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Acevedo-Barrios R, Tirado-Ballestas I, Bertel-Sevilla A, Cervantes-Ceballos L, Gallego JL, Leal MA, Tovar D, Olivero-Verbel J. Bioprospecting of extremophilic perchlorate-reducing bacteria: report of promising Bacillus spp. isolated from sediments of the bay of Cartagena, Colombia. Biodegradation 2024; 35:601-620. [PMID: 38625437 DOI: 10.1007/s10532-024-10079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/06/2024] [Indexed: 04/17/2024]
Abstract
Three extremophile bacterial strains (BBCOL-009, BBCOL-014 and BBCOL-015), capable of degrading high concentrations of perchlorate at a range of pH (6.5 to 10.0), were isolated from Colombian Caribbean Coast sediments. Morphological features included Gram negative strain bacilli with sizes averaged of 1.75 × 0.95, 2.32 × 0.65 and 3.08 × 0.70 μm, respectively. The reported strains tolerate a wide range of pH (6.5 to 10.0); concentrations of NaCl (3.5 to 7.5% w/v) and KClO4- (250 to 10000 mg/L), reduction of KClO4- from 10 to 25%. LB broth with NaCl (3.5-30% w/v) and KClO4- (250-10000 mg/L) were used in independent trials to evaluate susceptibility to salinity and perchlorate, respectively. Isolates increased their biomass at 7.5 % (w/v) NaCl with optimal development at 3.5 % NaCl. Subsequently, ClO4- reduction was assessed using LB medium with 3.5% NaCl and 10000 mg/L ClO4-. BBCOL-009, BBCOL-014 and BBCOL-015 achieved 10%, 17%, and 25% reduction of ClO4-, respectively. The 16 S rRNA gene sequence grouped them as Bacillus flexus T6186-2, Bacillus marisflavi TF-11 (T), and Bacillus vietnamensis 15 - 1 (T) respectively, with < 97.5% homology. In addition, antimicrobial resistance to ertapenem, vancomycine, amoxicillin clavulanate, penicillin, and erythromycin was present in all the isolates, indicating their high adaptability to stressful environments. The isolated strains from marine sediments in Cartagena Bay, Colombia are suitable candidates to reduce perchlorate contamination in different environments. Although the primary focus of the study of perchlorate-reducing and resistant bacteria is in the ecological and agricultural realms, from an astrobiological perspective, perchlorate-resistant bacteria serve as models for astrobiological investigations.
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Affiliation(s)
- Rosa Acevedo-Barrios
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia.
- Grupo de Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, POB 130001, Cartagena de Indias D. T. y C, Colombia.
| | - Irina Tirado-Ballestas
- GENOMA Group, Health Sciences Department, Universidad del Sinú, Santillana Campus, Cartagena, 130015, Colombia
- Group of Functional Toxicology, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
| | - Angela Bertel-Sevilla
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
| | - Leonor Cervantes-Ceballos
- Group of Functional Toxicology, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
| | - Jorge L Gallego
- Department of Engineering, University of Medellin, Medellín, 050026, Colombia
| | - María Angélica Leal
- Planetary Sciences and Astrobiology Research Group (GCPA), Universidad Nacional de Colombia and Corporación Científica Laguna, Bogotá, 111321, Colombia
- Biosphere and Cosmos Research Group (BIOC). Corporación Científica Laguna, Bogotá, 111163, Colombia
| | - David Tovar
- Planetary Sciences and Astrobiology Research Group (GCPA), Universidad Nacional de Colombia and Corporación Científica Laguna, Bogotá, 111321, Colombia
- Biosphere and Cosmos Research Group (BIOC). Corporación Científica Laguna, Bogotá, 111163, Colombia
| | - Jesús Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
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2
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Akabuogu E, Zhang L, Krašovec R, Roberts IS, Waigh TA. Electrical Impedance Spectroscopy with Bacterial Biofilms: Neuronal-like Behavior. NANO LETTERS 2024; 24:2234-2241. [PMID: 38320294 PMCID: PMC10885197 DOI: 10.1021/acs.nanolett.3c04446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/08/2024]
Abstract
Negative capacitance at low frequencies for spiking neurons was first demonstrated in 1941 (K. S. Cole) by using extracellular electrodes. The phenomenon subsequently was explained by using the Hodgkin-Huxley model and is due to the activity of voltage-gated potassium ion channels. We show that Escherichia coli (E. coli) biofilms exhibit significant stable negative capacitances at low frequencies when they experience a small DC bias voltage in electrical impedance spectroscopy experiments. Using a frequency domain Hodgkin-Huxley model, we characterize the conditions for the emergence of this feature and demonstrate that the negative capacitance exists only in biofilms containing living cells. Furthermore, we establish the importance of the voltage-gated potassium ion channel, Kch, using knock-down mutants. The experiments provide further evidence for voltage-gated ion channels in E. coli and a new, low-cost method to probe biofilm electrophysiology, e.g., to understand the efficacy of antibiotics. We expect that the majority of bacterial biofilms will demonstrate negative capacitances.
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Affiliation(s)
- Emmanuel
U. Akabuogu
- Division
of Infection, Lydia Becker Institute of Immunology and Inflammation,
School of Biological Sciences, University
of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
- Biological
Physics, Department of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Lin Zhang
- Biological
Physics, Department of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Rok Krašovec
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United
Kingdom
| | - Ian S. Roberts
- Division
of Infection, Lydia Becker Institute of Immunology and Inflammation,
School of Biological Sciences, University
of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Thomas A. Waigh
- Biological
Physics, Department of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Photon
Science Institute, Alan
Turing Building, Oxford Road, Manchester, M13 9PY, United
Kingdom
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3
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Maisat W, Yuki K. Volatile anesthetic isoflurane exposure facilitates Enterococcus biofilm infection. FASEB J 2023; 37:e23186. [PMID: 37665578 PMCID: PMC10495085 DOI: 10.1096/fj.202301128r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Enterococcus faecalis (E. faecalis) is one of the major pathogenic bacteria responsible for surgical site infections. Biofilm infections are major hospital-acquired infections. Previous studies suggested that ions could regulate biofilm formation in microbes. Volatile anesthetics, frequently administered in surgical setting, target ion channels. Here, we investigated the role of ion channels/transporters and volatile anesthetics in the biofilm formation by E. faecalis MMH594 strain and its ion transporter mutants. We found that a chloride transporter mutant significantly reduced biofilm formation compared to the parental strain. Downregulation of teichoic acid biosynthesis in the chloride transporter mutant impaired biofilm matrix formation and cellular adhesion, leading to mitigated biofilm formation. Among anesthetics, isoflurane exposure enhanced biofilm formation in vitro and in vivo. The upregulation of de novo purine biosynthesis pathway by isoflurane exposure potentially enhanced biofilm formation, an essential process for DNA, RNA, and ATP synthesis. We also demonstrated that isoflurane exposure to E. faecalis increased cyclic-di-AMP and extracellular DNA production, consistent with the increased purine biosynthesis. We further showed that isoflurane enhanced the enzymatic activity of phosphoribosyl pyrophosphate synthetase (PRPP-S). With the hypothesis that isoflurane directly bound to PRPP-S, we predicted isoflurane binding site on it using rigid docking. Our study provides a better understanding of the underlying mechanisms of E. faecalis biofilm formation and highlights the potential impact of an ion transporter and volatile anesthetic on this process. These findings may lead to the development of novel strategies for preventing E. faecalis biofilm formation and improving patient outcomes in clinical settings.
