Pergolizzi
- Department of Clinical and Biological Science, University of Turin, Turin, Italy
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15
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Woo V, Eshleman EM, Hashimoto-Hill S, Whitt J, Wu SE, Engleman L, Rice T, Karns R, Qualls JE, Haslam DB, Vallance BA, Alenghat T. Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. Cell Host Microbe 2021; 29:1744-1756.e5. [PMID: 34678170 DOI: 10.1016/j.chom.2021.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 07/14/2021] [Accepted: 09/21/2021] [Indexed: 12/30/2022]
Abstract
Interactions between the microbiota and mammalian host are essential for defense against infection, but the microbial-derived cues that mediate this relationship remain unclear. Here, we find that intestinal epithelial cell (IEC)-associated commensal bacteria, segmented filamentous bacteria (SFB), promote early protection against the pathogen Citrobacter rodentium, independent of CD4+ T cells. SFB induced histone modifications in IECs at sites enriched for retinoic acid receptor motifs, suggesting that SFB may enhance defense through retinoic acid (RA). Consistent with this, inhibiting RA signaling suppressed SFB-induced protection. Intestinal RA levels were elevated in SFB mice, despite the inhibition of mammalian RA production, indicating that SFB directly modulate RA. Interestingly, RA was produced by intestinal bacteria, and the loss of bacterial-intrinsic aldehyde dehydrogenase activity decreased the RA levels and increased infection. These data reveal RA as an unexpected microbiota-derived metabolite that primes innate defense and suggests that pre- and probiotic approaches to elevate RA could prevent or combat infections.
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Affiliation(s)
- Vivienne Woo
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Emily M Eshleman
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Seika Hashimoto-Hill
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Jordan Whitt
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Shu-En Wu
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Laura Engleman
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Taylor Rice
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joseph E Qualls
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - David B Haslam
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Bruce A Vallance
- Department of Pediatrics, BC Children's Hospital Research Institute and the University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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16
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Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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17
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Antifungal Effects of Fusion Puroindoline B on the Surface and Intracellular Environment of Aspergillus flavus. Probiotics Antimicrob Proteins 2021; 13:249-260. [PMID: 32488675 DOI: 10.1007/s12602-020-09667-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aspergillus flavus infection is a major issue for safe food storage. In this study, we constructed an efficient prokaryotic expression system for puroindoline B (PINB) protein to detect its antifungal activity. The Puroindoline b gene was cloned into pET-28a (+) vector and expressed in Escherichia coli. Treatment with fusion PINB revealed that it inhibits mycelial growth of A. flavus, a common grain mold. Moreover, fusion PINB-treated A. flavus mycelium withered and exhibited a sunken spore head. As fusion PINB concentration increased, electrical conductivity in mycelium also increased, indicative of cell membrane damage. Furthermore, intracellular malate dehydrogenase and succinate dehydrogenase activity decreased, revealing a disruption in the tricarboxylic acid cycle. Moreover, the dampened activity of the ion pump Na+K+-ATPase negatively affected the intracellular regulation of both ions. Catalase and superoxide dismutase activity decreased, thus reducing antioxidant capacity, a result confirmed with an increase in malondialdehyde content. Changes to the GSH/GSSG ratio indicated a shift to an intracellular oxidative state. At the same time, laser scanning confocal microscopy assay showed the accumulation of reactive oxygen species and nuclear damage. Therefore, the PINB fusion protein may have the potential to control A. flavus in grain storage and food preservation.
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18
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Abstract
Bacteria are electrically powered organisms; cells maintain an electrical potential across their plasma membrane as a source of free energy to drive essential processes. In recent years, however, bacterial membrane potential has been increasingly recognized as dynamic. Those dynamics have been implicated in diverse physiological functions and behaviors, including cell division and cell-to-cell signaling. In eukaryotic cells, such dynamics play major roles in coupling bioelectrical stimuli to changes in internal cell states. Neuroscientists and physiologists have established detailed molecular pathways that transduce eukaryotic membrane potential dynamics to physiological and gene expression responses. We are only just beginning to explore these intracellular responses to bioelectrical activity in bacteria. In this review, we summarize progress in this area, including evidence of gene expression responses to stimuli from electrodes and mechanically induced membrane potential spikes. We argue that the combination of provocative results, missing molecular detail, and emerging tools makes the investigation of bioelectrically induced long-term intracellular responses an important and rewarding effort in the future of microbiology.
