1
|
Sarkar S, Kumari A, Tiwari M, Tiwari V. Interaction and simulation studies suggest the possible molecular targets of intrinsically disordered amyloidogenic antimicrobial peptides in Acinetobacter baumannii. J Biomol Struct Dyn 2024; 42:2747-2764. [PMID: 37144752 DOI: 10.1080/07391102.2023.2208219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
Acinetobacter baumannii is one of the causing agents of nosocomial infections. A wide range of antibiotics fails to work against these pathogens. Hence, there is an urgent requirement to develop other therapeutics to solve this problem. Antimicrobial peptides (AMPs) are a diverse group of naturally occurring peptides that have the ability to kill diverse groups of microorganisms. The major challenge of using AMPs as therapeutics is their unstable nature and the fact that most of their molecular targets are still unknown. In this study, we have selected intrinsically disordered and amyloidogenic AMPs, showing activity against A. baumannii, that is, Bactenecin, Cath BF, Citropin 1.1, DP7, NA-CATH, Tachyplesin, and WAM-1. To identify the probable target of these AMPs in A. baumannii, calculation of docking score, binding energy, dissociation constant, and molecular dynamics analysis was performed with selected seventeen possible molecular targets. The result showed that the most probable molecular targets of most of the intrinsically disordered amyloidogenic AMPs were UDP-N-acetylenol-pyruvoyl-glucosamine reductase (MurB), followed by 33-36 kDa outer membrane protein (Omp 33-36), UDP-N-acetylmuramoyl-l-alanyl-d-glutamate-2,6-diaminopimelate ligase (MurE), and porin Subfamily Protein (PorinSubF). Further, molecular dynamics analysis concluded that the target of antimicrobial peptide Bactenecin is MurB of A. baumannii, and identified other molecular targets of selected AMPs. Additionally, the oligomerization capacity of the selected AMPs was also investigated, and it was shown that the selected AMPs form oligomeric states, and interact with their molecular targets in that state. Experimental validation using purified AMPs and molecular targets needs to be done to confirm the interaction.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sayani Sarkar
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Aruna Kumari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| |
Collapse
|
2
|
Wu J, Zhang HL, Guo S, Li X, Dong T, Zhu Y, Tsim KWK. Acori Tatarinowii Rhizoma prevents the fluoxetine-induced multiple-drug resistance of Escherichia coli against antibiotics. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 123:155232. [PMID: 38006809 DOI: 10.1016/j.phymed.2023.155232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/12/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND In treating depression, the residual anti-depressant in gut interacts with the microbiome, leading to the appearance of multiple drug resistant (MDR) mutants, which poses a challenge for the treatment of infectious complications. Strategy is needed to combat this issue. Acori Tatarinowii Rhizoma (ATR, rhizome of Acorus tatarinowii Schott, Araceae), a traditional Chinese medicine, has been widely used for treatment of neurological disorders and gastrointestinal digestive disease in China. Here, ATR was demonstrated an excellent MDR-preventing effect in fluoxetine-induced Escherichia coli (E. coli). AIM OF THE STUDY This study aimed to reveal the effective role of ATR and its signaling cascades involved in preventing fluoxetine-induced MDR. MATERIALS AND METHODS The water extract of ATR was co-applied with sub-minimum inhibitory concentration (100 mg/l) of fluoxetine in E. coli to evaluate its anti-MDR potential. Formation of reactive oxygen species (ROS) and expression of MDR-related genes in bacteria were measured by dichloro-dihydro-fluorescein diacetate assay and real-time PCR, respectively. Two fluorescent dyes, 1-N-phenylnapthylamine and 3,3'-dipropylthiadicarbocyanine were used to analyze the outer membrane permeability and inner membrane depolarization of E. coli. The accumulation of fluoxetine in the treated E. coli was determined via HPLC. The active fraction of ATR was identified. RESULTS The water extract of ATR significantly decreased the number of MDR mutants induced by fluoxetine and had half effective concentrations (EC50) of 55.5 μg/ml and 16.8 μg/ml for chloramphenicol and tetracycline, respectively. ATR robustly reversed the fluoxetine-induced superoxide response and membrane damage in E. coli. In addition, the inclusion of ATR significantly reduced the accumulation of fluoxetine in E. coli. After further fractionation, the polysaccharide of ATR was demonstrated as the fraction with the most significant anti-MDR activity. CONCLUSIONS This is the first report to investigate the MDR-preventing effect of ATR. The results of this study proposed ATR as an excellent herbal product to prevent MDR issues, as induced by fluoxetine, with the potential to reduce the side effects during the drug therapy of depression.
Collapse
Affiliation(s)
- Jiahui Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hoi Lam Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Suisui Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xin Li
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae and Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nan Jing, Jiangsu Province, China
| | - Tingxia Dong
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Shenzhen, China
| | - Yue Zhu
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae and Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nan Jing, Jiangsu Province, China
| | - Karl Wah Keung Tsim
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Shenzhen, China.
| |
Collapse
|
3
|
Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K. Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress. mSystems 2023; 8:e0103723. [PMID: 37909716 PMCID: PMC10746267 DOI: 10.1128/msystems.01037-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.
Collapse
Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| |
Collapse
|
4
|
Nestorovich EM, Bezrukov SM. Beta-Barrel Channel Response to High Electric Fields: Functional Gating or Reversible Denaturation? Int J Mol Sci 2023; 24:16655. [PMID: 38068977 PMCID: PMC10706840 DOI: 10.3390/ijms242316655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Ion channels exhibit gating behavior, fluctuating between open and closed states, with the transmembrane voltage serving as one of the essential regulators of this process. Voltage gating is a fundamental functional aspect underlying the regulation of ion-selective, mostly α-helical, channels primarily found in excitable cell membranes. In contrast, there exists another group of larger, and less selective, β-barrel channels of a different origin, which are not directly associated with cell excitability. Remarkably, these channels can also undergo closing, or "gating", induced by sufficiently strong electric fields. Once the field is removed, the channels reopen, preserving a memory of the gating process. In this study, we explored the hypothesis that the voltage-induced closure of the β-barrel channels can be seen as a form of reversible protein denaturation by the high electric fields applied in model membranes experiments-typically exceeding twenty million volts per meter-rather than a manifestation of functional gating. Here, we focused on the bacterial outer membrane channel OmpF reconstituted into planar lipid bilayers and analyzed various characteristics of the closing-opening process that support this idea. Specifically, we considered the nearly symmetric response to voltages of both polarities, the presence of multiple closed states, the stabilization of the open conformation in channel clusters, the long-term gating memory, and the Hofmeister effects in closing kinetics. Furthermore, we contemplate the evolutionary aspect of the phenomenon, proposing that the field-induced denaturation of membrane proteins might have served as a starting point for their development into amazing molecular machines such as voltage-gated channels of nerve and muscle cells.
Collapse
Affiliation(s)
- Ekaterina M. Nestorovich
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Sergey M. Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| |
Collapse
|
5
|
Li S, Chen D, Liu Z, Tao S, Zhang T, Chen Y, Bao L, Ma J, Huang Y, Xu S, Wu L, Chen S. Directed evolution of TetR for constructing sensitive and broad-spectrum tetracycline antibiotics whole-cell biosensor. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132311. [PMID: 37633019 DOI: 10.1016/j.jhazmat.2023.132311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/02/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Antibiotic abuse is the main reason for the drug resistance of pathogenic bacteria, posing a potential health risk. Antibiotic surveillance is critical for preventing antibiotic contamination. This study aimed to develop a sensitive and broad-spectrum whole-cell biosensor for tetracycline antibiotics (TCs) detection. Wild-type TCs-responsive biosensor was constructed by introducing a tetracycline operon into a sfGFP reporter plasmid. Using error-prone PCR, mutation libraries containing approximately 107 variants of the tetracycline repressor (TetR) gene were generated. The tigecycline-senstive mutants were isolated using high-throughput flow cytometric sorting. After 2 rounds of directed evolution, a mutant epS2-22 of TerR was isolated and assembled as a TCs biosensor. The epS2-22 biosensor was more sensitive and broad-spectrum than the wild-type biosensors. The detection limits of the epS2-22 biosensor for seven TCs were 4- to 62-fold lower than the wild-type biosensor (no response to tigecycline). Meanwhile, the epS2-22 biosensor had a shorter detection time and a stronger signal output than the wild type. In addition, the evolved epS2-22 biosensor showed excellent performance in detecting low traces of TCs in environmental water. These results suggest that directed evolution is a powerful tool for developing high-performance whole-cell biosensors, and the evolved epS2-22 biosensors have the potential for wider applications in real-world TCs detection.