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Affiliation(s)
- Wiriya Maisat
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Anesthesiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care and Pain Medicine, Cardiac Anesthesia Division, Boston Children’s Hospital, Boston, MA, USA
- Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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4
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Kantiwal U, Pandey J. Efficient Inhibition of Bacterial Biofilm Through Interference of Protein-Protein Interaction of Master Regulator Proteins: a Proof of Concept Study with SinR- SinI Complex of Bacillus subtilis. Appl Biochem Biotechnol 2023; 195:1947-1967. [PMID: 36401726 DOI: 10.1007/s12010-022-04231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 11/21/2022]
Abstract
Biofilm-associated microbial growth is a major cause of environmental, industrial, and public health concern. Therefore, there is a pressing need to discover and develop efficient antibiofilm strategies. Regulatory proteins vital for biofilm formation might be ideal targets for developing novel antibiofilm therapeutics. Their activities often depend on protein-protein interactions. Therefore, such targets present unique opportunities and challenges to drug discovery. In Bacillus subtilis, a model organism for studying biofilms, SinR acts as the master regulator of the biofilm formation cascade. Under favourable growth conditions, it represses the epsA-O and tapA-sipW-tasA operons, which encode for essential structural components of biofilms. Under unfavourable growth conditions, SinI, an agonist protein, inactivates SinR by forming a heterotrimeric complex. This results in derepression of epsA-O and tapA-sipW-tasA operons and leads to the phenotypic switch from planktonic to biofilm-associated form. We hypothesized that inhibiting SinR-SinI interaction might warrant repression of epsA-O and tapA-sipW-tasA operons and inhibit biofilm formation. To evaluate this hypothesis, we carried out a drug repurposing study for identifying potential inhibitors of SinI. Cefoperazone and itraconazole were identified as potential inhibitors with virtual screening. The stability of their interaction with SinI was assessed in extended MD performed over 100 ns. Both cefoperazone and itraconazole showed stable interaction. In in vitro studies, cefoperazone hindered the interaction of purified recombinant SinI and SinR. In the whole cell-based biofilm inhibition assays also cefoperazone was found to efficiently inhibited biofilm formation. These results provide proof of concept for targeting protein-protein interaction of master regulators as potential target for discovery and development of antibiofilm therapeutics. We propose that similar drug repurposing studies targeting key regulators of biofilm formation cascade could be an efficient approach for discovering novel anti-biofilm therapeutics against priority pathogens.
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Affiliation(s)
- Usha Kantiwal
- Laboratory of Molecular Microbiology, Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, NH-8, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Janmejay Pandey
- Laboratory of Molecular Microbiology, Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, NH-8, Kishangarh, Ajmer, 305817, Rajasthan, India.
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5
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Kikuchi K, Galera-Laporta L, Weatherwax C, Lam JY, Moon EC, Theodorakis EA, Garcia-Ojalvo J, Süel GM. Electrochemical potential enables dormant spores to integrate environmental signals. Science 2022; 378:43-49. [PMID: 36201591 PMCID: PMC10593254 DOI: 10.1126/science.abl7484] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The dormant state of bacterial spores is generally thought to be devoid of biological activity. We show that despite continued dormancy, spores can integrate environmental signals over time through a preexisting electrochemical potential. Specifically, we studied thousands of individual Bacillus subtilis spores that remain dormant when exposed to transient nutrient pulses. Guided by a mathematical model of bacterial electrophysiology, we modulated the decision to exit dormancy by genetically and chemically targeting potassium ion flux. We confirmed that short nutrient pulses result in step-like changes in the electrochemical potential of persistent spores. During dormancy, spores thus gradually release their stored electrochemical potential to integrate extracellular information over time. These findings reveal a decision-making mechanism that operates in physiologically inactive cells.
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Affiliation(s)
- Kaito Kikuchi
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Colleen Weatherwax
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Jamie Y Lam
- Department of Chemistry and Biochemistry, University of California San Diego; La Jolla, CA 92093, USA
| | - Eun Chae Moon
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
| | - Emmanuel A Theodorakis
- Department of Chemistry and Biochemistry, University of California San Diego; La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra; 08003 Barcelona, Spain
- Senior author
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego; La Jolla, CA 92093, USA
- San Diego Center for Systems Biology, University of California San Diego; La Jolla, CA 92093-0380, USA
- Center for Microbiome Innovation, University of California San Diego; La Jolla, CA 92093-0380, USA
- Senior author
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6
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Yun Z, Qin D, Wei F, Xiaobing L. Application of antibacterial nanoparticles in orthodontic materials. NANOTECHNOLOGY REVIEWS 2022. [DOI: 10.1515/ntrev-2022-0137] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
During the orthodontic process, increased microbial colonization and dental plaque formation on the orthodontic appliances and auxiliaries are major complications, causing oral infectious diseases, such as dental caries and periodontal diseases. To reduce plaque accumulation, antimicrobial materials are increasingly being investigated and applied to orthodontic appliances and auxiliaries by various methods. Through the development of nanotechnology, nanoparticles (NPs) have been reported to exhibit excellent antibacterial properties and have been applied in orthodontic materials to decrease dental plaque accumulation. In this review, we present the current development, antibacterial mechanisms, biocompatibility, and application of antibacterial NPs in orthodontic materials.
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Affiliation(s)
- Zhang Yun
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University , Chengdu , Sichuan 610041 , China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University , Chengdu , Sichuan 610041 , China
| | - Du Qin
- Department of Stomatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China , Chengdu , 610072 , China
| | - Fei Wei
- Department of Stomatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China , Chengdu , 610072 , China
| | - Li Xiaobing
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University , Chengdu , Sichuan 610041 , China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University , Chengdu , Sichuan 610041 , China
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7
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Ivshina I, Bazhutin G, Tyan S, Polygalov M, Subbotina M, Tyumina E. Cellular Modifications of Rhodococci Exposed to Separate and Combined Effects of Pharmaceutical Pollutants. Microorganisms 2022; 10:microorganisms10061101. [PMID: 35744619 PMCID: PMC9227840 DOI: 10.3390/microorganisms10061101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Actinomycetes of the genus Rhodococcus (class Actinomycetia) are dominant dwellers of biotopes with anthropogenic load. They serve as a natural system of primary response to xenobiotics in open ecosystems, initiate defensive responses in the presence of pollutants, and are regarded as ideal agents capable of transforming and degrading pharmaceuticals. Here, the ability of selected Rhodococcus strains to co-metabolize nonsteroidal anti-inflammatory drugs (ibuprofen, meloxicam, and naproxen) and information on the protective mechanisms of rhodococci against toxic effects of pharmaceuticals, individually or in a mixture, have been demonstrated. For the first time, R. ruber IEGM 439 provided complete decomposition of 100 mg/L meloxicam after seven days. It was shown that versatile cellular modifications occurring at the early development stages of nonspecific reactions of Rhodococcus spp. in response to separate and combined effects of the tested pharmaceuticals included changes in electrokinetic characteristics and catalase activity; transition from unicellular to multicellular life forms accompanied by pronounced morphological abnormalities; changes in the average size of vegetative cells and surface area-to-volume ratio; and the formation of linked cell assemblages. The obtained data are considered as adaptation mechanisms in rhodococci, and consequently their increased resistance to separate and combined effects of ibuprofen, meloxicam, and naproxen.