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Affiliation(s)
- Joshua M Jones
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Joseph W Larkin
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
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19
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Zinatullina KM, Kasaikina OT, Khrameeva NP, Indeykina MI, Kononikhin AS. Interaction between Glutathione and Resveratrol in the Presence of Hydrogen Peroxide: A Kinetic Model. KINETICS AND CATALYSIS 2021. [DOI: 10.1134/s0023158421020130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Barraud N, Létoffé S, Beloin C, Vinh J, Chiappetta G, Ghigo JM. Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress. NPJ Biofilms Microbiomes 2021; 7:34. [PMID: 33850153 PMCID: PMC8044216 DOI: 10.1038/s41522-021-00203-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/18/2021] [Indexed: 02/03/2023] Open
Abstract
Communities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen, and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteine S-nitrosylation in aerobic and anaerobic biofilm and planktonic Escherichia coli cultures and we identified proteins with biofilm-specific S-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairing S-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG, and GltD altered important biofilm properties, including motility, biofilm maturation, or resistance to oxidative stress. Our study therefore revealed that S-nitrosylation constitutes a physiological basis underlying functions critical for E. coli adaptation to the biofilm environment.
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Affiliation(s)
- Nicolas Barraud
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France
| | - Sylvie Létoffé
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France
| | - Joelle Vinh
- Biological Mass Spectrometry and Proteomics (SMBP), ESPCI Paris, Université PSL, CNRS FRE2032, 75005, Paris, France
| | - Giovanni Chiappetta
- Biological Mass Spectrometry and Proteomics (SMBP), ESPCI Paris, Université PSL, CNRS FRE2032, 75005, Paris, France.
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, Paris, France.
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21
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Antibiofilm properties of copper (II) and iron (III) complexes with an EDTA-based phenylene macrocycle and its acyclic analogue against food and clinical related pathogens. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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22
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Lee IG, Lee BJ. How Bacterial Redox Sensors Transmit Redox Signals via Structural Changes. Antioxidants (Basel) 2021; 10:antiox10040502. [PMID: 33804871 PMCID: PMC8063818 DOI: 10.3390/antiox10040502] [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: 02/17/2021] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 01/17/2023] Open
Abstract
Bacteria, like humans, face diverse kinds of stress during life. Oxidative stress, which is produced by cellular metabolism and environmental factors, can significantly damage cellular macromolecules, ultimately negatively affecting the normal growth of the cell. Therefore, bacteria have evolved a number of protective strategies to defend themselves and respond to imposed stress by changing the expression pattern of genes whose products are required to convert harmful oxidants into harmless products. Structural biology combined with biochemical studies has revealed the mechanisms by which various bacterial redox sensor proteins recognize the cellular redox state and transform chemical information into structural signals to regulate downstream signaling pathways.
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Affiliation(s)
- In-Gyun Lee
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Korea;
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
- Correspondence:
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23
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Nothling MD, Cao H, McKenzie TG, Hocking DM, Strugnell RA, Qiao GG. Bacterial Redox Potential Powers Controlled Radical Polymerization. J Am Chem Soc 2021; 143:286-293. [PMID: 33373526 DOI: 10.1021/jacs.0c10673] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microbes employ a remarkably intricate electron transport system to extract energy from the environment. The respiratory cascade of bacteria culminates in the terminal transfer of electrons onto higher redox potential acceptors in the extracellular space. This general and inducible mechanism of electron efflux during normal bacterial proliferation leads to a characteristic fall in bulk redox potential (Eh), the degree of which is dependent on growth phase, the microbial taxa, and their physiology. Here, we show that the general reducing power of bacteria can be subverted to induce the abiotic production of a carbon-centered radical species for targeted bioorthogonal molecular synthesis. Using two species, Escherichia coli and Salmonella enterica serovar Typhimurium as model microbes, a common redox active aryldiazonium salt is employed to intervene in the terminal respiratory electron flow, affording radical production that is mediated by native redox-active molecular shuttles and active bacterial metabolism. The aryl radicals are harnessed to initiate and sustain a bioorthogonal controlled radical polymerization via reversible addition-fragmentation chain transfer (BacRAFT), yielding a synthetic extracellular matrix of "living" vinyl polymers with predetermined molecular weight and low dispersity. The ability to interface the ubiquitous reducing power of bacteria into synthetic materials design offers a new means for creating engineered living materials with promising adaptive and self-regenerative capabilities.
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Affiliation(s)
- Mitchell D Nothling
- Department of Chemical Engineering, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thomas G McKenzie
- Department of Chemical Engineering, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Dianna M Hocking
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Greg G Qiao
- Department of Chemical Engineering, University of Melbourne, Melbourne, VIC 3010, Australia
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24
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Rode DK, Singh PK, Drescher K. Multicellular and unicellular responses of microbial biofilms to stress. Biol Chem 2020; 401:1365-1374. [DOI: 10.1515/hsz-2020-0213] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/11/2020] [Indexed: 12/28/2022]
Abstract
AbstractBiofilms are a ubiquitous mode of microbial life and display an increased tolerance to different stresses. Inside biofilms, cells may experience both externally applied stresses and internal stresses that emerge as a result of growth in spatially structured communities. In this review, we discuss the spatial scales of different stresses in the context of biofilms, and if cells in biofilms respond to these stresses as a collection of individual cells, or if there are multicellular properties associated with the response. Understanding the organizational level of stress responses in microbial communities can help to clarify multicellular functions of biofilms.