Collapse
Affiliation(s)
- Shunlan Li
- School of Public Health, Wannan Medical College, Wuhu 241002, China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Dongdong Chen
- School of Public Health, Wannan Medical College, Wuhu 241002, China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Ziqing Liu
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Shipin Tao
- School of Public Health, Wannan Medical College, Wuhu 241002, China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Tianyi Zhang
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Yiwen Chen
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Lingzhi Bao
- School of Public Health, Wannan Medical College, Wuhu 241002, China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Jie Ma
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Yuee Huang
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Lijun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Shaopeng Chen
- School of Public Health, Wannan Medical College, Wuhu 241002, China.
| |
Collapse
|
6
|
Sajeev-Sheeja A, Smorodina E, Zhang S. Structural bioinformatics studies of bacterial outer membrane beta-barrel transporters and their AlphaFold2 predicted water-soluble QTY variants. PLoS One 2023; 18:e0290360. [PMID: 37607179 PMCID: PMC10443868 DOI: 10.1371/journal.pone.0290360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Beta-barrel outer membrane proteins (OMP) are integral components of Gram-negative bacteria, eukaryotic mitochondria, and chloroplasts. They play essential roles in various cellular processes including nutrient transport, membrane stability, host-pathogen interactions, antibiotic resistance and more. The advent of AlphaFold2 for accurate protein structure predictions transformed structural bioinformatic studies. We previously used a QTY code to convert hydrophobic alpha-helices to hydrophilic alpha-helices in over 50 membrane proteins with all alpha-helices. The QTY code systematically replaces hydrophobic leucine (L), isoleucine (I), valine (V), and phenylalanine (F) with hydrophilic glutamine (Q), threonine (T), and tyrosine (Y). We here present a structural bioinformatic analysis of five outer membrane beta-barrel proteins with known molecular structures, including a) BamA, b) Omp85 (also called Sam50), c) FecA, d) Tsx, and e) OmpC. We superposed the structures of five native beta-barrel outer membrane proteins and their AlphaFold2-predicted corresponding QTY variant structures. The superposed structures of OMPs and their QTY variants exhibit remarkable structural similarity, as evidenced by residue mean square distance (RMSD) values between 0.206Å to 0.414Å despite the replacement of at least 22% (Transmembrane variation) of the amino acids in the transmembrane regions. We also show that native outer membrane proteins and QTY variants have different hydrophobicity patches. Our study provides important insights into the differences between hydrophobic and hydrophilic beta-barrels and validates the QTY code for studying beta-barrel membrane proteins and perhaps other hydrophobic aggregated proteins. Our findings demonstrate that the QTY code can be used as a simple tool for designing hydrophobic proteins in various biological contexts.
Collapse
Affiliation(s)
- Akash Sajeev-Sheeja
- Department of Chemistry, Indian Institute of Science Education and Research, Srinivasapuram, Yerpedu Mandal, Tirupati Dist, Tirupati, Andhra Pradesh, India
| | - Eva Smorodina
- Department of Immunology, Laboratory for Computational and Systems Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| |
Collapse
|
7
|
Kadeřábková N, Mahmood AJS, Furniss RCD, Mavridou DAI. Making a chink in their armor: Current and next-generation antimicrobial strategies against the bacterial cell envelope. Adv Microb Physiol 2023; 83:221-307. [PMID: 37507160 PMCID: PMC10517717 DOI: 10.1016/bs.ampbs.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Gram-negative bacteria are uniquely equipped to defeat antibiotics. Their outermost layer, the cell envelope, is a natural permeability barrier that contains an array of resistance proteins capable of neutralizing most existing antimicrobials. As a result, its presence creates a major obstacle for the treatment of resistant infections and for the development of new antibiotics. Despite this seemingly impenetrable armor, in-depth understanding of the cell envelope, including structural, functional and systems biology insights, has promoted efforts to target it that can ultimately lead to the generation of new antibacterial therapies. In this article, we broadly overview the biology of the cell envelope and highlight attempts and successes in generating inhibitors that impair its function or biogenesis. We argue that the very structure that has hampered antibiotic discovery for decades has untapped potential for the design of novel next-generation therapeutics against bacterial pathogens.
Collapse
Affiliation(s)
- Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Ayesha J S Mahmood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, United States.
| |
Collapse
|
8
|
Rojas-Luna L, Posadas-Modragón A, Avila-Trejo AM, Alcántara-Farfán V, Rodríguez-Páez LI, Santiago-Cruz JA, Pastor-Alonso MO, Aguilar-Faisal JL. Inhibition of chikungunya virus replication by N-ω-Chloroacetyl-L-Ornithine in C6/36, Vero cells and human fibroblast BJ. Antivir Ther 2023; 28:13596535231155263. [PMID: 36724136 DOI: 10.1177/13596535231155263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Polyamines are involved in several cellular processes and inhibiting their synthesis affects chikungunya virus (CHIKV) replication and translation, and, therefore, reduces the quantity of infectious viral particles produced. In this study, we evaluated the inhibition of CHIKV replication by N-ω-chloroacetyl-L-ornithine (NCAO), a competitive inhibitor of ornithine decarboxylase, an enzyme which is key in the biosynthesis of polyamines (PAs). METHODS The cytotoxicity of NCAO was evaluated by MTT in cell culture. The inhibitory effect of CHIKV replication by NCAO was evaluated in Vero and C6/36 cells. The intracellular polyamines were quantified by HPLC in CHIKV-infected cells. We evaluated the yield of CHIKV in titres via the addition of PAs in Vero, C6/36 cells and human fibroblast BJ treated with NCAO. RESULTS We found that NCAO inhibits the replication of CHIKV in Vero and C6/36 cells in a dose-dependent manner, causing a decrease in the PFU/mL of at least 4 logarithms (p < 0.01) in both cell lines. Viral yields were restored by the addition of exogenous polyamines, mainly putrescine. The HPLC analyses showed that NCAO decreases the content of intracellular PAs, even though it is predominantly spermidines and spermines which are present in infected cells. Inhibition of CHIKV replication was observed in human fibroblast BJ treated with 100 μM NCAO 24 h before and 48 h after the infection at a MOI 1. CONCLUSIONS NCAO inhibits CHIKV replication by depleting the intracellular polyamines in Vero, C6/36 cells and human fibroblast BJ, suggesting that this compound is a possible antiviral agent for CHIKV.
Collapse
Affiliation(s)
- Lucero Rojas-Luna
- Laboratorio de Medicina de Conservación, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, 27740Instituto Politécnico Nacional, Mexico City, Mexico
| | - Araceli Posadas-Modragón
- Laboratorio de Medicina de Conservación, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, 27740Instituto Politécnico Nacional, Mexico City, Mexico
| | - Amanda M Avila-Trejo
- Laboratorio de Medicina de Conservación, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, 27740Instituto Politécnico Nacional, Mexico City, Mexico.,Laboratorio de Bioquímica Farmacológica, 61735Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Verónica Alcántara-Farfán
- Laboratorio de Bioquímica Farmacológica, 61735Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Lorena I Rodríguez-Páez
- Laboratorio de Bioquímica Farmacológica, 61735Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - José Angel Santiago-Cruz
- Laboratorio de Medicina de Conservación, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, 27740Instituto Politécnico Nacional, Mexico City, Mexico
| | - Marvin O Pastor-Alonso
- Laboratorio de Medicina de Conservación, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, 27740Instituto Politécnico Nacional, Mexico City, Mexico
| | - J Leopoldo Aguilar-Faisal
- Laboratorio de Medicina de Conservación, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, 27740Instituto Politécnico Nacional, Mexico City, Mexico
| |
Collapse
|
9
|
Zhan L, Hou Z, Wang Y, Liu H, Liu Y, Huang G. Rapid Profiling of Metabolic Perturbations to Antibiotics in Living Bacteria by Induced Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1960-1966. [PMID: 36106750 DOI: 10.1021/jasms.2c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rapid monitoring of real bacterial metabolic perturbations to antibiotics may be helpful to better understand the mechanisms of action and more targeted treatment. In this study, the real metabolic responses to antibiotic treatment in living bacteria were profiled rapidly by induced electrospray ionization mass spectrometry. Significant metabolic perturbations were profiled after antibiotic treatment compared with untreated bacteria. Similar and unique metabolic responses were observed with different antibiotic treatments. Further multivariable analysis was performed to determine significant metabolites as potential biomarkers. Moreover, different metabolic disturbances were detected for serial dilutions of antibiotic treatments. Overall, combined with induced electrospray ionization mass spectrometry, the rapid and real bacterial metabolic status caused by antibiotics was monitored, suggesting the potential application of our method in mechanism exploration and clinical diagnosis.
Collapse
Affiliation(s)
- Liujuan Zhan
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China
- School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China
| | - Zhuanghao Hou
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China
- School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China
| | - Yu Wang
- School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China
| | - Huimin Liu
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China
- School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China
| | - Yangzhong Liu
- School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China
| | - Guangming Huang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China
- School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China
| |
Collapse
|
10
|
Liu D, Shi H, Chen G, Zhang X, Gu T, Zhu M, Tan W. Strategies for anti-oxidative stress and anti-acid stress in bioleaching of LiCoO 2 using an acidophilic microbial consortium. Extremophiles 2022; 26:22. [PMID: 35767155 DOI: 10.1007/s00792-022-01270-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/17/2022] [Indexed: 11/04/2022]
Abstract
High metal ion concentrations and low pH cause severely inhibit the activity of an acidophilic microbial consortium (AMC) in bioleaching. This work investigated the effects of exogenous spermine on biofilm formation and the bioleaching efficiency of LiCoO2 by AMC in 9K medium. After the addition of 1 mM spermine, the activities of glutathione peroxidase and catalase increased, while the amount of H2O2, intracellular reactive oxygen species (ROS) and malondialdehyde in AMC decreased. These results indicated that the ability of AMC biofilm to resist oxidative stress introduced by 3.5 g/L Li+ and 30.1 g/L Co2+ was improved by spermine. The activity of glutamate decarboxylase was promoted to restore the intracellular pH buffering ability of AMC. Electrochemical measurements showed that the oxidation rate of pyrite was increased by exogenous spermine. As a result, high bioleaching efficiencies of 97.1% for Li+ and 96.1% for Co2+ from a 5.0% (w v-1) lithium cobalt oxide powder slurry were achieved. This work demonstrated that Tafel polarization can be used to monitor the AMC biofilm's ability of uptaking electrons from pyrite during bioleaching. The corrosion current density increased with 1 mM spermine, indicating enhanced electron uptake by the biofilm from pyrite.