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Affiliation(s)
- Irina Ivshina
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
- Correspondence:
| | - Grigory Bazhutin
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Semyon Tyan
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Maxim Polygalov
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Maria Subbotina
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Elena Tyumina
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
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8
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Bavaharan A, Skilbeck C. Electrical signalling in prokaryotes and its convergence with quorum sensing in Bacillus. Bioessays 2022; 44:e2100193. [PMID: 35195292 DOI: 10.1002/bies.202100193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
The importance of electrical signalling in bacteria is an emerging paradigm. Bacillus subtilis biofilms exhibit electrical communication that regulates metabolic activity and biofilm growth. Starving cells initiate oscillatory extracellular potassium signals that help even the distribution of nutrients within the biofilm and thus help regulate biofilm development. Quorum sensing also regulates biofilm growth and crucially there is convergence between electrical and quorum sensing signalling axes. This makes B. subtilis an interesting model for cell signalling research. SpoOF is predicted to act as a logic gate for signalling pathway convergence, raising interesting questions about the functional nature of this gate and the relative importance of these disparate signals on biofilm behaviour. How is an oscillating signal integrated with a quorum signal? The model presented offers rich opportunities for future experimental and theoretical modelling research. The importance of direct cell-to-cell electrical signalling in prokaryotes, so characteristic of multicellular eukaryotes, is also discussed.
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9
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Wendel BM, Pi H, Krüger L, Herzberg C, Stülke J, Helmann JD. A Central Role for Magnesium Homeostasis during Adaptation to Osmotic Stress. mBio 2022; 13:e0009222. [PMID: 35164567 PMCID: PMC8844918 DOI: 10.1128/mbio.00092-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
Osmotic stress is a significant physical challenge for free-living cells. Cells from all three domains of life maintain viability during osmotic stress by tightly regulating the major cellular osmolyte potassium (K+) and by import or synthesis of compatible solutes. It has been widely established that in response to high salt stress, many bacteria transiently accumulate high levels of K+, leading to bacteriostasis, with growth resuming only when compatible solutes accumulate and K+ levels are restored to biocompatible levels. Using Bacillus subtilis as a model system, we provide evidence that K+ fluxes perturb Mg2+ homeostasis: import of K+ upon osmotic upshift is correlated with Mg2+ efflux, and Mg2+ reimport is critical for adaptation. The transient growth inhibition resulting from hyperosmotic stress is coincident with loss of Mg2+ and a decrease in protein translation. Conversely, the reimport of Mg2+ is a limiting factor during resumption of growth. Furthermore, we show the essential signaling dinucleotide cyclic di-AMP fluctuates dynamically in coordination with Mg2+ and K+ levels, consistent with the proposal that cyclic di-AMP orchestrates the cellular response to osmotic stress. IMPORTANCE Environments with high concentrations of salt or other solutes impose an osmotic stress on cells, ultimately limiting viability by dehydration of the cytosol. A very common cellular response to high osmolarity is to immediately import high levels of potassium ion (K+), which helps prevent dehydration and allows time for the import or synthesis of biocompatible solutes that allow a resumption of growth. Here, using Bacillus subtilis as a model, we demonstrate that concomitant with K+ import there is a large reduction in intracellular magnesium (Mg2+) mediated by specific efflux pumps. Further, it is the reimport of Mg2+ that is rate-limiting for the resumption of growth. These coordinated fluxes of K+ and Mg2+ are orchestrated by cyclic-di-AMP, an essential second messenger in Firmicutes. These findings amend the conventional model for osmoadaptation and reveal that Mg2+ limitation is the proximal cause of the bacteriostasis that precedes resumption of growth.
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Affiliation(s)
- Brian M. Wendel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Hualiang Pi
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Larissa Krüger
- Department of General Microbiology, GZMB, Georg August University, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, GZMB, Georg August University, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg August University, Göttingen, Germany
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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10
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Unappreciated Roles for K+ Channels in Bacterial Physiology. Trends Microbiol 2021; 29:942-950. [DOI: 10.1016/j.tim.2020.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 01/03/2023]
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11
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Stolarek P, Bernat P, Szczerbiec D, Różalski A. Phospholipids and Fatty Acids Affect the Colonization of Urological Catheters by Proteus mirabilis. Int J Mol Sci 2021; 22:ijms22168452. [PMID: 34445157 PMCID: PMC8395112 DOI: 10.3390/ijms22168452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
Proteus mirabilis-mediated CAUTIs are usually initiated by the adherence of bacteria to a urinary catheter surface. In this paper, three isolates of different origin and exhibiting different adhesion abilities were investigated in search of any changes in lipidome components which might contribute to P. mirabilis adhesion to catheters. Using GC-MS and LC-MS/MS techniques, 21 fatty acids and 27 phospholipids were identified in the examined cells. The comparison of the profiles of phospholipids and fatty acids obtained for catheter-attached cells and planktonic cells of the pathogens indicated C11:0 and PE 37:2 levels as values which could be related to P. mirabilis adhesion to a catheter, as well as cis C16:1, PE 32:0, PE 33:0, PE 38:2, PG 33:1, PG 34:0, PE 30:1, PE 32:1 and PG 30:2 levels as values which could be associated with cell hydrophobicity. Based on DiBAC4 (3) fluorescence intensity and an affinity to p-xylene, it was found that the inner membrane depolarization, as well as strong cell-surface hydrophobicity, were important for P. mirabilis adhesion to a silicone catheter. A generalized polarization of Laurdan showed lower values for P. mirabilis cells attached to the catheter surface than for planktonic cells, suggesting lower packing density of membrane components of the adherent cells compared with tightly packed, stiffened membranes of the planktonic cells. Taken together, these data indicate that high surface hydrophobicity, fluidization and depolarization of P. mirabilis cell membranes enable colonization of a silicone urinary catheter surface.
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Affiliation(s)
- Paulina Stolarek
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (D.S.); (A.R.)
- Correspondence: ; Tel.: +48-42-635-43-24; Fax: +48-42-665-58-18
| | - Przemysław Bernat
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Dominika Szczerbiec
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (D.S.); (A.R.)
| | - Antoni Różalski
- Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (D.S.); (A.R.)
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12
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Huang L, Zhang J, Xiang Z, Wu D, Huang X, Huang X, Liang Z, Tang ZY, Deng H. Faradaic Counter for Liposomes Loaded with Potassium, Sodium Ions, or Protonated Dopamine. Anal Chem 2021; 93:9495-9504. [PMID: 34196181 DOI: 10.1021/acs.analchem.1c01336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collisional electrochemistry between single particles and a biomimetic polarized micro-liquid/liquid interface has emerged as a novel and powerful analytical method for measurements of single particles. Using this platform, rapid detection of liposomes at the single particle level is reported herein. Individual potassium, sodium, or protonated dopamine-encapsulated (pristine or protein-decorated) liposomes collide and fuse with the polarized micro-liquid/liquid interface accompanying the release of ions, which are recorded as spike-like current transients of stochastic nature. The sizing and concentration of the liposomes can be readily estimated by quantifying the amount of encapsulated ions in individual liposomes via integrating each current spike versus time and the spike frequency, respectively. We call this type of nanosensing technology "Faradaic counter". The estimated liposome size distribution by this method is in line with the dynamic light scattering (DLS) measurements, implying that the quantized current spikes are indeed caused by the collisions of individual liposomes. The reported electrochemical sensing technology may become a viable alternative to DLS and other commercial nanoparticle analysis systems, for example, nanoparticle tracking analysis.
