1
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Bin Mohammad Muzaki MZ, Subramoni S, Summers S, Kjelleberg S, Rice SA. Klebsiella pneumoniae AI-2 transporters mediate interspecies interactions and composition in a three-species biofilm community. NPJ Biofilms Microbiomes 2024; 10:91. [PMID: 39341797 PMCID: PMC11439081 DOI: 10.1038/s41522-024-00546-0] [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: 02/14/2023] [Accepted: 08/06/2024] [Indexed: 10/01/2024] Open
Abstract
Biofilms in nature often exist as communities. In this study, an experimental mixed-species community consisting of Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was used to investigate how AI-2 transporters affect interspecies interactions and composition. The K. pneumoniae lsrB/lsrD deletion mutants had a 10-25-fold higher concentration of extracellular AI-2 compared to the wild-type. Although these deletion mutants produced monospecies biofilms of similar biomass, the substitution of these mutants for the parental strain significantly altered composition. Dual-species biofilm assays demonstrated that the changes in composition were due to the cumulative effect of pairwise interactions. It was further revealed that K. pneumoniae being present physically in the consortium was important in AI-2 mediating composition in the consortium, and that AI-2 transporters were crucial in achieving maximum biomass in the community. In conclusion, these findings demonstrate that AI-2 transporters mediate interspecies interactions and is important in maintaining the compositional equilibrium of the community.
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Affiliation(s)
- Muhammad Zulfadhly Bin Mohammad Muzaki
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
- The Australian Institute for Microbiology and Infection, The University of Technology Sydney, Sydney, NSW, Australia.
- Microbiomes for One Systems Health and Agriculture and Food, CSIRO, Westmead, NSW, Australia.
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2
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Geng Y, Nguyen TVP, Homaee E, Golding I. Using bacterial population dynamics to count phages and their lysogens. Nat Commun 2024; 15:7814. [PMID: 39242585 PMCID: PMC11379933 DOI: 10.1038/s41467-024-51913-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 08/20/2024] [Indexed: 09/09/2024] Open
Abstract
Traditional assays for counting bacteriophages and their lysogens are labor-intensive and perturbative to the host cells. Here, we present a high-throughput infection method in a microplate reader, where the growth dynamics of the infected culture is measured using the optical density (OD). We find that the OD at which the culture lyses scales linearly with the logarithm of the initial phage concentration, providing a way of measuring phage numbers over nine orders of magnitude and down to single-phage sensitivity. Interpreting the measured dynamics using a mathematical model allows us to infer the phage growth rate, which is a function of the phage-cell encounter rate, latent period, and burst size. Adding antibiotic selection provides the ability to measure the rate of host lysogenization. Using this method, we found that when E. coli growth slows down, the lytic growth rate of lambda phages decreases, and the propensity for lysogeny increases, demonstrating how host physiology influences the viral developmental program.
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Affiliation(s)
- Yuncong Geng
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Thu Vu Phuc Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Ehsan Homaee
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ido Golding
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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3
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Šoltysová M, Řezáčová P. Structure and function of bacterial transcription regulators of the SorC family. Transcription 2024:1-22. [PMID: 39223991 DOI: 10.1080/21541264.2024.2387895] [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: 06/19/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
The SorC family is a large group of bacterial transcription regulators involved in controlling carbohydrate catabolism and quorum sensing. SorC proteins consist of a conserved C-terminal effector-binding domain and an N-terminal DNA-binding domain, whose type divides the family into two subfamilies: SorC/DeoR and SorC/CggR. Proteins of the SorC/CggR subfamily are known to regulate the key node of glycolysis-triose phosphate interconversion. On the other hand, SorC/DeoR proteins are involved in a variety of peripheral carbohydrate catabolic pathways and quorum sensing functions, including virulence. Despite the abundance and importance of this family, SorC proteins seem to be on the periphery of scientific interest, which might be caused by the fragmentary information about its representatives. This review aims to compile the existing knowledge and provide material to inspire future questions about the SorC protein family.
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Affiliation(s)
- Markéta Šoltysová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, Czechia
| | - Pavlína Řezáčová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, Czechia
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4
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Gao Y, Peng D, Wang X, Lin S. Effects of the quorum sensing related luxS gene and lsr operon on Klebsiella michiganensis resisting copper stress. ENVIRONMENTAL RESEARCH 2024; 256:119244. [PMID: 38810822 DOI: 10.1016/j.envres.2024.119244] [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: 03/11/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
Industrial wastewater is a major environmental concern due to its high copper content, which poses significant toxicity to microbial life. Autoinducer-2 (AI-2) can participate in the inter- and intra-species communication and regulate the physiological functions of different bacterial species by producing AI-2 signal molecules. However, there are few research reports on the luxS gene and lsr operon functions for AI-2 in bacteria with a certain tolerance to copper. This study delves into the potential of quorum sensing mechanisms, particularly the AI-2 system, for enhancing microbial resistance to copper toxicity in Klebsiella michiganensis (KM). We detail the critical roles of the luxS gene in AI-2 synthesis and the lsr operon in AI-2 uptake, demonstrating their collective impact on enhancing copper resistance. Our findings show that mutations in the lsr operon, alongside the knockout of the luxS gene in KM strain (KMΔluxSΔlsr), significantly impair the strain's motility (p < 0.0001) and biofilm formation (p < 0.01), underscoring the operon's role in AI-2 transport. These genetic insights are pivotal for developing bioremediation strategies aimed at mitigating copper pollution in wastewater. By elucidating the mechanisms through which KM modulates copper resistance, this study highlights the broader ecological significance of leveraging microbial quorum sensing pathways for sustainable wastewater management.