Collapse
Affiliation(s)
- Dehong Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hongjie Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Guanglin Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, OH, USA.
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| |
Collapse
|
11
|
Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH, Palsson BO. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Sci Rep 2022; 12:7274. [PMID: 35508583 PMCID: PMC9068703 DOI: 10.1038/s41598-022-11134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/14/2022] [Indexed: 11/24/2022] Open
Abstract
Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YcaN, YbhD, YgfI, YiaU, YneJ. We show that: (1) YbdO (tentatively re-named CitR) regulation has an effect on bacterial growth at low pH with citrate supplementation. CitR is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); (2) YgfI (tentatively re-named DhfA) activates the dhaKLM operon that encodes the phosphotransferase system, DhfA is involved in formate, glycerol and dihydroxyacetone utilization; (3) YiaU (tentatively re-named LpsR) regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase and resistance to oxacillin microaerobically; (4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of l-glutamate and putrescine as nitrogen/energy sources; and (5) YbhD and YcaN regulate adjacent y-genes on the genome. We have thus established the functions for four LTFs and identified the target genes for three LTFs.
Collapse
Affiliation(s)
- Irina A Rodionova
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA. .,Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA.
| | - Ye Gao
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA.,Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Jonathan Monk
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Ying Hefner
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Nicholas Wong
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Dmitry A Rodionov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Zhongge Zhang
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Milton H Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0116, USA. .,Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
| |
Collapse
|
12
|
Thiel CS, Vahlensieck C, Bradley T, Tauber S, Lehmann M, Ullrich O. Metabolic Dynamics in Short- and Long-Term Microgravity in Human Primary Macrophages. Int J Mol Sci 2021; 22:ijms22136752. [PMID: 34201720 PMCID: PMC8269311 DOI: 10.3390/ijms22136752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/24/2022] Open
Abstract
Microgravity acts on cellular systems on several levels. Cells of the immune system especially react rapidly to changes in gravity. In this study, we performed a correlative metabolomics analysis on short-term and long-term microgravity effects on primary human macrophages. We could detect an increased amino acid concentration after five minutes of altered gravity, that was inverted after 11 days of microgravity. The amino acids that reacted the most to changes in gravity were tightly clustered. The observed effects indicated protein degradation processes in microgravity. Further, glucogenic and ketogenic amino acids were further degraded to Glucose and Ketoleucine. The latter is robustly accumulated in short-term and long-term microgravity but not in hypergravity. We detected highly dynamic and also robust adaptative metabolic changes in altered gravity. Metabolomic studies could contribute significantly to the understanding of gravity-induced integrative effects in human cells.
Collapse
Affiliation(s)
- Cora S. Thiel
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
- Correspondence: (C.S.T.); (O.U.)
| | - Christian Vahlensieck
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
| | - Timothy Bradley
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
| | - Svantje Tauber
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
| | - Martin Lehmann
- Biocenter LMU Muenchen, Department of Biology I–Botany, Großhaderner Strasse 2–4, 82152 Planegg-Martinsried, Germany;
| | - Oliver Ullrich
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; (C.V.); (T.B.); (S.T.)
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, Überlandstrasse 271, 8600 Dübendorf, Switzerland
- Space Biotechnology, Department of Machine Design, Engineering Design and Product Development, Institute of Mechanical Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
- Space Medicine, Ernst-Abbe-Hochschule (EAH) Jena, Department of Industrial Engineering, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Space Life Sciences Laboratory (SLSL), Kennedy Space Center (KSC), 505 Odyssey Way, Exploration Park, FL 32953, USA
- Correspondence: (C.S.T.); (O.U.)
| |
Collapse
|
13
|
Iwadate Y, Ramezanifard R, Golubeva YA, Fenlon LA, Slauch JM. PaeA (YtfL) protects from cadaverine and putrescine stress in Salmonella Typhimurium and E. coli. Mol Microbiol 2021; 115:1379-1394. [PMID: 33481283 PMCID: PMC10923242 DOI: 10.1111/mmi.14686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Salmonella and E. coli synthesize, import, and export cadaverine, putrescine, and spermidine to maintain physiological levels and provide pH homeostasis. Both low and high intracellular levels of polyamines confer pleiotropic phenotypes or lethality. Here, we demonstrate that the previously uncharacterized inner membrane protein PaeA (YtfL) is required for reducing cytoplasmic cadaverine and putrescine concentrations. We identified paeA as a gene involved in stationary phase survival when cells were initially grown in acidic medium, in which they produce cadaverine. The paeA mutant is also sensitive to putrescine, but not to spermidine or spermine. Sensitivity to external cadaverine in stationary phase is only observed at pH > 8, suggesting that the polyamines need to be deprotonated to passively diffuse into the cell cytoplasm. In the absence of PaeA, intracellular polyamine levels increase and the cells lose viability. Degradation or modification of the polyamines is not relevant. Ectopic expression of the known cadaverine exporter, CadB, in stationary phase partially suppresses the paeA phenotype, and overexpression of PaeA in exponential phase partially complements a cadB mutant grown in acidic medium. These data support the hypothesis that PaeA is a cadaverine/putrescine exporter, reducing potentially toxic levels under certain stress conditions.
Collapse
Affiliation(s)
- Yumi Iwadate
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Rouhallah Ramezanifard
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Yekaterina A. Golubeva
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Luke A. Fenlon
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
- Current address: Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, Utah 84132
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| |
Collapse
|
14
|
Queralt-Martín M, Perini DA, Alcaraz A. Specific adsorption of trivalent cations in biological nanopores determines conductance dynamics and reverses ionic selectivity. Phys Chem Chem Phys 2021; 23:1352-1362. [PMID: 33367433 DOI: 10.1039/d0cp04486e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Adsorption processes are central to ionic transport in industrial and biological membrane systems. Multivalent cations modulate the conductive properties of nanofluidic devices through interactions with charged surfaces that depend principally on the ion charge number. Considering that ion channels are specialized valves that demand a sharp specificity in ion discrimination, we investigate the adsorption dynamics of trace amounts of different salts of trivalent cations in biological nanopores. We consider here OmpF from Escherichia coli, an archetypical protein nanopore, to probe the specificity of biological nanopores to multivalent cations. We systematically compare the effect of three trivalent electrolytes on OmpF current-voltage relationships and characterize the degree of rectification induced by each ion. We also analyze the open channel current noise to determine the existence of equilibrium/non-equilibrium mechanisms of ion adsorption and evaluate the extent of charge inversion through selectivity measurements. We show that the interaction of trivalent electrolytes with biological nanopores occurs via ion-specific adsorption yielding differential modulation of ion conduction and selectivity inversion. We also demonstrate the existence of non-equilibrium fluctuations likely related to ion-dependent trapping-detrapping processes. Our study provides fundamental information relevant to different biological and electrochemical systems where transport phenomena involve ion adsorption in charged surfaces under nanoscale confinement.
Collapse
Affiliation(s)
- María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - D Aurora Perini
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| |
Collapse
|
15
|
Gagic M, Kociova S, Smerkova K, Michalkova H, Setka M, Svec P, Pribyl J, Masilko J, Balkova R, Heger Z, Richtera L, Adam V, Milosavljevic V. One-pot synthesis of natural amine-modified biocompatible carbon quantum dots with antibacterial activity. J Colloid Interface Sci 2020; 580:30-48. [PMID: 32679365 DOI: 10.1016/j.jcis.2020.06.125] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 10/23/2022]
Abstract
In the present study, the thermal decomposition of citric acid in the presence of biogenic amine was used to synthesize four different functionalized carbon quantum dots (CQDs), namely, histamine-(HCQDs), putrescine-(PCQDs), cadaverine-(CCQDs) and spermine-(SCQDs). The thermal decomposition of the precursors resulted in a decrease in stability and the formation of surface amides via a cross-linking process between the carboxyl and amine groups. The deposition of biogenic amines was confirmed by a structural characterization of the synthesized CQDs. The resulting CQDs, with a net zero charge, exhibited excellent stability in environments with different pH values. Through a set of different cytotoxicity tests, the absence of gene mutations, apoptosis, necrosis or disruption in cell membranes revealed the high biocompatibility of the CQDs. The antimicrobial activity of the synthesized CQDs was investigated against different bacterial species (Staphylococcus aureus, Escherichia coli, and Klebsiella pneumonia). We determined the growth kinetics, production of reactive oxygen species (ROS), cell viability and changes in membrane integrity by scanning electron microscopy (SEM). The minimal inhibitory concentrations (MICs) for S. aureus ranged from 3.4 to 6.9 µg/mL. Regarding E.coli and K. pneumonia, all CQD formulations reduced growth, and the MICs were determined for CCQDs and HCQDs (6.9-19.4 µg/mL). The antibacterial activity mechanism was attributed to the oxidative stress generated after CQD treatment, which resulted in the destabilization of the bacterial membrane. The bacterial permeability to propidium iodide indicated a change in membrane integrity, and the effect of CQDs on the morphology of the bacterial cells was evidenced by SEM.