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Affiliation(s)
- Linhan Huang
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China
| | - Jingcheng Zhang
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China
| | - Zhipeng Xiang
- Key Laboratory on Fuel Cell Technology of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China
| | - Di Wu
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China
| | - Xinjian Huang
- Institute of Intelligent Perception, Midea Corporate Research Center, Foshan 528311, China
| | - Xizhe Huang
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China
| | - Zhenxing Liang
- Key Laboratory on Fuel Cell Technology of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China
| | - Zhen-Yu Tang
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Haiqiang Deng
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China
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13
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Galera-Laporta L, Comerci CJ, Garcia-Ojalvo J, Süel GM. IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria. Cell Syst 2021; 12:497-508. [PMID: 34139162 PMCID: PMC8570674 DOI: 10.1016/j.cels.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
Metal ions are essential for life and represent the second most abundant constituent (after water) of any living cell. While the biological importance of inorganic ions has been appreciated for over a century, we are far from a comprehensive understanding of the functional roles that ions play in cells and organisms. In particular, recent advances are challenging the traditional view that cells maintain constant levels of ion concentrations (ion homeostasis). In fact, the ionic composition (metallome) of cells appears to be purposefully dynamic. The scientific journey that started over 60 years ago with the seminal work by Hodgkin and Huxley on action potentials in neurons is far from reaching its end. New evidence is uncovering how changes in ionic composition regulate unexpected cellular functions and physiology, especially in bacteria, thereby hinting at the evolutionary origins of the dynamic metallome. It is an exciting time for this field of biology, which we discuss and refer to here as IonoBiology.
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Affiliation(s)
- Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colin J Comerci
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093- 0380, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093-0380, USA.
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14
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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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15
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The Many Roles of the Bacterial Second Messenger Cyclic di-AMP in Adapting to Stress Cues. J Bacteriol 2020; 203:JB.00348-20. [PMID: 32839175 DOI: 10.1128/jb.00348-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to changes in environmental conditions through adaptation to external cues. Frequently, bacteria employ nucleotide signaling molecules to mediate a specific, rapid response. Cyclic di-AMP (c-di-AMP) was recently discovered to be a bacterial second messenger that is essential for viability in many species. In this review, we highlight recent work that has described the roles of c-di-AMP in bacterial responses to various stress conditions. These studies show that depending on the lifestyle and environmental niche of the bacterial species, the c-di-AMP signaling network results in diverse outcomes, such as regulating osmolyte transport, controlling plant attachment, or providing a checkpoint for spore formation. c-di-AMP achieves this signaling specificity through expression of different classes of synthesis and catabolic enzymes as well as receptor proteins and RNAs, which will be summarized.
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16
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Yang CY, Bialecka-Fornal M, Weatherwax C, Larkin JW, Prindle A, Liu J, Garcia-Ojalvo J, Süel GM. Encoding Membrane-Potential-Based Memory within a Microbial Community. Cell Syst 2020; 10:417-423.e3. [PMID: 32343961 PMCID: PMC7286314 DOI: 10.1016/j.cels.2020.04.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 04/02/2020] [Indexed: 12/29/2022]
Abstract
Cellular membrane potential plays a key role in the formation and retrieval of memories in the metazoan brain, but it remains unclear whether such memory can also be encoded in simpler organisms like bacteria. Here, we show that single-cell-level memory patterns can be imprinted in bacterial biofilms by light-induced changes in the membrane potential. We demonstrate that transient optical perturbations generate a persistent and robust potassium-channel-mediated change in the membrane potential of bacteria within the biofilm. The light-exposed cells respond in an anti-phase manner, relative to unexposed cells, to both natural and induced oscillations in extracellular ion concentrations. This anti-phase response, which persists for hours following the transient optical stimulus, enables a direct single-cell resolution visualization of spatial memory patterns within the biofilm. The ability to encode robust and persistent membrane-potential-based memory patterns could enable computations within prokaryotic communities and suggests a parallel between neurons and bacteria.
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Affiliation(s)
- Chih-Yu Yang
- Division of Biological Sciences, University of California, San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Maja Bialecka-Fornal
- Division of Biological Sciences, University of California, San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Colleen Weatherwax
- Division of Biological Sciences, University of California, San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joseph W Larkin
- Division of Biological Sciences, University of California, San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Arthur Prindle
- Division of Biological Sciences, University of California, San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jintao Liu
- Division of Biological Sciences, University of California, San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Infectious Diseases Research and Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, People's Republic of China
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona 08003, Spain
| | - Gürol M Süel
- Division of Biological Sciences, University of California, San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093-0380, USA.
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17
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Benarroch JM, Asally M. The Microbiologist’s Guide to Membrane Potential Dynamics. Trends Microbiol 2020; 28:304-314. [DOI: 10.1016/j.tim.2019.12.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
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18
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Blee JA, Roberts IS, Waigh TA. Spatial propagation of electrical signals in circular biofilms: A combined experimental and agent-based fire-diffuse-fire study. Phys Rev E 2019; 100:052401. [PMID: 31870031 DOI: 10.1103/physreve.100.052401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Indexed: 11/07/2022]
Abstract
Bacterial biofilms are a risk to human health, playing critical roles in persistent infections. Recent studies have observed electrical signaling in biofilms and thus biofilms represent a new class of active excitable matter in which cell division is the active process and the spiking of the individual bacterial cells is the excitable process. Electrophysiological models have predominantly been developed to describe eukaryotic systems, but we demonstrate their use in understanding bacterial biofilms. Our agent-based fire-diffuse-fire (ABFDF) model successfully simulates the propagation of both centrifugal (away from the center) and centripetal (toward the center) electrical signals through biofilms of Bacillus subtilis. Furthermore, the ABFDF model allows realistic spatial positioning of the bacteria in two dimensions to be included in the fire-diffuse-fire model and this is the crucial factor that improves agreement with experiments. The speed of propagation is not constant and depends on the radius of the propagating electrical wave front. Centripetal waves are observed to move faster than centrifugal waves, which is a curvature driven effect and is correctly captured by our simulations.
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Affiliation(s)
- J A Blee
- Biological Physics, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.,Photon Science Institute, Alan Turing Building, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation Immunity & Respiratory Medicine, Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Michael Smith Building, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - I S Roberts
- Lydia Becker Institute of Immunology and Inflammation Immunity & Respiratory Medicine, Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Michael Smith Building, University of Manchester, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - T A Waigh
- Biological Physics, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.,Photon Science Institute, Alan Turing Building, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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19
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Mikušević V, Schrecker M, Kolesova N, Patiño-Ruiz M, Fendler K, Hänelt I. A channel profile report of the unusual K + channel KtrB. J Gen Physiol 2019; 151:1357-1368. [PMID: 31624134 PMCID: PMC6888753 DOI: 10.1085/jgp.201912384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/03/2019] [Accepted: 09/27/2019] [Indexed: 11/20/2022] Open
Abstract
KtrAB is a key player in bacterial K+ uptake required for K+ homeostasis and osmoadaptation. The system is unique in structure and function. It consists of the K+-translocating channel subunit KtrB, which forms a dimer in the membrane, and the soluble regulatory subunit KtrA, which attaches to the cytoplasmic side of the dimer as an octameric ring conferring Na+ and ATP dependency to the system. Unlike most K+ channels, KtrB lacks the highly conserved T(X)GYG selectivity filter sequence. Instead, only a single glycine residue is found in each pore loop, which raises the question of how selective the ion channel is. Here, we characterized the KtrB subunit from the Gram-negative pathogen Vibrio alginolyticus by isothermal titration calorimetry, solid-supported membrane-based electrophysiology, whole-cell K+ uptake, and ACMA-based transport assays. We found that, despite its simple selectivity filter, KtrB selectively binds K+ with micromolar affinity. Rb+ and Cs+ bind with millimolar affinities. However, only K+ and the poorly binding Na+ are efficiently translocated, based on size exclusion by the gating loop. Importantly, the physiologically required K+ over Na+ selectivity is provided by the channel's high affinity for potassium, which interestingly results from the presence of the sodium ions themselves. In the presence of the KtrA subunit, sodium ions further decrease the Michaelis-Menten constant for K+ uptake from milli- to micromolar concentrations and increase the Vmax, suggesting that Na+ also facilitates channel gating. In conclusion, high binding affinity and facilitated K+ gating allow KtrAB to function as a selective K+ channel.