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Affiliation(s)
- Ya Gao
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Dongyu Peng
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Xinlong Wang
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Shanshan Lin
- School of Environment, Northeast Normal University, Changchun, 130117, China.
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5
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Möller AM, Vázquez-Hernández M, Kutscher B, Brysch R, Brückner S, Marino EC, Kleetz J, Senges CHR, Schäkermann S, Bandow JE, Narberhaus F. Common and varied molecular responses of Escherichia coli to five different inhibitors of the lipopolysaccharide biosynthetic enzyme LpxC. J Biol Chem 2024; 300:107143. [PMID: 38458396 PMCID: PMC10998244 DOI: 10.1016/j.jbc.2024.107143] [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: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024] Open
Abstract
A promising yet clinically unexploited antibiotic target in difficult-to-treat Gram-negative bacteria is LpxC, the key enzyme in the biosynthesis of lipopolysaccharides, which are the major constituents of the outer membrane. Despite the development of dozens of chemically diverse LpxC inhibitor molecules, it is essentially unknown how bacteria counteract LpxC inhibition. Our study provides comprehensive insights into the response against five different LpxC inhibitors. All compounds bound to purified LpxC from Escherichia coli. Treatment of E. coli with these compounds changed the cell shape and stabilized LpxC suggesting that FtsH-mediated proteolysis of the inactivated enzyme is impaired. LpxC inhibition sensitized E. coli to vancomycin and rifampin, which poorly cross the outer membrane of intact cells. Four of the five compounds led to an accumulation of lyso-phosphatidylethanolamine, a cleavage product of phosphatidylethanolamine, generated by the phospholipase PldA. The combined results suggested an imbalance in lipopolysaccharides and phospholipid biosynthesis, which was corroborated by the global proteome response to treatment with the LpxC inhibitors. Apart from LpxC itself, FabA and FabB responsible for the biosynthesis of unsaturated fatty acids were consistently induced. Upregulated compound-specific proteins are involved in various functional categories, such as stress reactions, nucleotide, or amino acid metabolism and quorum sensing. Our work shows that antibiotics targeting the same enzyme do not necessarily elicit identical cellular responses. Moreover, we find that the response of E. coli to LpxC inhibition is distinct from the previously reported response in Pseudomonas aeruginosa.
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Affiliation(s)
- Anna-Maria Möller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Blanka Kutscher
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Raffael Brysch
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Simon Brückner
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Emily C Marino
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia Kleetz
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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6
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Gifford DR, Bhattacharyya A, Geim A, Marshall E, Krašovec R, Knight CG. Environmental and genetic influence on the rate and spectrum of spontaneous mutations in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001452. [PMID: 38687010 PMCID: PMC11084559 DOI: 10.1099/mic.0.001452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024]
Abstract
Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests, we characterized the spectrum of spontaneous mutations in Escherichia coli grown in low and high glucose environments. These conditions are known to affect the rate of spontaneous mutation in wild-type MG1655, but not in a ΔluxS deletant strain - a gene with roles in both quorum sensing and the recycling of methylation products used in E. coli's DNA repair process. We find an increase in AT>GC transitions in the low glucose environment, suggesting that processes relating to the production or repair of this mutation could drive the response of overall mutation rate to glucose concentration. Interestingly, this increase in AT>GC transitions is maintained by the glucose non-responsive ΔluxS deletant. Instead, an elevated rate of GC>TA transversions, more common in a high glucose environment, leads to a net non-responsiveness of overall mutation rate for this strain. Our results show how relatively subtle changes, such as the concentration of a carbon substrate or loss of a regulatory gene, can substantially influence the amount and nature of genetic variation available to selection.
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Affiliation(s)
- Danna R. Gifford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Anish Bhattacharyya
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Alexandra Geim
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Pembroke College, University of Cambridge, Cambridge, UK
| | - Eleanor Marshall
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Rok Krašovec
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Christopher G. Knight
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
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7
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Scheidweiler D, Bordoloi AD, Jiao W, Sentchilo V, Bollani M, Chhun A, Engel P, de Anna P. Spatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media. Nat Commun 2024; 15:191. [PMID: 38167276 PMCID: PMC10761857 DOI: 10.1038/s41467-023-44267-y] [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: 03/28/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Biological tissues, sediments, or engineered systems are spatially structured media with a tortuous and porous structure that host the flow of fluids. Such complex environments can influence the spatial and temporal colonization patterns of bacteria by controlling the transport of individual bacterial cells, the availability of resources, and the distribution of chemical signals for communication. Yet, due to the multi-scale structure of these complex systems, it is hard to assess how different biotic and abiotic properties work together to control the accumulation of bacterial biomass. Here, we explore how flow-mediated interactions allow the gut commensal Escherichia coli to colonize a porous structure that is composed of heterogenous dead-end pores (DEPs) and connecting percolating channels, i.e. transmitting pores (TPs), mimicking the structured surface of mammalian guts. We find that in presence of flow, gradients of the quorum sensing (QS) signaling molecule autoinducer-2 (AI-2) promote E. coli chemotactic accumulation in the DEPs. In this crowded environment, the combination of growth and cell-to-cell collision favors the development of suspended bacterial aggregates. This results in hot-spots of resource consumption, which, upon resource limitation, triggers the mechanical evasion of biomass from nutrients and oxygen depleted DEPs. Our findings demonstrate that microscale medium structure and complex flow coupled with bacterial quorum sensing and chemotaxis control the heterogenous accumulation of bacterial biomass in a spatially structured environment, such as villi and crypts in the gut or in tortuous pores within soil and filters.