Collapse
Affiliation(s)
- Milica Gagic
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Silvia Kociova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Kristyna Smerkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; Central European Institute of Technology, Purkyňova 123, 61 200 Brno, Czech Republic
| | - Hana Michalkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Milena Setka
- Central European Institute of Technology, Purkyňova 123, 61 200 Brno, Czech Republic
| | - Pavel Svec
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Jan Pribyl
- CEITEC MU, Masaryk University, Kamenice 5/A35, 62 500 Brno, Czech Republic
| | - Jiri Masilko
- Brno University of Technology, Institute of Materials Chemistry, Purkyňova 464/118, 612 00 Brno, Czech Republic
| | - Radka Balkova
- Brno University of Technology, Institute of Materials Chemistry, Purkyňova 464/118, 612 00 Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; Central European Institute of Technology, Purkyňova 123, 61 200 Brno, Czech Republic
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; Central European Institute of Technology, Purkyňova 123, 61 200 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; Central European Institute of Technology, Purkyňova 123, 61 200 Brno, Czech Republic
| | - Vedran Milosavljevic
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; Central European Institute of Technology, Purkyňova 123, 61 200 Brno, Czech Republic.
| |
Collapse
|
16
|
Lee J, Kim M, Jeong SE, Park HY, Jeon CO, Park W. Amentoflavone, a novel cyanobacterial killing agent from Selaginella tamariscina. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121312. [PMID: 31699478 DOI: 10.1016/j.jhazmat.2019.121312] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 05/10/2023]
Abstract
Harmful cyanobacterial bloom (HCB) by Microcystis aeruginosa is increasingly becoming a serious concern to the environment and human health alike. Currently, many physical, chemical, and biological controls are underway to eliminate HCB, but natural chemicals are rarely used. To find a control agent with low environmental toxicity and high potential for practical use, 60 plant extracts were screened. Only Selaginella tamariscina extract killed all four Microcystis aeruginosa strains, but not the other tested bacteria. Chloroform fraction of S. tamariscina extract (CSE) showed the highest killing activity. The effects of CSE on M. aeruginosa were monitored using differential interference contrast microscopy and flow-cytometry analysis, scanning electron microscopy, and transmission electron microscopy. The images showed that CSE-treated cells were abnormally altered, with damaged cell membranes, peptidoglycan layers, and cytoplasm. Quadrupole time-of-flight liquid chromatography-mass spectrometry was used to identify amentoflavone as a major active compound. Pure amentoflavone, even at low concentrations showed a powerful killing effect on M. aeruginosa, but not on other non-cyanobacteria. Overall, in this study, we have highlighted the potentials of S. tamariscina extracts and amentoflavone as selective HCB control agents.
Collapse
Affiliation(s)
- Jaebok Lee
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hye Yoon Park
- National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
| |
Collapse
|
17
|
Graça-Lopes G, Graça G, Barahona S, Moreira RN, Arraiano CM, Gonçalves LG. NMR-Metabolomics Shows That BolA Is an Important Modulator of Salmonella Typhimurium Metabolic Processes under Virulence Conditions. Metabolites 2019; 9:metabo9110243. [PMID: 31652780 PMCID: PMC6918366 DOI: 10.3390/metabo9110243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/28/2022] Open
Abstract
BolA is a ubiquitous global transcription factor. Despite its clear role in the induction of important stress-resistant physiological changes and its recent implication in the virulence of Salmonella, further research is required to shed light on the pathways modulated by BolA. In this study, we resorted to untargeted 1H-NMR metabolomics to understand the impact of BolA on the metabolic profile of Salmonella Typhimurium, under virulence conditions. Three strains of S. Typhimurium SL1344 were studied: An SL1344 strain transformed with an empty plasmid (control), a bolA knockout mutant (ΔbolA), and a strain overexpressing bolA (bolA+). These strains were grown in a minimal virulence-inducing medium and cells were collected at the end of the exponential and stationary phases. The extracts were analyzed by NMR, and multivariate and univariate statistical analysis were performed to identify significant alterations. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) of 1H-NMR data allowed the discrimination between the metabolic profiles of these strains, revealing increased levels of acetate, valine, alanine, NAD+, succinate, coenzyme A, glutathione, and putrescine in bolA+. These results indicate that BolA regulates pathways related to stress resistance and virulence, being an important modulator of the metabolic processes needed for S. Typhimurium infection.
Collapse
Affiliation(s)
- Gil Graça-Lopes
- ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Gonçalo Graça
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK.
| | - Susana Barahona
- ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Ricardo N Moreira
- ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Cecília M Arraiano
- ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Luís G Gonçalves
- ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| |
Collapse
|
18
|
Pulmonary Surfactant Promotes Virulence Gene Expression and Biofilm Formation in Klebsiella pneumoniae. Infect Immun 2018; 86:IAI.00135-18. [PMID: 29712730 DOI: 10.1128/iai.00135-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/24/2018] [Indexed: 12/18/2022] Open
Abstract
The interactions between Klebsiella pneumoniae and the host environment at the site of infection are largely unknown. Pulmonary surfactant serves as an initial point of contact for inhaled bacteria entering the lung and is thought to contain molecular cues that aid colonization and pathogenesis. To gain insight into this ecological transition, we characterized the transcriptional response of K. pneumoniae MGH 78578 to purified pulmonary surfactant. This work revealed changes within the K. pneumoniae transcriptome that likely contribute to host colonization, adaptation, and virulence in vivo Notable transcripts expressed under these conditions include genes involved in capsule synthesis, lipopolysaccharide modification, antibiotic resistance, biofilm formation, and metabolism. In addition, we tested the contributions of other surfactant-induced transcripts to K. pneumoniae survival using engineered isogenic KPPR1 deletion strains in a murine model of acute pneumonia. In these infection studies, we identified the MdtJI polyamine efflux pump and the ProU glycine betaine ABC transporter to be significant mediators of K. pneumoniae survival within the lung and confirmed previous evidence for the importance of de novo leucine synthesis to bacterial survival during infection. Finally, we determined that pulmonary surfactant promoted type 3 fimbria-mediated biofilm formation in K. pneumoniae and identified two surfactant constituents, phosphatidylcholine and cholesterol, that drive this response. This study provides novel insight into the interactions occurring between K. pneumoniae and the host at an important infection site and demonstrates the utility of purified lung surfactant preparations for dissecting host-lung pathogen interactions in vitro.
Collapse
|
19
|
Wang J, Lu X, Ying H, Ma W, Xu S, Wang X, Chen K, Ouyang P. A Novel Process for Cadaverine Bio-Production Using a Consortium of Two Engineered Escherichia coli. Front Microbiol 2018; 9:1312. [PMID: 29971056 PMCID: PMC6018084 DOI: 10.3389/fmicb.2018.01312] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/29/2018] [Indexed: 01/03/2023] Open
Abstract
Bio-production of cadaverine from cheap carbon sources for synthesizing bio-based polyamides is becoming more common. Here, a novel fermentation process for cadaverine bio-production from glucose was implemented by using a microbial consortium of two engineered Escherichia coli strains to relieve the toxic effect of cadaverine on fermentation efficiency. To achieve controllable growth of strains in the microbial consortium, two engineered E. coli strains grown separately on different carbon sources were first constructed. The strains were, an L-lysine-producing E. coli NT1004 with glucose as carbon source, and a cadaverine-producing E. coli CAD03 with glucose metabolism deficiency generated by modifying the PTSGlc system with CRISPR-Cas9 technology and inactivating cadaverine degradation pathways. Co-culturing these two engineered E. coli strains with a mixture of glucose and glycerol led to successful production of cadaverine. After optimizing cultivation conditions, a cadaverine titer of 28.5 g/L was achieved with a multi-stage constant-speed feeding strategy.
Collapse
Affiliation(s)
- Jing Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xiaolu Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanxiao Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Weichao Ma
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| |
Collapse
|
20
|
Nabu S, Lawung R, Isarankura-Na-Ayudhya P, Roytrakul S, Dolprasit S, Sengyee S, Isarankura-Na-Ayudhya C, Prachayasittikul V. Comparative proteomics analysis of Neisseria gonorrhoeae strains in response to extended-spectrum cephalosporins. EXCLI JOURNAL 2017; 16:1207-1229. [PMID: 29285017 PMCID: PMC5736987 DOI: 10.17179/excli2017-832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 10/18/2017] [Indexed: 01/02/2023]
Abstract
Neisseria gonorrhoeae strains displaying reduced susceptibility and resistance to extended-spectrum cephalosporins (ESCs) are major public health concerns. Although resistance mechanisms of ESCs have extensively been studied, the proteome-wide investigation on the biological response to the antibiotic stress is still limited. Herein, a proteomics approach based on two-dimensional gel electrophoresis and MALDI-TOF/TOF-MS analysis was applied to investigate the global protein expression under ESC stresses of ESC-susceptible and ESC-reduced susceptible N. gonorrhoeae strains. Upon exposure to ceftriaxone, 14 and 21 proteins of ESC-susceptible and ESC-reduced susceptible strains, respectively, were shown to be differentially expressed. In the meanwhile, differential expressions of 13 and 17 proteins were detected under cefixime stress for ESC-susceptible and ESC-reduced susceptible strains, respectively. ESC antibiotics have been proven to trigger the expression of several proteins implicated in a variety of biological functions including transport system, energy metabolism, stress response and pathogenic virulence factors. Interestingly, macrophage infectivity potentiators (Ng-MIP) showed increased expression for ESC-reduced susceptible strain under ESC stress. The altered expression of Ng-MIP was found to be a unique response to ESC stresses. Our finding proposes a broad view on proteomic changes in N. gonorrhoeae in response to ESC antibiotics that provides further insights into the gonococcal antimicrobial resistance and physiological adaptation mechanism.