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Affiliation(s)
- Vedrana Mikušević
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Marina Schrecker
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Natalie Kolesova
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Miyer Patiño-Ruiz
- Department of Biophysical Chemistry, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Klaus Fendler
- Department of Biophysical Chemistry, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
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20
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Wang T, Flint S, Palmer J. Magnesium and calcium ions: roles in bacterial cell attachment and biofilm structure maturation. BIOFOULING 2019; 35:959-974. [PMID: 31687841 DOI: 10.1080/08927014.2019.1674811] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
The ubiquitous divalent cations magnesium and calcium are important nutrients required by bacteria for growth and cell maintenance. Multi-faceted roles are shown both in bacterial initial attachment and biofilm maturation. The effects of calcium and magnesium can be highlighted in physio-chemical interactions, gene regulation and bio-macromolecular structural modification, which lead to either promotion or inhibition of biofilms. This review outlines recent research addressing phenotypic changes and mechanisms undertaken by calcium and magnesium in affecting bacterial biofilm formation.
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Affiliation(s)
- Tianyang Wang
- Institute of Food Science and Technology, School of Food and Advanced Technology, Massey University, New Zealand
| | - Steve Flint
- Institute of Food Science and Technology, School of Food and Advanced Technology, Massey University, New Zealand
| | - Jon Palmer
- Institute of Food Science and Technology, School of Food and Advanced Technology, Massey University, New Zealand
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21
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Chen M, Wu S, Tan Y, Li R, Liu Y, Huang Q. Rubidium-doped titanium surfaces with modulatory effects on MC3T3-E1 cell response and antibacterial capacity against
Staphylococcus aureus. Biomed Mater 2019; 14:045016. [DOI: 10.1088/1748-605x/ab2585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Frotscher E, Krainer G, Hartmann A, Schlierf M, Keller S. Conformational Dynamics Govern the Free-Energy Landscape of a Membrane-Interacting Protein. ACS OMEGA 2018; 3:12026-12032. [PMID: 31459283 PMCID: PMC6690567 DOI: 10.1021/acsomega.8b01609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/11/2018] [Indexed: 05/08/2023]
Abstract
The equilibrium stabilities and the folding rates of membrane-bound proteins are determined by hydrophobic and polar intermolecular contacts with their environment as well as by intramolecular packing and conformational dynamics. The contributions of these factors, however, remain elusive and might vary considerably among proteins. Mistic from Bacillus subtilis is a particularly intriguing example of an α-helical protein that associates with membranes in spite of its unusual hydrophilicity. In micelles, Mistic is stabilized by hydrophobic and polar interactions with detergents, but it is unclear whether and how these intermolecular contacts are coupled to structural and dynamic adaptations of the protein itself. Here, we investigated the packing and the conformational dynamics of Mistic as functions of detergent headgroup chemistry and chain length, employing single-molecule Förster resonance energy transfer spectroscopy and time-resolved intrinsic tryptophan fluorescence spectroscopy. Surprisingly, in nonionic detergents, more effective hydrophobic burial and, thus, greater protein stability with increasing hydrophobic micellar thickness were accompanied by a gradual loosening of the helical bundle. By contrast, Mistic was found to assume a stable, compact fold in zwitterionic detergents that allowed faster dynamics on the nanosecond timescale. Thus, intramolecular packing per se is insufficient for conferring high protein stability; instead, enhanced nanosecond dynamics and, consequently, greater conformational entropy in the compact folded state account for Mistic's high equilibrium stability and fast folding rates in zwitterionic micelles even at the expense of less effective hydrophobic burial.
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Affiliation(s)
- Erik Frotscher
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Georg Krainer
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Andreas Hartmann
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Michael Schlierf
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
- E-mail: (M.S.)
| | - Sandro Keller
- Molecular
Biophysics, Technische Universität
Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- E-mail: (S.K.)
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23
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Larkin JW, Zhai X, Kikuchi K, Redford SE, Prindle A, Liu J, Greenfield S, Walczak AM, Garcia-Ojalvo J, Mugler A, Süel GM. Signal Percolation within a Bacterial Community. Cell Syst 2018; 7:137-145.e3. [PMID: 30056004 DOI: 10.1016/j.cels.2018.06.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/08/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Signal transmission among cells enables long-range coordination in biological systems. However, the scarcity of quantitative measurements hinders the development of theories that relate signal propagation to cellular heterogeneity and spatial organization. We address this problem in a bacterial community that employs electrochemical cell-to-cell communication. We developed a model based on percolation theory, which describes how signals propagate through a heterogeneous medium. Our model predicts that signal transmission becomes possible when the community is organized near a critical phase transition between a disconnected and a fully connected conduit of signaling cells. By measuring population-level signal transmission with single-cell resolution in wild-type and genetically modified communities, we confirm that the spatial distribution of signaling cells is organized at the predicted phase transition. Our findings suggest that at this critical point, the population-level benefit of signal transmission outweighs the single-cell level cost. The bacterial community thus appears to be organized according to a theoretically predicted spatial heterogeneity that promotes efficient signal transmission.
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Affiliation(s)
- Joseph W Larkin
- Division of Biological Sciences, University of California San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xiaoling Zhai
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Kaito Kikuchi
- Division of Biological Sciences, University of California San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Samuel E Redford
- Division of Biological Sciences, University of California San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Arthur Prindle
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Jintao Liu
- Center for Infectious Diseases Research and Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, 100084 Beijing, China
| | - Sacha Greenfield
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA; Department of Physics and Astronomy, Carleton College, Northfield, MN 55057, USA
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, CNRS, PSL, Université Pierre et Marie Curie and École Normale Supérieure, Paris 75231, France
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Gürol M Süel
- Division of Biological Sciences, University of California San Diego, Pacific Hall Room 2225B, Mail Code 0347, 9500 Gilman Drive, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California San Diego, La Jolla, CA 92093, USA.
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24
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León MJ, Hoffmann T, Sánchez-Porro C, Heider J, Ventosa A, Bremer E. Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics. Front Microbiol 2018; 9:108. [PMID: 29497403 PMCID: PMC5818414 DOI: 10.3389/fmicb.2018.00108] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.
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Affiliation(s)
- María J León
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
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25
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Zhang M, Zhang X, Tong L, Wang Y, Ou D, Zhang J, Wu Q, Ye Y. Genes involved in tolerance to osmotic stress by random mutagenesis in Cronobacter malonaticus. J Dairy Sci 2018; 101:3851-3858. [PMID: 29454685 DOI: 10.3168/jds.2017-13995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/28/2017] [Indexed: 12/18/2022]
Abstract
Cronobacter malonaticus is one of the opportunistic food-borne pathogens in powdered infant formula and has unusual abilities to survive under environmental stresses such as osmotic conditions. However, the genes involved in osmotic stress have received little attention in C. malonaticus. Here, genes involved in osmotic stress were determined in C. malonaticus using a transposon mutagenesis approach. According to the growth of mutants (n = 215) under 5.0% NaCl concentration, the survival of 5 mutants under osmotic stress was significantly decreased compared with that of the wild type strain. Five mutating sites, including potassium efflux protein KefA, inner membrane protein YqjF, peptidylprolyl isomerase, Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase, and oligogalacturonate lyase were successfully identified. In addition, the biofilm formation of 5 mutants was determined using crystal violet staining, scanning electron microscopy, and confocal laser scanning microscopy, and the biofilms of 5 mutants significantly decreased within 72 h compared with that of wild type strain. This is the first report to determine the genes involved in osmotic tolerance in C. malonaticus. The findings provided valuable information for deep understanding of the mechanism of survival of C. malonaticus under osmotic stress, and a possible relationship between biofilm formation and tolerance to osmotic stress was also demonstrated in C. malonaticus.