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Affiliation(s)
- David Scheidweiler
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Ankur Deep Bordoloi
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Wenqiao Jiao
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | | | - Audam Chhun
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Pietro de Anna
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland.
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8
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Li J, Liu H, Zhao C, Zhang J, He W. Autoinducer-2 quorum sensing regulates biofilm formation and chain elongation metabolic pathways to enhance caproate synthesis in microbial electrochemical system. CHEMOSPHERE 2023; 344:140384. [PMID: 37806331 DOI: 10.1016/j.chemosphere.2023.140384] [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: 05/16/2023] [Revised: 08/26/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Quorum sensing (QS) have been explored extensively. However, most studies focused on N-acyl homoserine lactones (AHLs) participating in intraspecies QS. In this study, autoinducer-2 (AI-2, participating in interspecies QS) with different concentration was investigated for chain elongation in microbial electrosynthesis (MES). The results demonstrated that the R3 treatment, which involved adding 10 μM of 4,5-dihydroxy-2,3-pentanedione (DPD) in the reactor, exhibited the best performance. The concentration of caproate was increased by 66.88% and the redox activity of cathodic electroactive biofilms (EABs) was enhanced. Meanwhile, microbial community data indicated that Negativicutes relative abundance was increased obviously in R3 treatment. In this study, the transcriptome Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases were used to analyze the metabolic pathway of chain elongation involving fatty acid biosynthesis (FAB) pathway and reverse β-oxidization (RBO) pathway. KEGG analysis revealed that fatty acid elongation metabolism (p < 0.001), tryptophan metabolism (p < 0.01), arginine and proline metabolism (p < 0.05) were significantly improved in R3 treatment. GO analysis suggested that R3 treatment mainly upregulated significantly transmembrane signaling receptor activity (p < 0.01), oxidoreductase activity (p < 0.05), and phosphorelay signal transduction (p < 0.05). Moreover, metatranscriptomic analyses also showed that R3 treatment could upregulate the LuxP extracellular receptor, LuxO transcriptional activator, LsrB periplasmic protein, and were beneficial to both FAB and RBO pathways. These findings provided a new insight into chain elongation in MES system.
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Affiliation(s)
- Jing Li
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
| | - He Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, 215011, Jiangsu Province, PR China.
| | - Chao Zhao
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
| | - Jie Zhang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
| | - Wanying He
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
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9
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Cickovski T, Mathee K, Aguirre G, Tatke G, Hermida A, Narasimhan G, Stollstorff M. Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective. PLoS One 2023; 18:e0273890. [PMID: 37594987 PMCID: PMC10437823 DOI: 10.1371/journal.pone.0273890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Attention Deficit Hyperactivity Disorder (ADHD) is an increasingly prevalent neuropsychiatric disorder characterized by hyperactivity, inattention, and impulsivity. Symptoms emerge from underlying deficiencies in neurocircuitry, and recent research has suggested a role played by the gut microbiome. The gut microbiome is an ecosystem of interdependent taxa involved in an exponentially complex web of interactions, plus host gene and reaction pathways, some of which involve neurotransmitters with roles in ADHD neurocircuitry. Studies have analyzed the ADHD gut microbiome using macroscale metrics such as diversity and differential abundance, and have proposed several taxa as elevated or reduced in ADHD compared to Control. Few studies have delved into the complex underlying dynamics ultimately responsible for the emergence of such metrics, leaving a largely incomplete, sometimes contradictory, and ultimately inconclusive picture. We aim to help complete this picture by venturing beyond taxa abundances and into taxa relationships (i.e. cooperation and competition), using a publicly available gut microbiome dataset (targeted 16S, v3-4 region, qPCR) from an observational, case-control study of 30 Control (15 female, 15 male) and 28 ADHD (15 female, 13 male) undergraduate students. We first perform the same macroscale analyses prevalent in ADHD gut microbiome literature (diversity, differential abundance, and composition) to observe the degree of correspondence, or any new trends. We then estimate two-way ecological relationships by producing Control and ADHD Microbial Co-occurrence Networks (MCNs), using SparCC correlations (p ≤ 0.01). We perform community detection to find clusters of taxa estimated to mutually cooperate along with their centroids, and centrality calculations to estimate taxa most vital to overall gut ecology. We finally summarize our results, providing conjectures on how they can guide future experiments, some methods for improving our experiments, and general implications for the field.
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Affiliation(s)
- Trevor Cickovski
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, United States of America
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, FL, United States of America
| | - Gloria Aguirre
- Department of Biological Sciences, College of Arts, Sciences and Education, Florida International University, Miami, FL, United States of America
| | - Gorakh Tatke
- Department of Biological Sciences, College of Arts, Sciences and Education, Florida International University, Miami, FL, United States of America
| | - Alejandro Hermida
- Cognitive Neuroscience Laboratory, Department of Psychology, Florida International University, Miami, FL, United States of America
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, United States of America
| | - Melanie Stollstorff
- Cognitive Neuroscience Laboratory, Department of Psychology, Florida International University, Miami, FL, United States of America
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10
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Miller Conrad LC, Perez LJ. A Geneticist Transcribing the Chemical Language of Bacteria. Isr J Chem 2023; 63:e202200079. [PMID: 37469628 PMCID: PMC10353724 DOI: 10.1002/ijch.202200079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 12/05/2022]
Abstract
The study of quorum sensing, bacterial cell-to-cell communication mediated by the production and detection of small molecule signals, has skyrocketed since its discovery in the last third of the 20th century. Building from early investigations of bacterial bioluminescence, the process has been characterized to control a numerous and growing number of group behaviors, including virulence and biofilm formation. Bonnie Bassler has made key contributions to the understanding of quorum sensing, leading interdisciplinary efforts to characterize key signaling pathway components and their respective signaling molecules across a range of gram-negative bacteria. This review highlights her work in the field, with a particular emphasis on the chemical contributions of her work.