Collapse
Affiliation(s)
- Sunanta Nabu
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Ratana Lawung
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.,Center of Medical Laboratory Services, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Sittiruk Roytrakul
- Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Supamas Dolprasit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Sineenart Sengyee
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | | | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| |
Collapse
|
21
|
Abstract
One of the main fundamental mechanisms of antibiotic resistance in Gram-negative bacteria comprises an effective change in the membrane permeability to antibiotics. The Gram-negative bacterial complex cell envelope comprises an outer membrane that delimits the periplasm from the exterior environment. The outer membrane contains numerous protein channels, termed as porins or nanopores, which are mainly involved in the influx of hydrophilic compounds, including antibiotics. Bacterial adaptation to reduce influx through these outer membrane proteins (Omps) is one of the crucial mechanisms behind antibiotic resistance. Thus to interpret the molecular basis of the outer membrane permeability is the current challenge. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in antibiotic influx. Further, it aims to study the bacterial response to antibiotic membrane permeability and hopefully provoke a discussion toward understanding and further exploration of prospects to improve our knowledge on physicochemical parameters that direct the translocation of antibiotics through the bacterial membrane protein channels.
Collapse
Affiliation(s)
- Ishan Ghai
- School of Engineering and Life Sciences, Jacobs University, Bremen
| | | |
Collapse
|
22
|
Polyamine-binding protein PotD2 is required for stress tolerance and virulence in Actinobacillus pleuropneumoniae. Antonie van Leeuwenhoek 2017; 110:1647-1657. [DOI: 10.1007/s10482-017-0914-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
|
23
|
Li YJ, Harroun SG, Su YC, Huang CF, Unnikrishnan B, Lin HJ, Lin CH, Huang CC. Synthesis of Self-Assembled Spermidine-Carbon Quantum Dots Effective against Multidrug-Resistant Bacteria. Adv Healthc Mater 2016; 5:2545-2554. [PMID: 27448287 DOI: 10.1002/adhm.201600297] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/08/2016] [Indexed: 11/08/2022]
Abstract
This study reports a two-step method to synthesize spermidine-capped fluorescent carbon quantum dots (Spd-CQDs) and their potential application as an antibacterial agent. Fluorescent carbon quantum dots (CQDs) are synthesized by pyrolysis of ammonium citrate in the solid state and then modified with spermidine by a simple heating treatment without a coupling agent. Spermidine, a naturally occurring polyamine, binds with DNA, lipids, and proteins involved in many important processes within organisms such as DNA stability, and cell growth, proliferation, and death. The antimicrobial activity of the as-synthesized Spd-CQDs (size ≈4.6 nm) has been tested against non-multidrug-resistant E. coli, S. aureus, B. subtilis, and P. aeruginosa bacteria and also multidrug-resistant bacteria, methicillin-resistant S. aureus (MRSA). The minimal inhibitory concentration value of Spd-CQDs is much lower (>25 000-fold) than that of spermidine, indicating their promising antibacterial characteristics. The mechanism of antibacterial activity is investigated, and the results indicate that Spd-CQDs cause significant damage to the bacterial membrane. In vitro cytotoxicity and hemolysis analyses reveal the high biocompatibility of Spd-CQDs. To demonstrate its practical application, in vitro MRSA-infected wound healing studies in rats have been conducted, which show faster healing, better epithelialization, and formation of collagen fibers when Spd-CQDs are used as a dressing material.
Collapse
Affiliation(s)
- Yu-Jia Li
- Department of Bioscience and Biotechnology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Scott G. Harroun
- Department of Chemistry; Université de Montréal; Montréal Québec H3C 3J7 Canada
| | - Yu-Chia Su
- National Laboratory Animal Center; Taipei 11599 Taiwan
| | | | - Binesh Unnikrishnan
- Department of Bioscience and Biotechnology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Chia-Hua Lin
- Department of Biotechnology; National Formosa University; Yunlin 63208 Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology; National Taiwan Ocean University; Keelung 20224 Taiwan
- Center of Excellence for the Oceans; National Taiwan Ocean University; Keelung 20224 Taiwan
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung 80708 Taiwan
| |
Collapse
|
24
|
Remaining Mysteries of Molecular Biology: The Role of Polyamines in the Cell. J Mol Biol 2015; 427:3389-406. [DOI: 10.1016/j.jmb.2015.06.020] [Citation(s) in RCA: 401] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/12/2015] [Accepted: 06/29/2015] [Indexed: 11/23/2022]
|
25
|
Hadi-Alijanvand S, Mobasheri H, Hadi-Alijanvand H. Application of OmpF nanochannel forming protein in polynucleotide sequence recognition. J Mol Recognit 2015; 27:575-87. [PMID: 25178853 DOI: 10.1002/jmr.2381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/31/2014] [Accepted: 04/09/2014] [Indexed: 01/09/2023]
Abstract
Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to fabricate high-throughput systems capable to fulfill the task in an efficient manner. Here, voltage gating OmpF nanochannel, whose structure is known at an atomic level, was used to recognize and differentiate between polynucleotide primers through voltage clamp technique. Our results showed that poly(T) occasionally blocked the channel at both polarities, while poly(C) and poly(G) obstructed it only at positive polarity. The channel was blocked at potential differences of as low as 80 mV in the presence of poly(T). The conductance of channel decreased in the presence of poly(C) and poly(G) by 61 and 5% respectively. Analysis of the number of events showed that poly(T) caused more closing events at higher voltages, while poly(G) and poly(C) induced it at lower voltages. Application of the hazard function as a statistical parameter and analysis of event closing times in various voltages demonstrated the most efficient differentiation at 60 mV. The results of practical and theoretical approaches presented here show that OmpF porin channel possesses the structural and dynamic characteristics required to be considered as a biosensor capable for continuous polynucleotide sequencing.
Collapse
Affiliation(s)
- Saeid Hadi-Alijanvand
- Laboratory of Membrane Biophysics and Macromolecules, Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran
| | | | | |
Collapse
|
26
|
Lopes SC, Ferreira M, Sousa CF, Gameiro P. A fast way to track functional OmpF reconstitution in liposomes: Escherichia coli total lipid extract. Anal Biochem 2015; 479:54-9. [PMID: 25841673 DOI: 10.1016/j.ab.2015.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
Abstract
A major requirement to perform structural studies with membrane proteins is to define efficient reconstitution protocols that ensure a high incorporation degree and protein directionality and topology that mimics its in vivo conditions. For this kind of studies, protein reconstitution in membrane systems via a detergent-mediated pathway is usually successfully adopted because detergents are generally used in the initial isolation and purification of membrane proteins. This study reports OmpF reconstitution in preformed Escherichia coli liposomes followed by detection of its insertion by analyzing modifications on membrane structure by two different techniques: steady-state fluorescence anisotropy and dynamic light scattering. Another important issue is protein directionality. For OmpF, it is known that interaction with polyamines promotes channel blockage. In this work, the spermine-OmpF interaction was evaluated using surface plasmon resonance, and protein directionality was confirmed.
Collapse
Affiliation(s)
- S C Lopes
- UCIBIO@Requimte, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - M Ferreira
- UCIBIO@Requimte, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - C F Sousa
- UCIBIO@Requimte, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - P Gameiro
- UCIBIO@Requimte, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| |
Collapse
|
27
|
Goetze TA, Patil M, Jeshen I, Bölter B, Grahl S, Soll J. Oep23 forms an ion channel in the chloroplast outer envelope. BMC PLANT BIOLOGY 2015; 15:47. [PMID: 25849634 PMCID: PMC4331141 DOI: 10.1186/s12870-015-0445-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/30/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Metabolite, ion and protein translocation into chloroplasts occurs across two membranes, the inner and the outer envelope. Solute and metabolite channels fulfill very important functions in integrating the organelles into the metabolic network of the cell. However so far only a few have been identified. Here we describe the identification and the characterization of the outer envelope protein of 23 kDa, Oep23 from garden pea. RESULTS Oep23 is found in the entire plant lineage from green algae to flowering plants. It is expressed in all organs and developmental states tested so far. The reconstituted recombinant protein Oep23 from pea forms a high conductance ion channel with a maximal conductance in the fully open state of 466 ± 14pS at a holding potential of +100 mV (in 250 mM KCl). The Oep23 channel is cation selective (PK+ : PCl- = 15 : 1) with a voltage dependent open probability of maximal Vmem = 0 mV. CONCLUSION The data indicate that the Oep23 activity represents a single channel unit and does not assemble into a multiple pore complex like bacterial type porins or mitochondrial voltage dependent anion channel. Thus, Oep23 represents a new member of ion channels in the outer envelope of chloroplasts involved in solute exchange.
Collapse
Affiliation(s)
- Tom Alexander Goetze
- />Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- />Nanion Technologies GmbH, Gabrielenstr. 9, 80636 München, Germany
| | - Manali Patil
- />Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- />The Munich Center of Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 München, Germany
| | - Ingrid Jeshen
- />Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- />The Munich Center of Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 München, Germany
| | - Bettina Bölter
- />Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- />The Munich Center of Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 München, Germany
| | - Sabine Grahl
- />Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- />The Munich Center of Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 München, Germany
| | - Jürgen Soll
- />Department Biologie 1, Botanik, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- />The Munich Center of Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 München, Germany
| |
Collapse
|
28
|
Different sensitivity levels to norspermidine on biofilm formation in clinical and commensal Staphylococcus epidermidis strains. Microb Pathog 2015; 79:8-16. [DOI: 10.1016/j.micpath.2014.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 01/23/2023]
|
29
|
Abstract
Bacteria secrete and harbor in their membranes a number of pore-forming proteins. Some of these are bona fide ion channels that may respond to changes in membrane tension, voltage, or pH. Others may be large translocons used for the secretion of folded or unfolded polypeptide substrates. Additionally, many secreted toxins insert into target cell membranes and form pores that either collapse membrane electrochemical gradients or provide conduits for the delivery of virulence factors. In all cases, electrophysiological approaches have yielded much progress in past decades in understanding the functional mechanisms of these pores. By monitoring the changes in current due to ion flow through the pores, these techniques are used as high-resolution tools to gather detailed information on the kinetic and permeation properties of these proteins, including those whose physiological role is not ion flux. This review highlights some of the electrophysiological studies that have advanced the field of transport by pore-forming proteins of bacterial origin.