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Affiliation(s)
- Maofeng Zhang
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Xiyan Zhang
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Liaowang Tong
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yaping Wang
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Dexin Ou
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China.
| | - Yingwang Ye
- School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China.
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Krainer G, Hartmann A, Anandamurugan A, Gracia P, Keller S, Schlierf M. Ultrafast Protein Folding in Membrane-Mimetic Environments. J Mol Biol 2018; 430:554-564. [DOI: 10.1016/j.jmb.2017.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/12/2017] [Accepted: 10/27/2017] [Indexed: 01/06/2023]
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Abstract
How do neighboring bacterial biofilms sense and communicate with each other? In a recent paper, Liu et al. (2017) demonstrate how electrical signaling allows communication of metabolic states between adjacent B. subtilis biofilms, providing a possible generalizable mechanism for communication in multispecies biofilms with interdependent metabolism.
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Affiliation(s)
- Elizabeth A Libby
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jonathan Dworkin
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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Nielsen SM, Meyer RL, Nørskov-Lauritsen N. Differences in Gene Expression Profiles between Early and Late Isolates in Monospecies Achromobacter Biofilm. Pathogens 2017; 6:E20. [PMID: 28534862 PMCID: PMC5488654 DOI: 10.3390/pathogens6020020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/12/2017] [Accepted: 05/14/2017] [Indexed: 11/30/2022] Open
Abstract
Bacteria of genus Achromobacter are emerging pathogens in cystic fibrosis (CF) capable of biofilm formation and development of antimicrobial resistance. Evolutionary adaptions in the transition from primary to chronic infection were assessed by transcriptomic analysis of successive isolates of Achromobacter xylosoxidans from a single CF patient. Several efflux pump systems targeting antimicrobial agents were upregulated during the course of the disease, whereas all genes related to motility were downregulated. Genes annotated to subsystems of sulfur metabolism, protein metabolism and potassium metabolism exhibited the strongest upregulation. K+ channel genes were hyperexpressed, and a putative sulfite oxidase was more than 1500 times upregulated. The transcriptome patterns indicated a pivotal role of sulfur metabolism and electrical signalling in Achromobacter biofilms during late stage CF lung disease.
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Affiliation(s)
- Signe M Nielsen
- Department of Clinical Medicine, Health, Aarhus University, DK-8200 Aarhus, Denmark.
- Department of Clinical Microbiology, Aarhus University Hospital, DK-8200 Aarhus, Denmark.
| | - Rikke L Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus, Denmark.
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Liu J, Martinez-Corral R, Prindle A, Lee DYD, Larkin J, Gabalda-Sagarra M, Garcia-Ojalvo J, Süel GM. Coupling between distant biofilms and emergence of nutrient time-sharing. Science 2017; 356:638-642. [PMID: 28386026 DOI: 10.1126/science.aah4204] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 03/24/2017] [Indexed: 01/05/2023]
Abstract
Bacteria within communities can interact to organize their behavior. It has been unclear whether such interactions can extend beyond a single community to coordinate the behavior of distant populations. We discovered that two Bacillus subtilis biofilm communities undergoing metabolic oscillations can become coupled through electrical signaling and synchronize their growth dynamics. Coupling increases competition by also synchronizing demand for limited nutrients. As predicted by mathematical modeling, we confirm that biofilms resolve this conflict by switching from in-phase to antiphase oscillations. This results in time-sharing behavior, where each community takes turns consuming nutrients. Time-sharing enables biofilms to counterintuitively increase growth under reduced nutrient supply. Distant biofilms can thus coordinate their behavior to resolve nutrient competition through time-sharing, a strategy used in engineered systems to allocate limited resources.
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Affiliation(s)
- Jintao Liu
- Division of Biological Sciences, University of California, San Diego, CA 92093, USA
| | - Rosa Martinez-Corral
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Arthur Prindle
- Division of Biological Sciences, University of California, San Diego, CA 92093, USA
| | - Dong-Yeon D Lee
- Division of Biological Sciences, University of California, San Diego, CA 92093, USA
| | - Joseph Larkin
- Division of Biological Sciences, University of California, San Diego, CA 92093, USA
| | - Marçal Gabalda-Sagarra
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gürol M Süel
- Division of Biological Sciences, University of California, San Diego, CA 92093, USA. .,San Diego Center for Systems Biology, University of California, San Diego, CA 92093, USA.,Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
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Sadiq FA, Flint S, Li Y, Liu T, Lei Y, Sakandar HA, He G. New mechanistic insights into the motile-to-sessile switch in various bacteria with particular emphasis on Bacillus subtilis and Pseudomonas aeruginosa: a review. BIOFOULING 2017; 33:306-326. [PMID: 28347177 DOI: 10.1080/08927014.2017.1304541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/04/2017] [Indexed: 06/06/2023]
Abstract
A biofilm is a complex assemblage of microbial communities adhered to a biotic or an abiotic surface which is embedded within a self-produced matrix of extracellular polymeric substances. Many transcriptional regulators play a role in triggering a motile-sessile switch and in consequently producing the biofilm matrix. This review is aimed at highlighting the role of two nucleotide signaling molecules (c-di-GMP and c-di-AMP), toxin antitoxin modules and a novel transcriptional regulator BolA in biofilm formation in various bacteria. In addition, it highlights the common themes that have appeared in recent research regarding the key regulatory components and signal transduction pathways that help Bacillus subtilis and Pseudomonas aeruginosa to acquire the biofilm mode of life.
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Affiliation(s)
- Faizan A Sadiq
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Steve Flint
- b School of Food and Nutrition , Massey University , Palmerston North , New Zealand
| | - Yun Li
- c School of Life Sciences and Food Technology , Hanshan Normal University , Chaozhou , PR China
| | - TongJie Liu
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Yuan Lei
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | | | - GuoQing He
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
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Wang L, Hu C, Shao L. The antimicrobial activity of nanoparticles: present situation and prospects for the future. Int J Nanomedicine 2017; 12:1227-1249. [PMID: 28243086 PMCID: PMC5317269 DOI: 10.2147/ijn.s121956] [Citation(s) in RCA: 1535] [Impact Index Per Article: 219.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nanoparticles (NPs) are increasingly used to target bacteria as an alternative to antibiotics. Nanotechnology may be particularly advantageous in treating bacterial infections. Examples include the utilization of NPs in antibacterial coatings for implantable devices and medicinal materials to prevent infection and promote wound healing, in antibiotic delivery systems to treat disease, in bacterial detection systems to generate microbial diagnostics, and in antibacterial vaccines to control bacterial infections. The antibacterial mechanisms of NPs are poorly understood, but the currently accepted mechanisms include oxidative stress induction, metal ion release, and non-oxidative mechanisms. The multiple simultaneous mechanisms of action against microbes would require multiple simultaneous gene mutations in the same bacterial cell for antibacterial resistance to develop; therefore, it is difficult for bacterial cells to become resistant to NPs. In this review, we discuss the antibacterial mechanisms of NPs against bacteria and the factors that are involved. The limitations of current research are also discussed.