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Affiliation(s)
- Daniel K.H. Rode
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
| | - Praveen K. Singh
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
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25
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Bhatt AH, Ren ZJ, Tao L. Value Proposition of Untapped Wet Wastes: Carboxylic Acid Production through Anaerobic Digestion. iScience 2020; 23:101221. [PMID: 32563151 PMCID: PMC7305404 DOI: 10.1016/j.isci.2020.101221] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/28/2020] [Accepted: 05/28/2020] [Indexed: 02/02/2023] Open
Abstract
Although traditional anaerobic digestion (AD) process to produce methane-rich biogas from wet waste is deep-rooted, high carbon footprint and its low value as compared with other renewable sources demand advanced strategies to avoid its production. An emerging conversion pathway to arrest methanogenesis for producing value-added fuels and chemicals instead of biogas is sought as a sustainable alternative. This research provides a comprehensive analysis on current technology development, process challenges, applications, and economics for producing high-value short-chain carboxylic acids from AD of wet wastes. We show that (1) the theoretical energy yields of acids equal or exceed biogas, and (2) the cost of these acids is competitive with those produced from chemical markets, making this economically viable for mass production. With global abundance of wet waste feedstocks, this process of short-chain acid production provides a promising alternative to conventional biogas production technology, while achieving waste management and carbon mitigation goals.
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Affiliation(s)
- Arpit H Bhatt
- Strategic Energy Analysis Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Zhiyong Jason Ren
- Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Ling Tao
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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26
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The SrrAB two-component system regulates Staphylococcus aureus pathogenicity through redox sensitive cysteines. Proc Natl Acad Sci U S A 2020; 117:10989-10999. [PMID: 32354997 DOI: 10.1073/pnas.1921307117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus infections can lead to diseases that range from localized skin abscess to life-threatening toxic shock syndrome. The SrrAB two-component system (TCS) is a global regulator of S. aureus virulence and critical for survival under environmental conditions such as hypoxic, oxidative, and nitrosative stress found at sites of infection. Despite the critical role of SrrAB in S. aureus pathogenicity, the mechanism by which the SrrAB TCS senses and responds to these environmental signals remains unknown. Bioinformatics analysis showed that the SrrB histidine kinase contains several domains, including an extracellular Cache domain and a cytoplasmic HAMP-PAS-DHp-CA region. Here, we show that the PAS domain regulates both kinase and phosphatase enzyme activity of SrrB and present the structure of the DHp-CA catalytic core. Importantly, this structure shows a unique intramolecular cysteine disulfide bond in the ATP-binding domain that significantly affects autophosphorylation kinetics. In vitro data show that the redox state of the disulfide bond affects S. aureus biofilm formation and toxic shock syndrome toxin-1 production. Moreover, with the use of the rabbit infective endocarditis model, we demonstrate that the disulfide bond is a critical regulatory element of SrrB function during S. aureus infection. Our data support a model whereby the disulfide bond and PAS domain of SrrB sense and respond to the cellular redox environment to regulate S. aureus survival and pathogenesis.
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27
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Catovic C, Martin S, Desaint S, Borges C, Lesouhaitier H, Roullet F, Bresciani N, Jouault AM, Poulet V, Luc J, Joulia V, Jupin A, Masson C, Crozier A, Feuilloley MGJ. Development of a standardized method to evaluate the protective efficiency of cosmetic packaging against microbial contamination. AMB Express 2020; 10:81. [PMID: 32333203 PMCID: PMC7182652 DOI: 10.1186/s13568-020-01016-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/18/2020] [Indexed: 02/01/2023] Open
Abstract
Doubts surrounding the potential adverse effects of antimicrobial preservatives have modified the demand of consumers, who increasingly insist on the production of low-level and even preservative-free cosmetics. Protection of the product against microbial contamination is therefore focused on the packaging. This has prompted the emergence of a highly diverse array of so-called “protective”, “overprotective”, and “barrier” packaging. However, these designations are not normalized and the choice of the right packaging adapted to each cosmetic product is still essentially empirical, hazardous, and time consuming. The Cosmetic Valleys cluster has launched a commission to define a complete and experimentally-validated method to classify the level of protection of cosmetic packaging against microbial contamination. As reported herein, this required the development a specific bacteriostatic medium that can be used for 7 days and an in vitro procedure that reproduces in-use contamination and consumer practices. Based on tests performed on over 800 packages of different origin and performance characteristics, we propose a classification, divided into six grades, to differentiate the protective efficiency of cosmetic packaging. This work can be considered as a first step towards a regulatory text.