Collapse
Affiliation(s)
- Anne H Delcour
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001;
| |
Collapse
|
30
|
Ma J, McLeod S, MacCormack K, Sriram S, Gao N, Breeze AL, Hu J. Real-time monitoring of New Delhi metallo-β-lactamase activity in living bacterial cells by 1H NMR spectroscopy. Angew Chem Int Ed Engl 2014; 53:2130-3. [PMID: 24458501 PMCID: PMC4232273 DOI: 10.1002/anie.201308636] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/19/2013] [Indexed: 11/13/2022]
Abstract
Disconnections between in vitro responses and those observed in whole cells confound many attempts to design drugs in areas of serious medical need. A method based on 1D 1H NMR spectroscopy is reported that affords the ability to monitor the hydrolytic decomposition of the carbapenem antibiotic meropenem inside Escherichia coli cells expressing New Delhi metallo-β-lactamase subclass 1 (NDM-1), an emerging antibiotic-resistance threat. Cell-based NMR studies demonstrated that two known NDM-1 inhibitors, L-captopril and ethylenediaminetetraacetic acid (EDTA), inhibit the hydrolysis of meropenem in vivo. NDM-1 activity in cells was also shown to be inhibited by spermine, a porin inhibitor, although in an in vitro assay, the influence of spermine on the activity of isolated NDM-1 protein is minimal. This new approach may have generic utility for monitoring reactions involving diffusible metabolites in other complex biological matrices and whole-cell settings, including mammalian cells.
Collapse
Affiliation(s)
- Junhe Ma
- Discovery Sciences, AstraZeneca Boston, Waltham, MA 02451 (USA)
| | | | | | | | | | | | | |
Collapse
|
31
|
Ma J, McLeod S, MacCormack K, Sriram S, Gao N, Breeze AL, Hu J. Real-Time Monitoring of New Delhi Metallo-β-Lactamase Activity in Living Bacterial Cells by1H NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308636] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
32
|
Abstract
Copper resistance mechanisms are crucial for many pathogenic bacteria, including Mycobacterium tuberculosis, during infection because the innate immune system utilizes copper ions to kill bacterial intruders. Despite several studies detailing responses of mycobacteria to copper, the pathways by which copper ions cross the mycobacterial cell envelope are unknown. Deletion of porin genes in Mycobacterium smegmatis leads to a severe growth defect on trace copper medium but simultaneously increases tolerance for copper at elevated concentrations, indicating that porins mediate copper uptake across the outer membrane. Heterologous expression of the mycobacterial porin gene mspA reduced growth of M. tuberculosis in the presence of 2.5 μM copper by 40% and completely suppressed growth at 15 μM copper, while wild-type M. tuberculosis reached its normal cell density at that copper concentration. Moreover, the polyamine spermine, a known inhibitor of porin activity in Gram-negative bacteria, enhanced tolerance of M. tuberculosis for copper, suggesting that copper ions utilize endogenous outer membrane channel proteins of M. tuberculosis to gain access to interior cellular compartments. In summary, these findings highlight the outer membrane as the first barrier against copper ions and the role of porins in mediating copper uptake in M. smegmatis and M. tuberculosis.
Collapse
|
33
|
Petráčková D, Janeček J, Bezoušková S, Kalachová L, Techniková Z, Buriánková K, Halada P, Haladová K, Weiser J. Fitness and proteome changes accompanying the development of erythromycin resistance in a population of Escherichia coli grown in continuous culture. Microbiologyopen 2013; 2:841-52. [PMID: 23996919 PMCID: PMC3831644 DOI: 10.1002/mbo3.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/04/2013] [Accepted: 07/16/2013] [Indexed: 12/27/2022] Open
Abstract
We studied the impact of a sublethal concentration of erythromycin on the fitness and proteome of a continuously cultivated population of Escherichia coli. The development of resistance to erythromycin in the population was followed over time by the gradient plate method and minimum inhibitory concentration (MIC) measurements. We measured the growth rate, standardized efficiency of synthesis of radiolabeled proteins, and translation accuracy of the system. The proteome changes were followed over time in two parallel experiments that differed in the presence or absence of erythromycin. A comparison of the proteomes at each time point (43, 68, and 103 h) revealed a group of unique proteins differing in expression. From all 35 proteins differing throughout the cultivation, only three were common to more than one time point. In the final population, a significant proportion of upregulated proteins was localized to the outer or inner cytoplasmic membranes or to the periplasmic space. In a population growing for more than 100 generations in the presence of antibiotic, erythromycin-resistant bacterial clones with improved fitness in comparison to early resistant culture predominated. This phenomenon was accompanied by distinct changes in protein expression during a stepwise, population-based development of erythromycin resistance.
Collapse
Affiliation(s)
- Denisa Petráčková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Sarathy JP, Lee E, Dartois V. Polyamines inhibit porin-mediated fluoroquinolone uptake in mycobacteria. PLoS One 2013; 8:e65806. [PMID: 23755283 PMCID: PMC3670895 DOI: 10.1371/journal.pone.0065806] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 04/28/2013] [Indexed: 11/19/2022] Open
Abstract
Polyamines decrease the permeability of the outer membrane of Escherichia coli to fluoroquinolones and β-lactams. In this study, we tested the effect of four polyamines (spermidine, spermine, cadaverine and putrescine) on fluoroquinolone uptake in Mycobacterium bovis BCG. Our results show that polyamines are also capable of reducing the permeability of the mycobacterial outer membrane to fluoroquinolones. Spermidine was most effective and demonstrated reversible dose- and pH-dependent inhibition of ciprofloxacin accumulation. The extent of this inhibition was demonstrated across the fluoroquinolone compound class to varying degrees. Furthermore, we have shown that the addition of spermidine increases the survival of M. bovis BCG after a 5-day exposure to ciprofloxacin by up to 25 times. The treatment of actively-replicating Mycobacterium tuberculosis with spermidine reduced ciprofloxacin accumulation by half while non-replicating nutrient-starved M. tuberculosis cultures lacked similar sensitivity to polyamines. Gene expression studies showed that several outer membrane proteins are significantly down-regulated during the shift to non-replication. Collectively, these characteristics of fluoroquinolone uptake in M. bovis BCG are consistent with facilitated transport by porin-like proteins and suggest that a reduction in intracellular uptake contributes to the phenotypic drug resistance demonstrated by M. tuberculosis in the non-replicating state.
Collapse
|
35
|
Sarathy JP, Dartois V, Lee EJD. The role of transport mechanisms in mycobacterium tuberculosis drug resistance and tolerance. Pharmaceuticals (Basel) 2012; 5:1210-35. [PMID: 24281307 PMCID: PMC3816664 DOI: 10.3390/ph5111210] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/25/2012] [Accepted: 11/02/2012] [Indexed: 02/02/2023] Open
Abstract
In the fight against tuberculosis, cell wall permeation of chemotherapeutic agents remains a critical but largely unsolved question. Here we review the major mechanisms of small molecule penetration into and efflux from Mycobacterium tuberculosis and other mycobacteria, and outline how these mechanisms may contribute to the development of phenotypic drug tolerance and induction of drug resistance. M. tuberculosis is intrinsically recalcitrant to small molecule permeation thanks to its thick lipid-rich cell wall. Passive diffusion appears to account for only a fraction of total drug permeation. As in other bacterial species, influx of hydrophilic compounds is facilitated by water-filled open channels, or porins, spanning the cell wall. However, the diversity and density of M. tuberculosis porins appears lower than in enterobacteria. Besides, physiological adaptations brought about by unfavorable conditions are thought to reduce the efficacy of porins. While intracellular accumulation of selected drug classes supports the existence of hypothesized active drug influx transporters, efflux pumps contribute to the drug resistant phenotype through their natural abundance and diversity, as well as their highly inducible expression. Modulation of efflux transporter expression has been observed in phagocytosed, non-replicating persistent and multi-drug resistant bacilli. Altogether, M. tuberculosis has evolved both intrinsic properties and acquired mechanisms to increase its level of tolerance towards xenobiotic substances, by preventing or minimizing their entry. Understanding these adaptation mechanisms is critical to counteract the natural mechanisms of defense against toxic compounds and develop new classes of chemotherapeutic agents that positively exploit the influx and efflux pathways of mycobacteria.