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Affiliation(s)
- Linlin Wang
- Department of Stomatology, Hainan General Hospital, Haikou, Hainan
| | - Chen Hu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Longquan Shao
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
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Humphries J, Xiong L, Liu J, Prindle A, Yuan F, Arjes HA, Tsimring L, Süel GM. Species-Independent Attraction to Biofilms through Electrical Signaling. Cell 2017; 168:200-209.e12. [PMID: 28086091 DOI: 10.1016/j.cell.2016.12.014] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/17/2016] [Accepted: 12/09/2016] [Indexed: 12/30/2022]
Abstract
Bacteria residing within biofilm communities can coordinate their behavior through cell-to-cell signaling. However, it remains unclear if these signals can also influence the behavior of distant cells that are not part of the community. Using a microfluidic approach, we find that potassium ion channel-mediated electrical signaling generated by a Bacillus subtilis biofilm can attract distant cells. Integration of experiments and mathematical modeling indicates that extracellular potassium emitted from the biofilm alters the membrane potential of distant cells, thereby directing their motility. This electrically mediated attraction appears to be a generic mechanism that enables cross-species interactions, as Pseudomonas aeruginosa cells also become attracted to the electrical signal released by the B. subtilis biofilm. Cells within a biofilm community can thus not only coordinate their own behavior but also influence the behavior of diverse bacteria at a distance through long-range electrical signaling. PAPERCLIP.
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Affiliation(s)
- Jacqueline Humphries
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liyang Xiong
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jintao Liu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arthur Prindle
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fang Yuan
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi A Arjes
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5101, USA
| | - Lev Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gürol M Süel
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
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Kröber M, Verwaaijen B, Wibberg D, Winkler A, Pühler A, Schlüter A. Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing. J Biotechnol 2016; 231:212-223. [PMID: 27312701 DOI: 10.1016/j.jbiotec.2016.06.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/23/2016] [Accepted: 06/12/2016] [Indexed: 10/21/2022]
Abstract
The strain Bacillus amyloliquefaciens FZB42 is a plant growth promoting rhizobacterium (PGPR) and biocontrol agent known to keep infections of lettuce (Lactuca sativa) by the phytopathogen Rhizoctonia solani down. Several mechanisms, including the production of secondary metabolites possessing antimicrobial properties and induction of the host plant's systemic resistance (ISR), were proposed to explain the biocontrol effect of the strain. B. amyloliquefaciens FZB42 is able to form plaques (biofilm-like structures) on plant roots and this feature was discussed to be associated with its biocontrol properties. For this reason, formation of B. amyloliquefaciens biofilms was studied at the transcriptional level using high-throughput sequencing of whole transcriptome cDNA libraries from cells grown under biofilm-forming conditions vs. planktonic growth. Comparison of the transcriptional profiles of B. amyloliquefaciens FZB42 under these growth conditions revealed a common set of highly transcribed genes mostly associated with basic cellular functions. The lci gene, encoding an antimicrobial peptide (AMP), was among the most highly transcribed genes of cells under both growth conditions suggesting that AMP production may contribute to biocontrol. In contrast, gene clusters coding for synthesis of secondary metabolites with antimicrobial properties were only moderately transcribed and not induced in biofilm-forming cells. Differential gene expression revealed that 331 genes were significantly up-regulated and 230 genes were down-regulated in the transcriptome of B. amyloliquefaciens FZB42 under biofilm-forming conditions in comparison to planktonic cells. Among the most highly up-regulated genes, the yvqHI operon, coding for products involved in nisin (class I bacteriocin) resistance, was identified. In addition, an operon whose products play a role in fructosamine metabolism was enhanced in its transcription. Moreover, genes involved in the production of the extracellular biofilm matrix including exopolysaccharide genes (eps) and the yqxM-tasA-sipW operon encoding amyloid fiber synthesis were up-regulated in the B. amyloliquefaciens FZB42 biofilm. On the other hand, highly down-regulated genes in biofilms are associated with synthesis, assembly and regulation of the flagellar apparatus, the degradation of aromatic compounds and the export of copper. The obtained transcriptional profile for B. amyloliquefaciens biofilm cells uncovered genes involved in its development and enabled the assessment that synthesis of secondary metabolites among other factors may contribute to the biocontrol properties of the strain.
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Affiliation(s)
- Magdalena Kröber
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Bart Verwaaijen
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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Peng X, Zhang Y, Bai G, Zhou X, Wu H. Cyclic di-AMP mediates biofilm formation. Mol Microbiol 2016; 99:945-59. [PMID: 26564551 PMCID: PMC5003771 DOI: 10.1111/mmi.13277] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2015] [Indexed: 12/27/2022]
Abstract
Cyclic di-AMP (c-di-AMP) is an emerging second messenger in bacteria. It has been shown to play important roles in bacterial fitness and virulence. However, transduction of c-di-AMP signaling in bacteria and the role of c-di-AMP in biofilm formation are not well understood. The level of c-di-AMP is modulated by activity of di-adenylyl cyclase that produces c-di-AMP and phosphodiesterase (PDE) that degrades c-di-AMP. In this study, we determined that increased c-di-AMP levels by deletion of the pdeA gene coding for a PDE promoted biofilm formation in Streptococcus mutans. Deletion of pdeA upregulated expression of gtfB, the gene coding for a major glucan producing enzyme. Inactivation of gtfB blocked the increased biofilm by the pdeA mutant. Two c-di-AMP binding proteins including CabPA (SMU_1562) and CabPB (SMU_1708) were identified. Interestingly, only CabPA deficiency inhibited both the increased biofilm formation and the upregulated expression of GtfB observed in the pdeA mutant. In addition, CabPA but not CabPB interacted with VicR, a known transcriptional factor that regulates expression of gtfB, suggesting that a signaling link between CabPA and GtfB through VicR. Increased biofilm by the pdeA deficiency also enhanced bacterial colonization of Drosophila in vivo. Taken together, our studies reveal a new role of c-di-AMP in mediating biofilm formation through a CabPA/VicR/GtfB signaling network in S. mutans.
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Affiliation(s)
- Xian Peng
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, AL, USA
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
| | - Yang Zhang
- Center for Immunology and Microbial Disease, MC-151, Albany Medical College, 47 New Scotland Avenue, Albany, NY, USA
| | - Guangchun Bai
- Center for Immunology and Microbial Disease, MC-151, Albany Medical College, 47 New Scotland Avenue, Albany, NY, USA
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
| | - Hui Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, AL, USA
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Ion channels enable electrical communication in bacterial communities. Nature 2015; 527:59-63. [PMID: 26503040 DOI: 10.1038/nature15709] [Citation(s) in RCA: 408] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/10/2015] [Indexed: 12/15/2022]
Abstract
The study of bacterial ion channels has provided fundamental insights into the structural basis of neuronal signalling; however, the native role of ion channels in bacteria has remained elusive. Here we show that ion channels conduct long-range electrical signals within bacterial biofilm communities through spatially propagating waves of potassium. These waves result from a positive feedback loop, in which a metabolic trigger induces release of intracellular potassium, which in turn depolarizes neighbouring cells. Propagating through the biofilm, this wave of depolarization coordinates metabolic states among cells in the interior and periphery of the biofilm. Deletion of the potassium channel abolishes this response. As predicted by a mathematical model, we further show that spatial propagation can be hindered by specific genetic perturbations to potassium channel gating. Together, these results demonstrate a function for ion channels in bacterial biofilms, and provide a prokaryotic paradigm for active, long-range electrical signalling in cellular communities.