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Affiliation(s)
- Chloe Catovic
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), Normandie Univ, Univ. Rouen, 55 rue Saint-Germain, 27000, Evreux, France
| | | | - Stéphane Desaint
- Laboratoires de Biologie Végétale Yves Rocher, Innovation & Développement, 92130, Issy les Moulineaux, France
| | | | | | | | | | | | | | - Joelle Luc
- Laboratoires Pierre Fabre Dermo Cosmétique, 31322, Castanet Tolosan, France
| | - Valérie Joulia
- Laboratoires Pierre Fabre Dermo Cosmétique, 31322, Castanet Tolosan, France
| | | | | | - Alain Crozier
- Clean Cosmetic Consulting, 77420, Champs Sur Marne, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), Normandie Univ, Univ. Rouen, 55 rue Saint-Germain, 27000, Evreux, France.
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28
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Hengge R. Linking bacterial growth, survival, and multicellularity - small signaling molecules as triggers and drivers. Curr Opin Microbiol 2020; 55:57-66. [PMID: 32244175 DOI: 10.1016/j.mib.2020.02.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 02/05/2023]
Abstract
An overarching theme of cellular regulation in bacteria arises from the trade-off between growth and stress resilience. In addition, the formation of biofilms contributes to stress survival, since these dense multicellular aggregates, in which cells are embedded in an extracellular matrix of self-produced polymers, represent a self-constructed protective and homeostatic 'niche'. As shown here for the model bacterium Escherichia coli, the inverse coordination of bacterial growth with survival and the transition to multicellularity is achieved by a highly integrated regulatory network with several sigma subunits of RNA polymerase and a small number of transcriptional hubs as central players. By conveying information about the actual (micro)environments, nucleotide second messengers such as cAMP, (p)ppGpp, and in particular c-di-GMP are the key triggers and drivers that promote either growth or stress resistance and organized multicellularity in a world of limited resources.
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Affiliation(s)
- Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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Chu N, Liang Q, Jiang Y, Zeng RJ. Microbial electrochemical platform for the production of renewable fuels and chemicals. Biosens Bioelectron 2020; 150:111922. [DOI: 10.1016/j.bios.2019.111922] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 12/01/2022]
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Rodríguez-Arce I, Al-Jubair T, Euba B, Fernández-Calvet A, Gil-Campillo C, Martí S, Törnroth-Horsefield S, Riesbeck K, Garmendia J. Moonlighting of Haemophilus influenzae heme acquisition systems contributes to the host airway-pathogen interplay in a coordinated manner. Virulence 2019; 10:315-333. [PMID: 30973092 PMCID: PMC6550540 DOI: 10.1080/21505594.2019.1596506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Nutrient iron sequestration is the most significant form of nutritional immunity and causes bacterial pathogens to evolve strategies of host iron scavenging. Cigarette smoking contains iron particulates altering lung and systemic iron homeostasis, which may enhance colonization in the lungs of patients suffering chronic obstructive pulmonary disease (COPD) by opportunistic pathogens such as nontypeable. NTHi is a heme auxotroph, and the NTHi genome contains multiple heme acquisition systems whose role in pulmonary infection requires a global understanding. In this study, we determined the relative contribution to NTHi airway infection of the four heme-acquisition systems HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF that are located at the bacterial outer membrane or the periplasm. Our computational studies provided plausible 3D models for HbpA, SapA, PE, and HxuA interactions with heme. Generation and characterization of single mutants in the hxuCBA, hpe, sapA, and hbpA genes provided evidence for participation in heme binding-storage and inter-bacterial donation. The hxuA, sapA, hbpA, and hpe genes showed differential expression and responded to heme. Moreover, HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF presented moonlighting properties related to resistance to antimicrobial peptides or glutathione import, together likely contributing to the NTHi-host airway interplay, as observed upon cultured airway epithelia and in vivo lung infection. The observed multi-functionality was shown to be system-specific, thus limiting redundancy. Together, we provide evidence for heme uptake systems as bacterial factors that act in a coordinated and multi-functional manner to subvert nutritional- and other sources of host innate immunity during NTHi airway infection.
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Affiliation(s)
| | - Tamim Al-Jubair
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Begoña Euba
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | | | - Sara Martí
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento Microbiología, Hospital Universitari Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain
| | - Susanna Törnroth-Horsefield
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Rinaldo S, Giardina G, Mantoni F, Paone A, Cutruzzolà F. Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms. FEMS Microbiol Lett 2019; 365:4834012. [PMID: 29401255 DOI: 10.1093/femsle/fny029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.