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Affiliation(s)
- Laura C. Miller Conrad
- Department of Chemistry, San José State University, 1 Washington Sq, San Jose, CA 95192, USA
| | - Lark J. Perez
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
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11
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Nakamura Y, Watanabe K, Yoshioka Y, Ariyoshi W, Yamasaki R. Persister Cell Formation and Elevated lsrA and lsrC Gene Expression upon Hydrogen Peroxide Exposure in a Periodontal Pathogen Aggregatibacter actinomycetemcomitans. Microorganisms 2023; 11:1402. [PMID: 37374903 DOI: 10.3390/microorganisms11061402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The effect of hydrogen peroxide, an antiseptic dental treatment, on Aggregatibacter actinomycetemcomitans, the main causative agent of localized invasive periodontitis, was investigated. Hydrogen peroxide treatment (0.06%, 4× minimum inhibitory concentration) resulted in the persistence and survival of approximately 0.5% of the bacterial population. The surviving bacteria did not genetically acquire hydrogen peroxide resistance but exhibited a known persister behavior. Sterilization with mitomycin C significantly reduced the number of A. actinomycetemcomitans persister survivors. RNA sequencing of hydrogen peroxide-treated A. actinomycetemcomitans showed elevated expression of Lsr family members, suggesting a strong involvement of autoinducer uptake. In this study, we found a risk of A. actinomycetemcomitans persister residual from hydrogen peroxide treatment and hypothesized associated genetic mechanisms of persister from RNA sequencing.
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Affiliation(s)
- Yohei Nakamura
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
- Division of Developmental Stomatognathic Function Science, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Koji Watanabe
- Division of Developmental Stomatognathic Function Science, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Yoshie Yoshioka
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Wataru Ariyoshi
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Ryota Yamasaki
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
- Collaborative Research Centre for Green Materials on Environmental Technology, Kyushu Institute of Technology, 1-1 Sensui-chou, Tobata-ku, Kitakyushu 804-8550, Fukuoka, Japan
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12
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Shi Q, Wen H, Xu Y, Zhao X, Zhang J, Li Y, Meng Q, Yu F, Xiao J, Li X. Virtual screening-based discovery of AI-2 quorum sensing inhibitors that interact with an allosteric hydrophobic site of LsrK and their functional evaluation. Front Chem 2023; 11:1185224. [PMID: 37292175 PMCID: PMC10244669 DOI: 10.3389/fchem.2023.1185224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction: Quorum sensing (QS) is a bacterial intracellular and intercellular communication system that regulates virulence factor production, biofilm formation, and antibiotic sensitivity. Quorum-sensing inhibitors (QSIs) are a novel class of antibiotics that can effectively combat antibiotic resistance. Autoinducer-2 (AI-2) is a universal signaling molecule that mediates inter- and intraspecies QS systems among different bacteria. Furthermore, LsrK plays an important role in regulating the activity and stability of the intracellular AI-2 signaling pathway. Thus, LsrK is considered an important target for the development of QSIs. Methods: We designed a workflow integrating molecular dynamic (MD) simulations, virtual screening, LsrK inhibition assays, cell-based AI-2-mediated QS interference assays, and surface plasmon resonance (SPR)-based protein affinity assays to screen for potential LsrK kinase inhibitors. Results: MD simulation results of the LsrK/ATP complex revealed hydrogen bonds and salt bridge formation among four key residues, namely, Lys 431, Tyr 341, Arg 319, and Arg 322, which are critical for the binding of ATP to LsrK. Furthermore, MD simulation results indicated that the ATP-binding site has an allosteric pocket that can become larger and be occupied by small molecule compounds. Based on these MD simulation results, a constraint of forming at least one hydrogen bond with Arg 319, Arg 322, Lys 431, or Tyr 341 residues was introduced when performing virtual screening using Glide's virtual screening workflow (VSW). In the meantime, compounds with hydrophobic group likely to interact with the allosteric hydrophobic pocket are preferred when performing visual inspection. Seventy-four compounds were selected for the wet laboratory assays based on virtual screening and the absorption, distribution, metabolism, and excretion (ADME) properties of these compounds. LsrK inhibition assays revealed 12 compounds inhibiting LsrK by more than 60% at a 200 μM concentration; four of these (Y205-6768, D135-0149, 3284-1358, and N025-0038) had IC50 values below 50 μM and were confirmed as ATP-competitive inhibitors. Six of these 12 LsrK inhibitors exhibited high AI-2 QS inhibition, of which, Y205-6768 had the highest activity with IC50 = 11.28 ± 0.70 μM. The SPR assay verified that compounds Y205-6768 and N025-0038 specifically bound to LsrK. MD simulation analysis of the docking complexes of the four active compounds with LsrK further confirmed the importance of forming hydrogen bonds and salt bridges with key basic amino acid residues including Lys 431, Tyr 341, Arg 319, and Arg 322 and filling the allosteric hydrophobic pocket next to the purine-binding site of LsrK. Discussion: Our study clarified for the first time that there is an allosteric site near the ATP-binding site of Lsrk and that it enriches the structure-activity relationship information of Lsrk inhibitors. The four identified compounds showed novel structures, low molecular weights, high activities, and novel LsrK binding modes, rendering them suitable for further optimization for effective AI-2 QSIs. Our work provides a valuable reference for the discovery of QSIs that do not inhibit bacterial growth, thereby avoiding the emergence of drug resistance.