Collapse
Affiliation(s)
- Jansy Passiflora Sarathy
- Novartis Institute for Tropical Diseases Pte Ltd, 10 Biopolis Road #05-01, Chromos, 138670, Singapore.
| | | | | |
Collapse
|
36
|
Deactivation of the E. coli pH Stress Sensor CadC by Cadaverine. J Mol Biol 2012; 424:15-27. [DOI: 10.1016/j.jmb.2012.08.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/12/2012] [Accepted: 08/27/2012] [Indexed: 11/15/2022]
|
37
|
Hahn A, Stevanovic M, Mirus O, Schleiff E. The TolC-like protein HgdD of the cyanobacterium Anabaena sp. PCC 7120 is involved in secondary metabolite export and antibiotic resistance. J Biol Chem 2012; 287:41126-38. [PMID: 23071120 DOI: 10.1074/jbc.m112.396010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The role of TolC has largely been explored in proteobacteria, where it functions as a metabolite and protein exporter. In contrast, little research has been carried out on the function of cyanobacterial homologues, and as a consequence, not much is known about the mechanism of cyanobacterial antibiotic uptake and metabolite secretion in general. It has been suggested that the TolC-like homologue of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120, termed heterocyst glycolipid deposition protein D (HgdD), is involved in both protein and lipid secretion. To describe its function in secondary metabolite secretion, we established a system to measure the uptake of antibiotics based on the fluorescent molecule ethidium bromide. We analyzed the rate of porin-dependent metabolite uptake and confirmed the functional relation between detoxification and the action of HgdD. Moreover, we identified two major facilitator superfamily proteins that are involved in this process. It appears that anaOmp85 (Alr2269) is not required for insertion or assembly of HgdD, because an alr2269 mutant does not exhibit a phenotype similar to the hgdD mutant. Thus, we could assign components of the metabolite efflux system and describe parameters of detoxification by Anabaena sp. PCC 7120.
Collapse
Affiliation(s)
- Alexander Hahn
- Department of Biosciences, Center of Membrane Proteomics, Cluster of Excellence Frankfurt, Goethe University, 60438 Frankfurt, Germany
| | | | | | | |
Collapse
|
38
|
El-Halfawy OM, Valvano MA. Non-genetic mechanisms communicating antibiotic resistance: rethinking strategies for antimicrobial drug design. Expert Opin Drug Discov 2012; 7:923-33. [PMID: 22860901 DOI: 10.1517/17460441.2012.712512] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Infections by multidrug-resistant bacteria are of great concern worldwide. In many cases, resistance is not due to the presence of specific antibiotic-modifying enzymes, but rather associated with a general impermeability of the bacterial cell envelope. The molecular bases of this intrinsic resistance are not completely understood. Moreover, horizontal gene transfers cannot solely explain the spread of intrinsic resistance among bacterial strains. AREAS COVERED This review focuses on the increased intrinsic antibiotic resistance mediated by small molecules. These small molecules can either be secreted from bacterial cells of the same or different species (e.g., indole, polyamines, ammonia, and the Pseudomonas quinolone signal) or be present in the bacterial cell milieu, whether in the environment, such as indole acetic acid and other plant hormones, or in human tissues and body fluids, such as polyamines. These molecules are metabolic byproducts that act as infochemicals and modulate bacterial responses toward antibiotics leading to increasing or decreasing resistance levels. EXPERT OPINION The non-genetic mechanisms of antibiotic response modulation and communication discussed in this review should reorient our thinking of the mechanisms of intrinsic resistance to antibiotics and its spread across bacterial cell populations. The identification of chemical signals mediating increased intrinsic antibiotic resistance will expose novel critical targets for the development of new antimicrobial strategies.
Collapse
Affiliation(s)
- Omar M El-Halfawy
- University of Western Ontario, Center for Human Immunology, Departments of Microbiology and Immunology, and Medicine, London, Ontario, Canada
| | | |
Collapse
|
39
|
Pavlenok M, Derrington IM, Gundlach JH, Niederweis M. MspA nanopores from subunit dimers. PLoS One 2012; 7:e38726. [PMID: 22719928 PMCID: PMC3377714 DOI: 10.1371/journal.pone.0038726] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/14/2012] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium smegmatis porin A (MspA) forms an octameric channel and represents the founding member of a new family of pore proteins. Control of subunit stoichiometry is important to tailor MspA for nanotechnological applications. In this study, two MspA monomers were connected by linkers ranging from 17 to 62 amino acids in length. The oligomeric pore proteins were purified from M. smegmatis and were shown to form functional channels in lipid bilayer experiments. These results indicated that the peptide linkers did not prohibit correct folding and localization of MspA. However, expression levels were reduced by 10-fold compared to wild-type MspA. MspA is ideal for nanopore sequencing due to its unique pore geometry and its robustness. To assess the usefulness of MspA made from dimeric subunits for DNA sequencing, we linked two M1-MspA monomers, whose constriction zones were modified to enable DNA translocation. Lipid bilayer experiments demonstrated that this construct also formed functional channels. Voltage gating of MspA pores made from M1 monomers and M1-M1 dimers was identical indicating similar structural and dynamic channel properties. Glucose uptake in M. smegmatis cells lacking porins was restored by expressing the dimeric mspA M1 gene indicating correct folding and localization of M1-M1 pores in their native membrane. Single-stranded DNA hairpins produced identical ionic current blockades in pores made from monomers and subunit dimers demonstrating that M1-M1 pores are suitable for DNA sequencing. This study provides the proof of principle that production of single-chain MspA pores in M. smegmatis is feasible and paves the way for generating MspA pores with altered stoichiometries. Subunit dimers enable better control of the chemical and physical properties of the constriction zone of MspA. This approach will be valuable both in understanding transport across the outer membrane in mycobacteria and in tailoring MspA for nanopore sequencing of DNA.
Collapse
Affiliation(s)
- Mikhail Pavlenok
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ian M. Derrington
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, Washington, United States of America
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
40
|
Tkachenko AG, Akhova AV, Shumkov MS, Nesterova LY. Polyamines reduce oxidative stress in Escherichia coli cells exposed to bactericidal antibiotics. Res Microbiol 2012; 163:83-91. [DOI: 10.1016/j.resmic.2011.10.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 10/11/2011] [Indexed: 11/17/2022]
|
41
|
Kanjee U, Gutsche I, Ramachandran S, Houry WA. The enzymatic activities of the Escherichia coli basic aliphatic amino acid decarboxylases exhibit a pH zone of inhibition. Biochemistry 2011; 50:9388-98. [PMID: 21957966 DOI: 10.1021/bi201161k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stringent response regulator ppGpp has recently been shown by our group to inhibit the Escherichia coli inducible lysine decarboxylase, LdcI. As a follow-up to this observation, we examined the mechanisms that regulate the activities of the other four E. coli enzymes paralogous to LdcI: the constitutive lysine decarboxylase LdcC, the inducible arginine decarboxylase AdiA, the inducible ornithine decarboxylase SpeF, and the constitutive ornithine decarboxylase SpeC. LdcC and SpeC are involved in cellular polyamine biosynthesis, while LdcI, AdiA, and SpeF are involved in the acid stress response. Multiple mechanisms of regulation were found for these enzymes. In addition to LdcI, LdcC and SpeC were found to be inhibited by ppGpp; AdiA activity was found to be regulated by changes in oligomerization, while SpeF and SpeC activities were regulated by GTP. These findings indicate the presence of multiple mechanisms regulating the activity of this important family of decarboxylases. When the enzyme inhibition profiles are analyzed in parallel, a "zone of inhibition" between pH 6 and pH 8 is observed. Hence, the data suggest that E. coli utilizes multiple mechanisms to ensure that these decarboxylases remain inactive around neutral pH possibly to reduce the consumption of amino acids at this pH.
Collapse
Affiliation(s)
- Usheer Kanjee
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | | | | |
Collapse
|
42
|
Balasubramanian R, Kenney GE, Rosenzweig AC. Dual pathways for copper uptake by methanotrophic bacteria. J Biol Chem 2011; 286:37313-9. [PMID: 21900235 DOI: 10.1074/jbc.m111.284984] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Methanobactin (Mb), a 1217-Da copper chelator produced by the methanotroph Methylosinus trichosporium OB3b, is hypothesized to mediate copper acquisition from the environment, particularly from insoluble copper mineral sources. Although indirect evidence suggests that Mb provides copper for the regulation and activity of methane monooxygenase enzymes, experimental data for direct uptake of copper loaded Mb (Cu-Mb) are lacking. Uptake of intact Cu-Mb by M. trichosporium OB3b was demonstrated by isotopic and fluorescent labeling experiments. Confocal microscopy data indicate that Cu-Mb is localized in the cytoplasm. Both Cu-Mb and unchelated Cu are taken up by M. trichosporium OB3b, but by different mechanisms. Uptake of unchelated Cu is inhibited by spermine, suggesting a porin-dependent passive transport process. By contrast, uptake of Cu-Mb is inhibited by the uncoupling agents carbonyl cyanide m-chlorophenylhydrazone and methylamine, but not by spermine, consistent with an active transport process. Cu-Mb from M. trichosporium OB3b can also be internalized by other strains of methanotroph, but not by Escherichia coli, suggesting that Cu-Mb uptake is specific to methanotrophic bacteria. These findings are consistent with a key role for Cu-Mb in copper acquisition by methanotrophs and have important implications for further investigation of the copper uptake machinery.
Collapse
|
43
|
Potential analytical applications of lysenin channels for detection of multivalent ions. Anal Bioanal Chem 2011; 401:1871-9. [PMID: 21818682 DOI: 10.1007/s00216-011-5277-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 07/13/2011] [Accepted: 07/21/2011] [Indexed: 11/27/2022]
Abstract
Transmembrane protein transporters possessing binding sites for ions, toxins, pharmaceutical drugs, and other molecules constitute excellent candidates for developing sensitive and selective biosensing devices. Their attractiveness for analytical purposes is enhanced by the intrinsic amplification capabilities shown when the binding event leads to major changes in the transportation of ions or molecules other than the analyte itself. The large-scale implementation of such transmembrane proteins in biosensing devices is limited by the difficulties encountered in inserting functional transporters into artificial bilayer lipid membranes and by the limitations in understanding and exploiting the changes induced by the interaction with the analyte for sensing purposes. Here, we show that lysenin, a pore-forming toxin extracted from earthworm Eisenia foetida, which inserts stable and large conductance channels into artificial bilayer lipid membranes, functions as a multivalent ion-sensing device. The analytical response consists of concentration and ionic-species-dependent macroscopic conductance inhibition most probably linked to a ligand-induced gating mechanism. Multivalent ion removal by chelation or precipitation restores, in most cases, the initial conductance and demonstrates reversibility. Changes in lipid bilayer membrane compositions leading to the absence of voltage-induced gating do not affect the analytical response to multivalent ions. Microscopic current analysis performed on individual lysenin channels in the presence of Cu(2+) revealed complex open-closed transitions characterized by unstable intermediate sub-conducting states. Lysenin channels provide an analytical tool with a built-in sensing mechanism for inorganic and organic multivalent ions, and the excellent stability in an artificial environment recommend lysenin as a potential candidate for single-molecule detection and analysis.