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Affiliation(s)
- Serena Rinaldo
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Federico Mantoni
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
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Universal Molecular Triggers of Stress Responses in Cyanobacterium Synechocystis. Life (Basel) 2019; 9:life9030067. [PMID: 31434306 PMCID: PMC6789579 DOI: 10.3390/life9030067] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/15/2019] [Accepted: 08/17/2019] [Indexed: 02/07/2023] Open
Abstract
Systemic analysis of stress-induced transcription in the cyanobacterium Synechocystis sp. strain PCC 6803 identifies a number of genes as being induced in response to most abiotic stressors (heat, osmotic, saline, acid stress, strong light, and ultraviolet radiation). Genes for heat-shock proteins (HSPs) are activated by all these stresses and form a group that universally responds to all environmental changes. The functions of universal triggers of stress responses in cyanobacteria can be performed by reactive oxygen species (ROS), in particular H2O2, as well as changes in the redox potential of the components of the photosynthetic electron transport chain. The double mutant of Synechocystis sp. PCC 6803 (katG/tpx, or sll1987/sll0755), which is defective in antioxidant enzymes catalase (KatG) and thioredoxin peroxidase (Tpx), cannot grow in the presence of exogenous hydrogen peroxide (H2O2); and it is extremely sensitive to low concentrations of H2O2, especially under conditions of cold stress. Experiments on this mutant demonstrate that H2O2 is involved in regulation of gene expression that responds to a decrease in ambient temperature, and affects both the perception and the signal transduction of cold stress. In addition, they suggest that formation of ROS largely depends on the physical state of the membranes such as fluidity or viscosity. In cyanobacteria, an increase in membrane turnover leads to a decrease in the formation of ROS and an increase in resistance to cold stress. Therefore: (1) H2O2 is the universal trigger of stress responses in cyanobacterial cells; (2) ROS formation (in particular, H2O2) depends on the physical properties of both cytoplasmic and thylakoid membranes; (3) The destructive effect of H2O2 is reduced by increasing of fluidity of biological membranes.
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Vasieva O, Goryanin I. Is there a Function for a Sex Pheromone Precursor? J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2019-0016/jib-2019-0016.xml. [PMID: 31301673 PMCID: PMC7074142 DOI: 10.1515/jib-2019-0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/07/2019] [Indexed: 12/29/2022] Open
Abstract
Functional coupling and comparative genomics analysis have been applied to study functional associations of orthologs of enterococcal cAD1 sex pheromone (P13268) known to be responsible for biofilm formation, conjugative plasmid transfer and spreading of bacterial antibiotics resistance. cAD1 peptide pheromone is released from the membrane lipoprotein with the peptide precursor encoded by a gene cad (tr|C2JQE7). Our analysis of genomic neighbourhood of cad and motifs of the encoded polypeptide and its orthologs suggests a close functional association between cAD1 and ApbE protein (Q82Z24), a FMN insertion and trafficking facilitator. The cad and apbE orthologs were coupled in the genomes and ApbE-specific motifs for FMN covalent attachment were identified in cad-encoded protein sequence and its orthologs. These findings suggest a potential role of FMN-based reductase function of the cAD1 lipoprotein precursor in its processing and release of the active sex pheromone peptide. They may lead to a new approach in prevention of antibiotic resistance spread via targeting sex pheromone processing chaperones or by suppression of the FMN availability and covalent binding. This methods can be also applied to a controlled evolution of bacterial pathogenicity in microbial fuel cells, as the findings suggest the crosstalk between bacterial pathogenicity and bacterial electro-activity.
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Affiliation(s)
- O Vasieva
- University of Liverpool, Crown street, Liverpool, UK.,Ingenet ltd, 3d floor, 207 Regent street, London, UK
| | - I Goryanin
- University of Edinburgh, Edinburgh, UK.,Okinawa Institute Science and Technology, Okinawa, Japan.,Tianjin Institute of Industrial Biotechnology, Tianjin, China
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Reguera G. Microbial nanowires and electroactive biofilms. FEMS Microbiol Ecol 2019; 94:5000162. [PMID: 29931163 DOI: 10.1093/femsec/fiy086] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/14/2022] Open
Abstract
Geobacter bacteria are the only microorganisms known to produce conductive appendages or pili to electronically connect cells to extracellular electron acceptors such as iron oxide minerals and uranium. The conductive pili also promote cell-cell aggregation and the formation of electroactive biofilms. The hallmark of these electroactive biofilms is electronic heterogeneity, mediated by coordinated interactions between the conductive pili and matrix-associated cytochromes. Collectively, the matrix-associated electron carriers discharge respiratory electrons from cells in multilayered biofilms to electron-accepting surfaces such as iron oxide coatings and electrodes poised at a metabolically oxidizable potential. The presence of pilus nanowires in the electroactive biofilms also promotes the immobilization and reduction of soluble metals, even when present at toxic concentrations. This review summarizes current knowledge about the composition of the electroactive biofilm matrix and the mechanisms that allow the wired Geobacter biofilms to generate electrical currents and participate in metal redox transformations.