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Affiliation(s)
- Qianqian Shi
- School of Petrochemical Engineering, Liaoning Petrochemical University, Fushun, China
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yijie Xu
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xu Zhao
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jing Zhang
- Qionglai Medical Center Hospital, Chengdu, China
| | - Ye Li
- The No 968 Hospital of PLA, Jinzhou, China
| | - Qingbin Meng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Fang Yu
- School of Petrochemical Engineering, Liaoning Petrochemical University, Fushun, China
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Junhai Xiao
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xingzhou Li
- National Engineering Research Center for the Emergency Strategic Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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Xu Y, Zeng C, Wen H, Shi Q, Zhao X, Meng Q, Li X, Xiao J. Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein-Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation. Pharmaceuticals (Basel) 2023; 16:ph16050737. [PMID: 37242520 DOI: 10.3390/ph16050737] [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: 04/04/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Quorum sensing (QS) is a cell-to-cell communication mechanism that regulates bacterial pathogenicity, biofilm formation, and antibiotic sensitivity. Among the identified quorum sensing, AI-2 QS exists in both Gram-negative and Gram-positive bacteria and is responsible for interspecies communication. Recent studies have highlighted the connection between the phosphotransferase system (PTS) and AI-2 QS, with this link being associated with protein-protein interaction (PPI) between HPr and LsrK. Here, we first discovered several AI-2 QSIs targeting the LsrK/HPr PPI site through molecular dynamics (MD) simulation, virtual screening, and bioassay evaluation. Of the 62 compounds purchased, eight compounds demonstrated significant inhibition in LsrK-based assays and AI-2 QS interference assays. Surface plasmon resonance (SPR) analysis confirmed that the hit compound 4171-0375 specifically bound to the LsrK-N protein (HPr binding domain, KD = 2.51 × 10-5 M), and therefore the LsrK/HPr PPI site. The structure-activity relationships (SARs) emphasized the importance of hydrophobic interactions with the hydrophobic pocket and hydrogen bonds or salt bridges with key residues of LsrK for LsrK/HPr PPI inhibitors. These new AI-2 QSIs, especially 4171-0375, exhibited novel structures, significant LsrK inhibition, and were suitable for structural modification to search for more effective AI-2 QSIs.
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Affiliation(s)
- Yijie Xu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Chunlan Zeng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Huiqi Wen
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Qianqian Shi
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Xu Zhao
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Qingbin Meng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Xingzhou Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Junhai Xiao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
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14
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Structural Insights into the Ligand–LsrK Kinase Binding Mode: A Step Forward in the Discovery of Novel Antimicrobial Agents. Molecules 2023; 28:molecules28062542. [PMID: 36985513 PMCID: PMC10056567 DOI: 10.3390/molecules28062542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
LsrK is a bacterial kinase that triggers the quorum sensing, and it represents a druggable target for the identification of new agents for fighting antimicrobial resistance. Herein, we exploited tryptophan fluorescence spectroscopy (TFS) as a suitable technique for the identification of potential LsrK ligands from an in-house library of chemicals comprising synthetic compounds as well as secondary metabolites. Three secondary metabolites (Hib-ester, Hib-carbaldehyde and (R)-ASME) showed effective binding to LsrK, with KD values in the sub-micromolar range. The conformational changes were confirmed via circular dichroism and molecular docking results further validated the findings and displayed the specific mode of interaction. The activity of the identified compounds on the biofilm formation by some Staphylococcus spp. was investigated. Hib-carbaldehyde and (R)-ASME were able to reduce the production of biofilm, with (R)-ASME resulting in the most effective compound with an EC50 of 14 mg/well. The successful application of TFS highlights its usefulness in searching for promising LsrK inhibitor candidates with inhibitor efficacy against biofilm formation.
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Laganenka L, Lee JW, Malfertheiner L, Dieterich CL, Fuchs L, Piel J, von Mering C, Sourjik V, Hardt WD. Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nat Microbiol 2023; 8:204-217. [PMID: 36624229 DOI: 10.1038/s41564-022-01286-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/09/2022] [Indexed: 01/11/2023]
Abstract
Bacteria communicate and coordinate their behaviour at the intra- and interspecies levels by producing and sensing diverse extracellular small molecules called autoinducers. Autoinducer 2 (AI-2) is produced and detected by a variety of bacteria and thus plays an important role in interspecies communication and chemotaxis. Although AI-2 is a major autoinducer molecule present in the mammalian gut and can influence the composition of the murine gut microbiota, its role in bacteria-bacteria and bacteria-host interactions during gut colonization remains unclear. Combining competitive infections in C57BL/6 mice with microscopy and bioinformatic approaches, we show that chemotaxis (cheY) and AI-2 signalling (via lsrB) promote gut colonization by Escherichia coli, which is in turn connected to the ability of the bacteria to utilize fructoselysine (frl operon). We further show that the genomic diversity of E. coli strains with respect to AI-2 signalling allows ecological niche segregation and stable co-existence of different E. coli strains in the mammalian gut.