Collapse
|
44
|
Wager B, Baslé A, Delcour AH. Disulfide bond tethering of extracellular loops does not affect the closure of OmpF porin at acidic pH. Proteins 2011; 78:2886-94. [PMID: 20665474 DOI: 10.1002/prot.22807] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The permeability of the outer membrane of gram-negative bacteria is essentially controlled by pore-forming proteins of the porin family. The trimeric E. coli porin OmpF is assembled as a triple β-barrel, where each monomer contains a central pore and extracellular loops. Electrophysiological analysis of the behavior of OmpF at acidic pH reveals that the protein undergoes a conformational change leading to the sequential step-wise closure of the three monomers. A previous atomic force microscopy study suggested that the conformational change might be due to a bending of extracellular loops over the pore opening, and loop deletion experiments suggested that loops L1, L7, and L8 are involved. In order to test the hypothesis for loop movement, we engineered a series of double cysteine mutants in loops L1, L6, L7 and L8 in order to create disulfide bonds linking two loops to each other, or the two branches of a loop, or a loop to the β-barrel. Five out of the six mutants showed the formation of the disulfide bond. However, none of these had an altered response to acidic pH relative to the wildtype channel. Although we cannot dismiss the possibility that the mobility restriction introduced by each disulfide bond was too localized to impact a more global conformational change of the three loops, the fact that all of the different types of disulfide bond tethering were similarly ineffective suggests that the extracellular loops L1, L7, and L8 may not undergo a major acidic-pH induced conformational change leading to channel closure.
Collapse
Affiliation(s)
- Beau Wager
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | | | | |
Collapse
|
45
|
Fologea D, Krueger E, Al Faori R, Lee R, Mazur YI, Henry R, Arnold M, Salamo GJ. Multivalent ions control the transport through lysenin channels. Biophys Chem 2010; 152:40-5. [PMID: 20724059 DOI: 10.1016/j.bpc.2010.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/27/2010] [Accepted: 07/28/2010] [Indexed: 11/30/2022]
Abstract
We report the effect of different ions on the conducting properties of lysenin channels inserted into planar lipid bilayer membranes. Our observations indicated that multivalent ions inhibited the lysenin channels conductance in a concentration dependent manner. The analysis performed on single channels revealed that multivalent ions induced reversible sub-conducting or closed states depending on the ionic charge and size. Good agreement is reported between experimental results and a theoretical model that is proposed to describe the interaction between divalent ions and lysenin channels as a simple isothermal absorption process.
Collapse
Affiliation(s)
- Daniel Fologea
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Vinson HM, Gautam A, Olet S, Gibbs PS, Barigye R. Molecular analysis of porin gene transcription in heterogenotypic multidrug-resistant Escherichia coli isolates from scouring calves. J Antimicrob Chemother 2010; 65:1926-35. [PMID: 20639525 DOI: 10.1093/jac/dkq246] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Despite evidence that altered membrane porins may impair microbial drug uptake thereby potentially compounding efflux pump-mediated multidrug resistance, few studies have evaluated gene transcription to identify multidrug-resistance-associated porins and other potential drug targets. METHODS Genes that encode six membrane porins (fadL, lamB, ompC, ompF, ompW and yiaT) and two membrane proteins (tolC and ompT) were assessed by PCR and by quantitative real-time PCR (qRT-PCR) analysis of 10 multidrug-resistant (MDR) and 10 antibiotic-susceptible (AS) Escherichia coli isolates. The mean DeltaDeltaCt values for the study E. coli genes were analysed by the Wilcoxon test (P = 0.05). RESULTS All 20 E. coli isolates tested positive for tolC, lamB, ompC, ompF genes, while 10 MDR and 9/10 (90%) AS isolates were positive for the fadL gene. Seven out of 10 (70%) MDR and 7/10 (70%) AS isolates were positive for the yiaT gene, while 7/10 (70%) MDR and only 4/10 (40%) AS isolates were positive for the ompT gene. The mean DeltaDeltaCt values for the tolC and yiaT genes were significantly higher in MDR than in AS isolates (Wilcoxon test; P < 0.05). No significant difference was seen with respect to fadL, lamB, ompC, ompF, ompT and ompW gene transcription (Wilcoxon test; P > 0.05). CONCLUSIONS Findings suggest up-regulated transcription of tolC and yiaT genes in the MDR E. coli isolates. These results indirectly suggest that TolC and YiaT proteins may play some role(s) in multidrug resistance, but proteomic studies are needed before the two proteins are considered potential drug targets.
Collapse
Affiliation(s)
- Heather M Vinson
- Department of Veterinary and Microbiological Sciences, North Dakota State University, 1523 Centennial Blvd, Fargo, ND 58108, USA
| | | | | | | | | |
Collapse
|
47
|
Akhova AV, Tkachenko AG. Lysine decarboxylase activity as a factor of fluoroquinolone resistance in Escherichia coli. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709050075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
48
|
Becucci L, D'Amico M, Daniele S, Olivotto M, Pozzi A, Guidelli R. A metal-supported biomimetic micromembrane allowing the recording of single-channel activity and of impedance spectra of membrane proteins. Bioelectrochemistry 2009; 78:176-80. [PMID: 19726240 DOI: 10.1016/j.bioelechem.2009.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 08/09/2009] [Accepted: 08/11/2009] [Indexed: 10/20/2022]
Abstract
A novel tethered bilayer lipid micromembrane (tBLmicroM) was prepared and characterized. It consists of a mercury cap electrodeposited on a platinum microelectrode, about 20 microm in diameter. The micromembrane was prepared by tethering to the mercury cap a thiolipid monolayer and by then self-assembling a lipid monolayer on top of it. The thiolipid consisted of a disulfidated tetraoxyethylene hydrophilic spacer covalently linked to two phytanyl chains. Upon incorporating OmpF porin in the tBLmicroM, its single-channel activity was recorded by the patch-clamp technique, and its particular features described. An electrochemical impedance spectrum of the tBLmicroM incorporating OmpF porin is also reported. To the best of our knowledge, this tBLmicroM is the first metal-supported biomimetic micromembrane capable of incorporating non-engineered channel proteins in a functionally active state from their detergent solutions, and of allowing the recording of single-channel activity and of impedance spectra of these proteins via ion translocation into the hydrophilic spacer. The limited spaciousness of the spacer prevents a statistical analysis based on current-amplitude or blockage-time histograms. Nonetheless, the robustness, stability, ease of preparation and disposability of the present tBLmicroM may open the way to the realization of a channel-protein microarray platform allowing a high throughput drug screening.
Collapse
Affiliation(s)
- Lucia Becucci
- Department of Chemistry, Florence University, Via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy.
| | | | | | | | | | | |
Collapse
|
49
|
Outer membrane permeability and antibiotic resistance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:808-16. [PMID: 19100346 DOI: 10.1016/j.bbapap.2008.11.005] [Citation(s) in RCA: 995] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 11/12/2008] [Accepted: 11/13/2008] [Indexed: 01/19/2023]
Abstract
To date most antibiotics are targeted at intracellular processes, and must be able to penetrate the bacterial cell envelope. In particular, the outer membrane of gram-negative bacteria provides a formidable barrier that must be overcome. There are essentially two pathways that antibiotics can take through the outer membrane: a lipid-mediated pathway for hydrophobic antibiotics, and general diffusion porins for hydrophilic antibiotics. The lipid and protein compositions of the outer membrane have a strong impact on the sensitivity of bacteria to many types of antibiotics, and drug resistance involving modifications of these macromolecules is common. This review will describe the molecular mechanisms for permeation of antibiotics through the outer membrane, and the strategies that bacteria have deployed to resist antibiotics by modifications of these pathways.
Collapse
|
50
|
The porin and the permeating antibiotic: a selective diffusion barrier in Gram-negative bacteria. Nat Rev Microbiol 2008; 6:893-903. [PMID: 18997824 DOI: 10.1038/nrmicro1994] [Citation(s) in RCA: 599] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gram-negative bacteria are responsible for a large proportion of antibiotic-resistant bacterial diseases. These bacteria have a complex cell envelope that comprises an outer membrane and an inner membrane that delimit the periplasm. The outer membrane contains various protein channels, called porins, which are involved in the influx of various compounds, including several classes of antibiotics. Bacterial adaptation to reduce influx through porins is an increasing problem worldwide that contributes, together with efflux systems, to the emergence and dissemination of antibiotic resistance. An exciting challenge is to decipher the genetic and molecular basis of membrane impermeability as a bacterial resistance mechanism. This Review outlines the bacterial response towards antibiotic stress on altered membrane permeability and discusses recent advances in molecular approaches that are improving our knowledge of the physico-chemical parameters that govern the translocation of antibiotics through porin channels.
Collapse
|