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Affiliation(s)
- Gemma Reguera
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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A Novel Redox-Sensing Histidine Kinase That Controls Carbon Catabolite Repression in Azoarcus sp. CIB. mBio 2019; 10:mBio.00059-19. [PMID: 30967457 PMCID: PMC6456745 DOI: 10.1128/mbio.00059-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have identified and characterized the AccS multidomain sensor kinase that mediates the activation of the AccR master regulator involved in carbon catabolite repression (CCR) of the anaerobic catabolism of aromatic compounds in Azoarcus sp. CIB. A truncated AccS protein that contains only the soluble C-terminal autokinase module (AccS') accounts for the succinate-dependent CCR control. In vitro assays with purified AccS' revealed its autophosphorylation, phosphotransfer from AccS'∼P to the Asp60 residue of AccR, and the phosphatase activity toward its phosphorylated response regulator, indicating that the equilibrium between the kinase and phosphatase activities of AccS' may control the phosphorylation state of the AccR transcriptional regulator. Oxidized quinones, e.g., ubiquinone 0 and menadione, switched the AccS' autokinase activity off, and three conserved Cys residues, which are not essential for catalysis, are involved in such inhibition. Thiol oxidation by quinones caused a change in the oligomeric state of the AccS' dimer resulting in the formation of an inactive monomer. This thiol-based redox switch is tuned by the cellular energy state, which can change depending on the carbon source that the cells are using. This work expands the functional diversity of redox-sensitive sensor kinases, showing that they can control new bacterial processes such as CCR of the anaerobic catabolism of aromatic compounds. The AccSR two-component system is conserved in the genomes of some betaproteobacteria, where it might play a more general role in controlling the global metabolic state according to carbon availability.IMPORTANCE Two-component signal transduction systems comprise a sensor histidine kinase and its cognate response regulator, and some have evolved to sense and convert redox signals into regulatory outputs that allow bacteria to adapt to the altered redox environment. The work presented here expands knowledge of the functional diversity of redox-sensing kinases to control carbon catabolite repression (CCR), a phenomenon that allows the selective assimilation of a preferred compound among a mixture of several carbon sources. The newly characterized AccS sensor kinase is responsible for the phosphorylation and activation of the AccR master regulator involved in CCR of the anaerobic degradation of aromatic compounds in the betaproteobacterium Azoarcus sp. CIB. AccS seems to have a thiol-based redox switch that is modulated by the redox state of the quinone pool. The AccSR system is conserved in several betaproteobacteria, where it might play a more general role controlling their global metabolic state.
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Nzungize L, Ali MK, Wang X, Huang X, Yang W, Duan X, Yan S, Li C, Abdalla AE, Jeyakkumar P, Xie J. Mycobacterium tuberculosis metC (Rv3340) derived hydrogen sulphide conferring bacteria stress survival. J Drug Target 2019; 27:1004-1016. [DOI: 10.1080/1061186x.2019.1579820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Lambert Nzungize
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Md Kaisar Ali
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiaoyu Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Xue Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Wenmin Yang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiangke Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Shuangquan Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Chunyan Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Abualgasim Elgaili Abdalla
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
- Department of Clinical Microbiology, College of Medical Laboratory Sciences, Omdurman, Islamic University, Omdurman, Sudan
| | - Ponmani Jeyakkumar
- Institute of Bioorganic and Medical Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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Zerfaß C, Asally M, Soyer OS. Interrogating metabolism as an electron flow system. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 13:59-67. [PMID: 31008413 PMCID: PMC6472609 DOI: 10.1016/j.coisb.2018.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metabolism is generally considered as a neatly organised system of modular pathways, shaped by evolution under selection for optimal cellular growth. This view falls short of explaining and predicting a number of key observations about the structure and dynamics of metabolism. We highlight these limitations of a pathway-centric view on metabolism and summarise studies suggesting how these could be overcome by viewing metabolism as a thermodynamically and kinetically constrained, dynamical flow system. Such a systems-level, first-principles based view of metabolism can open up new avenues of metabolic engineering and cures for metabolic diseases and allow better insights to a myriad of physiological processes that are ultimately linked to metabolism. Towards further developing this view, we call for a closer interaction among physical and biological disciplines and an increased use of electrochemical and biophysical approaches to interrogate cellular metabolism together with the microenvironment in which it exists.