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Affiliation(s)
- Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Jae-Woo Lee
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Marburg, Germany
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Lea Fuchs
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Marburg, Germany
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16
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Rodrigues MV, Kis P, Xavier KB, Ventura MR. Synthesis and potential of Autoinducer‐2 and analogs to manipulate inter‐species Quorum Sensing. Isr J Chem 2023. [DOI: 10.1002/ijch.202200091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Miguel V. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Peter Kis
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
- Institute of Chemistry Slovak Academy of Sciences 845 38 Bratislava Slovakia
| | | | - M. Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
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17
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Stephens K, Bentley WE. Quorum Sensing from Two Engineers’ Perspectives. Isr J Chem 2023. [DOI: 10.1002/ijch.202200083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kristina Stephens
- Thayer School of Engineering Dartmouth College Hanover NH USA
- Center for Bioenergy Innovation Oak Ridge National Laboratory Oak Ridge TN USA
| | - William E. Bentley
- Fischell Department of Bioengineering University of Maryland College Park MD USA
- Institute for Bioscience and Biotechnology Research University of Maryland College Park MD USA [e]Robert E. Fischell Institute for Biomedical Devices University of Maryland College Park MD USA
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18
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Xue B, Shen Y, Zuo J, Song D, Fan Q, Zhang X, Yi L, Wang Y. Bringing Antimicrobial Strategies to a New Level: The Quorum Sensing System as a Target to Control Streptococcus suis. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122006. [PMID: 36556371 PMCID: PMC9782415 DOI: 10.3390/life12122006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022]
Abstract
Streptococcus suis (S. suis) is an important zoonotic pathogen. It mainly uses quorum sensing (QS) to adapt to complex and changeable environments. QS is a universal cell-to-cell communication system that has been widely studied for its physiological functions, including the regulation of bacterial adhesion, virulence, and biofilm formation. Quorum sensing inhibitors (QSIs) are highly effective at interfering with the QS system and bacteria have trouble developing resistance to them. We review the current research status of the S. suis LuxS/AI-2 QS system and QSIs. Studies showed that by inhibiting the formation of AI-2, targeting the LuxS protein, inhibiting the expression of luxs gene can control the LuxS/AI-2 QS system of S. suis. Other potential QSIs targets are summarized, which may be preventing and treating S. suis infections, including AI-2 production, transmission, LuxS protein, blockage of AI-2 binding to receptors, AI-2-mediated QS. Since antibiotics are becoming increasingly ineffective due to the emergence of resistant bacteria, including S. suis, it is thus critical to find new antibacterial drugs with different mechanisms of action. QSIs provide hope for the development of such drugs.
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Affiliation(s)
- Bingqian Xue
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Yamin Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Jing Zuo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Dong Song
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Qingying Fan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Xiaoling Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Li Yi
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
- College of Life Science, Luoyang Normal University, Luoyang 471000, China
- Correspondence: (L.Y.); (Y.W.)
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
- Correspondence: (L.Y.); (Y.W.)
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19
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Zhang Z, He P, Cai D, Chen S. Genetic and metabolic engineering for poly-γ-glutamic acid production: current progress, challenges, and prospects. World J Microbiol Biotechnol 2022; 38:208. [DOI: 10.1007/s11274-022-03390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/13/2022] [Indexed: 11/29/2022]
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Panayi T, Sarigiannis Y, Mourelatou E, Hapeshis E, Papaneophytou C. Anti-Quorum-Sensing Potential of Ethanolic Extracts of Aromatic Plants from the Flora of Cyprus. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192632. [PMID: 36235498 PMCID: PMC9572961 DOI: 10.3390/plants11192632] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/15/2022] [Accepted: 10/05/2022] [Indexed: 06/03/2023]
Abstract
Quorum sensing (QS) is a form of intra- and inter-species communication system employed by bacteria to regulate their collective behavior in a cell population-dependent manner. QS has been implicated in the virulence of several pathogenic bacteria. This work aimed to investigate the anti-QS potential of ethanolic extracts of eight aromatic plants of Cyprus, namely, Origanum vulgare subsp. hirtum, Rosmarinus officinalis, Salvia officinalis, Lavendula spp., Calendula officinalis, Melissa officinalis, Sideritis cypria, and Aloysia citriodora. We initially assessed the effects of the extracts on autoinducer 2 (AI-2) signaling activity, using Vibrio harveyi BB170 as a reported strain. We subsequently assessed the effect of the ethanolic extracts on QS-related processes, including biofilm formation and the swarming and swimming motilities of Escherichia coli MG1655. Of the tested ethanolic extracts, those of Origanum vulgare subsp. hirtum, Rosmarinus officinalis, and Salvia officinalis were the most potent AI-2 signaling inhibitors, while the extracts from the other plants exhibited low to moderate inhibitory activity. These three ethanolic extracts also inhibited the biofilm formation (>60%) of E. coli MG1655, as well as its swimming and swarming motilities, in a concentration-dependent manner. These extracts may be considered true anti-QS inhibitors because they disrupt QS-related activities of E. coli MG1655 without affecting bacterial growth. The results suggest that plants from the unexplored flora of Cyprus could serve as a source for identifying novel anti-QS inhibitors to treat infectious diseases caused by pathogens that are resistant to antibiotics.
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Wang S, Payne GF, Bentley WE. Quorum sensing componentry opens new lines of communication. EMBO J 2022; 41:e112162. [PMID: 35971916 PMCID: PMC9475535 DOI: 10.15252/embj.2022112162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Autoinducer-2 is a key molecule for bacterial quorum sensing. New exporter structures may now help narrow the gap between biology and engineering.