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Grau RR, de Oña P, Kunert M, Leñini C, Gallegos-Monterrosa R, Mhatre E, Vileta D, Donato V, Hölscher T, Boland W, Kuipers OP, Kovács ÁT. A Duo of Potassium-Responsive Histidine Kinases Govern the Multicellular Destiny of Bacillus subtilis. mBio 2015; 6:e00581. [PMID: 26152584 PMCID: PMC4495169 DOI: 10.1128/mbio.00581-15] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/01/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Multicellular biofilm formation and surface motility are bacterial behaviors considered mutually exclusive. However, the basic decision to move over or stay attached to a surface is poorly understood. Here, we discover that in Bacillus subtilis, the key root biofilm-controlling transcription factor Spo0A~Pi (phosphorylated Spo0A) governs the flagellum-independent mechanism of social sliding motility. A Spo0A-deficient strain was totally unable to slide and colonize plant roots, evidencing the important role that sliding might play in natural settings. Microarray experiments plus subsequent genetic characterization showed that the machineries of sliding and biofilm formation share the same main components (i.e., surfactin, the hydrophobin BslA, exopolysaccharide, and de novo-formed fatty acids). Sliding proficiency was transduced by the Spo0A-phosphorelay histidine kinases KinB and KinC. We discovered that potassium, a previously known inhibitor of KinC-dependent biofilm formation, is the specific sliding-activating signal through a thus-far-unnoticed cytosolic domain of KinB, which resembles the selectivity filter sequence of potassium channels. The differential expression of the Spo0A~Pi reporter abrB gene and the different levels of the constitutively active form of Spo0A, Sad67, in Δspo0A cells grown in optimized media that simultaneously stimulate motile and sessile behaviors uncover the spatiotemporal response of KinB and KinC to potassium and the gradual increase in Spo0A~Pi that orchestrates the sequential activation of sliding, followed by sessile biofilm formation and finally sporulation in the same population. Overall, these results provide insights into how multicellular behaviors formerly believed to be antagonistic are coordinately activated in benefit of the bacterium and its interaction with the host. IMPORTANCE Alternation between motile and sessile behaviors is central to bacterial adaptation, survival, and colonization. However, how is the collective decision to move over or stay attached to a surface controlled? Here, we use the model plant-beneficial bacterium Bacillus subtilis to answer this question. Remarkably, we discover that sessile biofilm formation and social sliding motility share the same structural components and the Spo0A regulatory network via sensor kinases, KinB and KinC. Potassium, an inhibitor of KinC-dependent biofilm formation, triggers sliding via a potassium-perceiving cytosolic domain of KinB that resembles the selectivity filter of potassium channels. The spatiotemporal response of these kinases to variable potassium levels and the gradual increase in Spo0A~Pi levels that orchestrates the activation of sliding before biofilm formation shed light on how multicellular behaviors formerly believed to be antagonistic work together to benefit the population fitness.
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Affiliation(s)
- Roberto R Grau
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Paula de Oña
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Maritta Kunert
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Cecilia Leñini
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Darío Vileta
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Verónica Donato
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR)-CONICET, Argentina
| | - Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Oscar P Kuipers
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
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Marino J, Hohl M, Seeger MA, Zerbe O, Geertsma ER. Bicistronic mRNAs to enhance membrane protein overexpression. J Mol Biol 2014; 427:943-954. [PMID: 25451035 DOI: 10.1016/j.jmb.2014.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/31/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
Abstract
Functional overexpression of membrane proteins is essential for their structural and functional characterization. However, functional overexpression is often difficult to achieve, and frequently either no expression or expression as misfolded aggregates is observed. We present an approach for improving the functional overexpression of membrane proteins in Escherichia coli using transcriptional fusions. The method involves the use of a small additional RNA sequence upstream to the RNA sequence of the target membrane protein and results in the production of a bicistronic mRNA. In contrast to the common approach of translational fusions to enhance protein expression, transcriptional fusions do not require protease treatment and subsequent removal of the fusion protein. Using this strategy, we observed improvements in the quantity and/or the quality of the produced material for several membrane proteins to levels compatible with structural studies. Our analysis revealed that translation of the upstream RNA sequence was not essential for increased expression. Rather, the sequence itself had a large impact on protein yields, suggesting that alternative folding of the transcript was responsible for the observed effect.
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Affiliation(s)
- Jacopo Marino
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Hohl
- Institute of Medical Microbiology, University of Zurich, 8057 Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, 8057 Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
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Marino J, Bordag N, Keller S, Zerbe O. Mistic's membrane association and its assistance in overexpression of a human GPCR are independent processes. Protein Sci 2014; 24:38-48. [PMID: 25297828 DOI: 10.1002/pro.2582] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/15/2014] [Accepted: 10/06/2014] [Indexed: 01/19/2023]
Abstract
The interaction of the Bacillus subtilis protein Mistic with the bacterial membrane and its role in promoting the overexpression of other membrane proteins are still matters of debate. In this study, we aimed to determine whether individual helical fragments of Mistic are sufficient for its interaction with membranes in vivo and in vitro. To this end, fragments encompassing each of Mistic's helical segments and combinations of them were produced as GFP-fusions, and their cellular localization was studied in Escherichia coli. Furthermore, peptides corresponding to the four helical fragments were synthesized by solid-phase peptide synthesis, and their ability to acquire secondary structure in a variety of lipids and detergents was studied by circular dichroism spectroscopy. Both types of experiments demonstrate that the third helical fragment of Mistic interacts only with LDAO micelles but does not partition into lipid bilayers. Interestingly, the other three helices interact with membranes in vivo and in vitro. Nevertheless, all of these short sequences can replace full-length Mistic as N-terminal fusions to achieve overexpression of a human G-protein-coupled receptor in E. coli, although with different effects on quantity and quality of the protein produced. A bioinformatic analysis of the Mistic family expanded the number of homologs from 4 to 20, including proteins outside the genus Bacillus. This information allowed us to discover a highly conserved Shine-Dalgarno sequence in the operon mstX-yugO that is important for downstream translation of the potassium ion channel yugO.
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Affiliation(s)
- Jacopo Marino
- Department of Chemistry, University of Zürich, Switzerland
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Broecker J, Fiedler S, Gimpl K, Keller S. Polar Interactions Trump Hydrophobicity in Stabilizing the Self-Inserting Membrane Protein Mistic. J Am Chem Soc 2014; 136:13761-8. [DOI: 10.1021/ja5064795] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jana Broecker
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
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Stress responses of the industrial workhorse Bacillus licheniformis to osmotic challenges. PLoS One 2013; 8:e80956. [PMID: 24348917 PMCID: PMC3858371 DOI: 10.1371/journal.pone.0080956] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Gram-positive endospore-forming bacterium Bacillus licheniformis can be found widely in nature and it is exploited in industrial processes for the manufacturing of antibiotics, specialty chemicals, and enzymes. Both in its varied natural habitats and in industrial settings, B. licheniformis cells will be exposed to increases in the external osmolarity, conditions that trigger water efflux, impair turgor, cause the cessation of growth, and negatively affect the productivity of cell factories in biotechnological processes. We have taken here both systems-wide and targeted physiological approaches to unravel the core of the osmostress responses of B. licheniformis. Cells were suddenly subjected to an osmotic upshift of considerable magnitude (with 1 M NaCl), and their transcriptional profile was then recorded in a time-resolved fashion on a genome-wide scale. A bioinformatics cluster analysis was used to group the osmotically up-regulated genes into categories that are functionally associated with the synthesis and import of osmostress-relieving compounds (compatible solutes), the SigB-controlled general stress response, and genes whose functional annotation suggests that salt stress triggers secondary oxidative stress responses in B. licheniformis. The data set focusing on the transcriptional profile of B. licheniformis was enriched by proteomics aimed at identifying those proteins that were accumulated by the cells through increased biosynthesis in response to osmotic stress. Furthermore, these global approaches were augmented by a set of experiments that addressed the synthesis of the compatible solutes proline and glycine betaine and assessed the growth-enhancing effects of various osmoprotectants. Combined, our data provide a blueprint of the cellular adjustment processes of B. licheniformis to both sudden and sustained osmotic stress.
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