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Affiliation(s)
- Christian Zerfaß
- Bio-Electrical Engineering (BEE) Innovation Hub, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Munehiro Asally
- Bio-Electrical Engineering (BEE) Innovation Hub, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, CV4 7AL, UK
| | - Orkun S. Soyer
- Bio-Electrical Engineering (BEE) Innovation Hub, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, CV4 7AL, UK
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Recent Advances and Current Trends in Nucleotide Second Messenger Signaling in Bacteria. J Mol Biol 2019; 431:908-927. [PMID: 30668970 DOI: 10.1016/j.jmb.2019.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/05/2019] [Accepted: 01/07/2019] [Indexed: 02/01/2023]
Abstract
The "International Symposium on Nucleotide Second Messenger Signaling in Bacteria" (September 30-October 3, 2018, Berlin), which was organized within the framework of DFG Priority Programme 1879 (www.spp1879.de), brought together 125 participants from 20 countries to discuss recent progress and future trends in this field. Even 50 years after its discovery, (p)ppGpp is venturing into exciting new fields, especially in gram-positive bacteria. After triggering the current renaissance in bacterial second messenger research, c-di-GMP is becoming ever more global with abounding new molecular mechanisms of action and physiological functions. The more recently discovered c-di-AMP is rapidly catching up and has now been found even in archaea, with its function in osmotic homeostasis being conserved across kingdom boundaries. Small modules associated with mobile genetic elements, which make and react to numerous novel mixed cyclic dinucleotides, seem to roam around rather freely in the bacterial world. Finally, many novel and old nucleotide molecules are still lurking around in search of a function. Across many talks it became apparent that (p)ppGpp, c-di-GMP and GTP/ATP can share and compete for binding sites (e.g., the Walker A motif in GTP/ATPases) with intriguing regulatory consequences, thus contributing to the emergent trend of systemwide networks that interconnect diverse signaling nucleotides. Overall, this inspiring conference made it clear that second messenger signaling is currently one of the most dynamic and exciting areas in microbial molecular biology and physiology, with major impacts ranging from microbial systems biology and ecology to infection biology.
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Pan X, Wu J, Xu S, Duan T, Duan Y, Wang J, Zhang F, Zhou M. Contribution of OxyR Towards Differential Sensitivity to Antioxidants in Xanthomonas oryzae pathovars oryzae and oryzicola. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1244-1256. [PMID: 29905495 DOI: 10.1094/mpmi-03-18-0074-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OxyR and SoxR are two transcriptional regulators in response to oxidative stress in most bacteria, and SoxR has been reported to be activated by the endogenous redox-cycling compound phenazine in phenazine-producing organisms. However, which transcriptional regulator is activated in pathogens treated with the antibiotic phenazine-1-carboxylic acid (PCA) has not been determined. In this study, we found that PCA treatment activated OxyR rather than SoxR in the phytopathogenic bacteria Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola. We also found that X. oryzae pv. oryzae was much more sensitive to PCA and H2O2 and had a defective antioxidant system (i.e., less of total antioxidant capacity and total catalase activity than X. oryzae pv. oryzicola, although X. oryzae pvs. oryzae and oryzicola are very closely related). Based on KEGG sequences, OxyR differs in 10 amino acids in X. oryzae pv. oryzae versus X. oryzae pv. oryzicola. By exchanging OxyR between X. oryzae pvs. oryzae and oryzicola, we elucidated that OxyR contributed to the differences in antioxidant capacity, total catalase activity, and sensitivity to PCA and H2O2. We also found that OxyR affected X. oryzae pvs. oryzae and oryzicola growth in a nutrient-poor medium, virulence on host plants (rice), and the hypersensitive response on nonhost plants (Nicotiana benthamiana). Thus, OxyR is a critical regulator that relates to the differences in antioxidative stress between X. oryzae pvs. oryzae and oryzicola and contributes to the differences in survival of them against oxidative stress.