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Affiliation(s)
- Sally Wang
- Fischell Department of BioengineeringUniversity of MarylandCollege ParkMDUSA
- Robert E. Fischell Institute for Biomedical DevicesUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandCollege ParkMDUSA
| | - Gregory F Payne
- Fischell Department of BioengineeringUniversity of MarylandCollege ParkMDUSA
- Robert E. Fischell Institute for Biomedical DevicesUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandCollege ParkMDUSA
| | - William E Bentley
- Fischell Department of BioengineeringUniversity of MarylandCollege ParkMDUSA
- Robert E. Fischell Institute for Biomedical DevicesUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandCollege ParkMDUSA
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22
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Yuan PB, Ling JH, Zhu JH, Peng C, Chen EZ, Zhong YX, Liu WT, Wang LJ, Yang L, Chen DQ. Proteomics profiling of ertapenem challenged major porin deficient carbapenem-resistant Klebsiella pneumoniae. J Proteomics 2022; 268:104715. [PMID: 36058541 DOI: 10.1016/j.jprot.2022.104715] [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: 01/30/2022] [Revised: 06/14/2022] [Accepted: 08/28/2022] [Indexed: 10/14/2022]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an urgent threat to human health. Major outer membrane proteins (OMPs) porin mutation is one important resistance mechanism of CRKP, and may also affect the inhibition activity of β-lactam and β-lactamase inhibitor combinations. The ertapenem-resistant K. pneumoniae strain 2018B120 with major porin mutations was isolated from a clinical patient. Genomic and time-series proteomic analyses were conducted to retrieve the ertapenem-challenged response of 2018B120. The abundance changing of proteins from PTS systems, ABC transporters, the autoinducer 2 (AI-2) quorum sensing system, and antioxidant systems can be observed. Overexpression of alternative porins was also noticed to balance major porins' defection. These findings added a detailed regulation network in bacterial resistance mechanisms and gave new insights into bypass adaptation mechanisms the porin deficient bacteria adopted under carbapenem antibiotics pressure. SIGNIFICANCE: Outer membrane porins deficiency is an important mechanism of carbapenem resistance in K. pneumoniae. Comprehensive genomic and proteomic profiling of an ertapenem-resistant K. pneumoniae strain 2018B120 gives a detailed systematic regulation network in bacterial resistance mechanisms. Overexpression of alternative porins to balance major porins' defection was noticed, giving new insights into bypass adaptation mechanisms of porin deficient bacteria.
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Affiliation(s)
- Pei-Bo Yuan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Hui Ling
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Hui Zhu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen Peng
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - En-Zhong Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Xia Zhong
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wan-Ting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lin-Jing Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ding-Qiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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23
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Henderson AL, Moreno A, Kram KE. Parallel Evolution towards Increased Motility in Long-Term Cultures of Escherichia coli, Even Though Motility was Not Required for Long-Term Survival. Microbiol Spectr 2022; 10:e0233021. [PMID: 35735986 PMCID: PMC9431438 DOI: 10.1128/spectrum.02330-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/31/2022] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli can survive for long periods in batch culture in the laboratory, where they experience a stressful and heterogeneous environment. During this incubation, E. coli acquires mutations that are selected in response to this environment, ultimately leading to evolved populations that are better adapted to these complex conditions, which can lead to a better understanding of evolutionary mechanisms. Mutations in regulatory genes often play a role in adapting to heterogeneous environments. To identify such mutations, we examined transcriptional differences during log phase growth in unaged cells compared to those that had been aged for 10 days and regrown. We identified expression changes in genes involved in motility and chemotaxis after adaptation to long-term cultures. We hypothesized that aged populations would also have phenotypic changes in motility and that motility may play a role in survival and adaptation to long-term cultures. While aged populations did show an increase in motility, this increase was not essential for survival in long-term cultures. We identified mutations in the regulatory gene sspA and other genes that may contribute to the observed differences in motility. Taken together, these data provide an overall picture of the role of mutations in regulatory genes for adaptation while underscoring that all changes that occur during evolution in stressful environments are not necessarily adaptive. IMPORTANCE Understanding how bacteria adapt in long-term cultures aids in both better treatment options for bacterial infections and gives insight into the mechanisms involved in bacterial evolution. In the past, it has been difficult to study these organisms in their natural environments. By using experimental evolution in heterogeneous and stressful laboratory conditions, we can more closely mimic natural environments and examine evolutionary mechanisms. One way to observe these mechanisms is to look at transcriptomic and genomic data from cells adapted to these complex conditions. Here, we found that although aged cells increase motility, this increase is not essential for survival in these conditions. These data emphasize that not all changes that occur due to evolutionary processes are adaptive, but these observations could still lead to hypotheses about the causative mutations. The information gained here allow us to make inferences about general mechanisms underlying phenotypic changes due to evolution.