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Affiliation(s)
- Xiayan Pan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Wu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shu Xu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yabing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Zhang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
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Modeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of Information. mSystems 2018; 3:mSystems00189-17. [PMID: 29946568 PMCID: PMC6009100 DOI: 10.1128/msystems.00189-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 06/03/2018] [Indexed: 12/11/2022] Open
Abstract
Bacteria sense and respond to their environments using a sophisticated array of sensors and regulatory networks to optimize their fitness and survival in a constantly changing environment. Understanding how these regulatory and sensory networks work will provide the capacity to predict bacterial behaviors and, potentially, to manipulate their interactions with an environment or host. Leveraging the information theory provides useful quantitative metrics for modeling the information processing capacity of bacterial regulatory networks. As our model accurately predicted gene expression profiles in a bacterial model system, we posit that the information theory-based approaches will be important to enhance our understanding of a wide variety of bacterial regulomes and our ability to engineer bacterial sensory and regulatory networks. Bacteria are not simply passive consumers of nutrients or merely steady-state systems. Rather, bacteria are active participants in their environments, collecting information from their surroundings and processing and using that information to adapt their behavior and optimize survival. The bacterial regulome is the set of physical interactions that link environmental information to the expression of genes by way of networks of sensors, transporters, signal cascades, and transcription factors. As bacteria cannot have one dedicated sensor and regulatory response system for every possible condition that they may encounter, the sensor systems must respond to a variety of overlapping stimuli and collate multiple forms of information to make “decisions” about the most appropriate response to a specific set of environmental conditions. Here, we analyze Pseudomonas fluorescens transcriptional responses to multiple sulfur nutrient sources to generate a predictive, computational model of the sulfur regulome. To model the regulome, we utilize a transmitter-channel-receiver scheme of information transfer and utilize principles from information theory to portray P. fluorescens as an informatics system. This approach enables us to exploit the well-established metrics associated with information theory to model the sulfur regulome. Our computational modeling analysis results in the accurate prediction of gene expression patterns in response to the specific sulfur nutrient environments and provides insights into the molecular mechanisms of Pseudomonas sensory capabilities and gene regulatory networks. In addition, modeling the bacterial regulome using the tools of information theory is a powerful and generalizable approach that will have multiple future applications to other bacterial regulomes. IMPORTANCE Bacteria sense and respond to their environments using a sophisticated array of sensors and regulatory networks to optimize their fitness and survival in a constantly changing environment. Understanding how these regulatory and sensory networks work will provide the capacity to predict bacterial behaviors and, potentially, to manipulate their interactions with an environment or host. Leveraging the information theory provides useful quantitative metrics for modeling the information processing capacity of bacterial regulatory networks. As our model accurately predicted gene expression profiles in a bacterial model system, we posit that the information theory-based approaches will be important to enhance our understanding of a wide variety of bacterial regulomes and our ability to engineer bacterial sensory and regulatory networks.
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Lee SJ, Kim DG, Lee KY, Koo JS, Lee BJ. Regulatory mechanisms of thiol-based redox sensors: lessons learned from structural studies on prokaryotic redox sensors. Arch Pharm Res 2018; 41:583-593. [PMID: 29777359 DOI: 10.1007/s12272-018-1036-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/01/2018] [Indexed: 01/29/2023]
Abstract
Oxidative stresses, such as reactive oxygen species, reactive electrophilic species, reactive nitrogen species, and reactive chlorine species, can damage cellular components, leading to cellular malfunction and death. In response to oxidative stress, bacteria have evolved redox-responsive sensors that enable them to simultaneously monitor and eradicate potential oxidative stress. Specifically, redox-sensing transcription regulators react to oxidative stress by means of modifying the thiol groups of cysteine residues, functioning as part of an efficient survival mechanism for many bacteria. In general, oxidative molecules can induce changes in the three-dimensional structures of redox sensors, which, in turn, affects the transcription of specific genes in detoxification pathways and defense mechanisms. Moreover, pathogenic bacteria utilize these redox sensors for adaptation and to evade subsequent oxidative attacks from host immune defense. For this reason, the redox sensors of pathogenic bacteria are potential antibiotic targets. Understanding the regulatory mechanisms of thiol-based redox sensors in bacteria will provide insight and knowledge into the discovery of new antibiotics.
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Affiliation(s)
- Sang Jae Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dong-Gyun Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Kyu-Yeon Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Ji Sung Koo
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Shewanella oneidensis as a living electrode for controlled radical polymerization. Proc Natl Acad Sci U S A 2018; 115:4559-4564. [PMID: 29666254 DOI: 10.1073/pnas.1800869115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metabolic engineering has facilitated the production of pharmaceuticals, fuels, and soft materials but is generally limited to optimizing well-defined metabolic pathways. We hypothesized that the reaction space available to metabolic engineering could be expanded by coupling extracellular electron transfer to the performance of an exogenous redox-active metal catalyst. Here we demonstrate that the electroactive bacterium Shewanella oneidensis can control the activity of a copper catalyst in atom-transfer radical polymerization (ATRP) via extracellular electron transfer. Using S. oneidensis, we achieved precise control over the molecular weight and polydispersity of a bioorthogonal polymer while similar organisms, such as Escherichia coli, showed no significant activity. We found that catalyst performance was a strong function of bacterial metabolism and specific electron transport proteins, both of which offer potential biological targets for future applications. Overall, our results suggest that manipulating extracellular electron transport pathways may be a general strategy for incorporating organometallic catalysis into the repertoire of metabolically controlled transformations.
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