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Affiliation(s)
- Autumn L. Henderson
- Department of Biology, California State University, Dominguez Hills, Carson, California, USA
| | - Angie Moreno
- Department of Biology, California State University, Dominguez Hills, Carson, California, USA
| | - Karin E. Kram
- Department of Biology, California State University, Dominguez Hills, Carson, California, USA
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Koga R, Moriyama M, Onodera-Tanifuji N, Ishii Y, Takai H, Mizutani M, Oguchi K, Okura R, Suzuki S, Gotoh Y, Hayashi T, Seki M, Suzuki Y, Nishide Y, Hosokawa T, Wakamoto Y, Furusawa C, Fukatsu T. Single mutation makes Escherichia coli an insect mutualist. Nat Microbiol 2022; 7:1141-1150. [PMID: 35927448 PMCID: PMC9352592 DOI: 10.1038/s41564-022-01179-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023]
Abstract
Microorganisms often live in symbiosis with their hosts, and some are considered mutualists, where all species involved benefit from the interaction. How free-living microorganisms have evolved to become mutualists is unclear. Here we report an experimental system in which non-symbiotic Escherichia coli evolves into an insect mutualist. The stinkbug Plautia stali is typically associated with its essential gut symbiont, Pantoea sp., which colonizes a specialized symbiotic organ. When sterilized newborn nymphs were infected with E. coli rather than Pantoea sp., only a few insects survived, in which E. coli exhibited specific localization to the symbiotic organ and vertical transmission to the offspring. Through transgenerational maintenance with P. stali, several hypermutating E. coli lines independently evolved to support the host's high adult emergence and improved body colour; these were called 'mutualistic' E. coli. These mutants exhibited slower bacterial growth, smaller size, loss of flagellar motility and lack of an extracellular matrix. Transcriptomic and genomic analyses of 'mutualistic' E. coli lines revealed independent mutations that disrupted the carbon catabolite repression global transcriptional regulator system. Each mutation reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that single carbon catabolite repression mutations can make E. coli an insect mutualist. These findings provide an experimental system for future work on host-microbe symbioses and may explain why microbial mutualisms are omnipresent in nature.
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Affiliation(s)
- Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Naoko Onodera-Tanifuji
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoshiko Ishii
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiroki Takai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masaki Mizutani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kohei Oguchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Reiko Okura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Suzuki
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yudai Nishide
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Takahiro Hosokawa
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Yuichi Wakamoto
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Chikara Furusawa
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan. .,Department of Biological Sciences, The University of Tokyo, Tokyo, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
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25
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Zhou Q, Feng F, Li FL, Liu J, Wang M, Huang S, Sun Y. Acylated homoserine lactones regulate the response of methane metabolism and nitrogen metabolism to florfenicol in anaerobic fermentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155035. [PMID: 35395307 DOI: 10.1016/j.scitotenv.2022.155035] [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: 01/17/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Antimicrobial agents enter the ecological environment through animal excreta and disrupt metabolism in environmental microorganisms. Quorum sensing (QS) can help bacteria adapt to their surroundings. To explore how acyl-homoserine lactone (AHL) can adjust the influence of florfenicol on nitrogen cycling and methane metabolism in anaerobic fermentation, a small indoor thermostatic anaerobic fermentation model was established by adding exogenous acylated homoserine lactone (AHL) signal molecules with florfenicol as the stress factor. Through bacterial function prediction by PICRUST, we found that the addition of AHL further increased the promotion of methanogenesis_by_CO2_reduction_with_H2 and hydrogenotrophic methanogenesis by florfenicol. Before the third sampling, florfenicol significantly inhibited the enrichment of the denitrification pathway microbiota, whereas the addition of AHL significantly promoted the enrichment of the denitrification pathway microbiota. Functional annotation showed that florfenicol exposure stress significantly affected nitrogen and methane metabolism, and the addition of AHLs reduced the response of functional genes to florfenicol. All nitrogen cycling enzymes with significantly different abundances in treatment groups were substantially associated with methane-metabolizing enzymes. Glutamate metabolism is significant in the process of anaerobic fermentation, and is a correlation point between nitrogen and methane metabolism. In our experiment, AHL was the influencing factor at the highest latitude that directly regulates the metabolism of NO3--N and the degradation process of florfenicol. The addition of AHL curbed the inhibitory effect of florfenicol on some functional microbiota, improved the stability of fermentation microbiota, and weakened the impact of antibiotic residues by improving its degradation efficiency.
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Affiliation(s)
- Qin Zhou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; College of Life Sciences and Engineering, Foshan University, 18 Jiangwan Road, Foshan 528011, Guangdong Province, China
| | - Fengling Feng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Fu Lin Li
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Junlin Liu
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Mianzhi Wang
- Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Shujian Huang
- College of Life Sciences and Engineering, Foshan University, 18 Jiangwan Road, Foshan 528011, Guangdong Province, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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Quorum quenching of autoinducer 2 increases methane production in anaerobic digestion of waste activated sludge. Appl Microbiol Biotechnol 2022; 106:4763-4774. [PMID: 35715650 DOI: 10.1007/s00253-022-12014-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
The ubiquitous signaling molecule autoinducer 2 (AI-2) is involved in intra- and interspecies communication, most notably between Gram-negative and Gram-positive bacteria. AI-2 accumulates during the exponential phase of the Escherichia coli (E. coli) monoculture and then rapidly decreases upon entry into the stationary phase. However, deleting both the genes encoding AI-2 synthase (LuxS) and the lsr operon regulator (LsrR) in the E. coli genome causes impaired AI-2 production and continuous AI-2 scavenging from the environment. This genetically-engineered E. coli mutant capable of quenching AI-2 quorum sensing (QS) system was utilized to evaluate the effect of AI-2 quenching on the anaerobic digestion of waste activated sludge (WAS) because the role of QS system via AI-2 in the process remains obscure. In this study, E. coli ∆luxS lsrR mutant cells were microencapsulated in sodium alginate beads and incubated with WAS anaerobically. After 15 days of anaerobic fermentation, the WAS containing double mutant cells produced significantly more methane than that of the parent E. coli cells. AI-2 quenching occurred concurrently with a shift of microbial communities that contribute to increasing acetate consumption by the Methanosarcina spp. resulting in an increase in methane production. KEY POINTS: • Impact of autoinducer 2 quenching in complex bacterial populations were determined. • Key microorganisms contributing to the increase of methane in WAS anaerobic digestion were found. • The AI-2 quenching is a potential regulatory in wastewater treatment and bioenergy research.
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27
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Sionov RV, Steinberg D. Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:1239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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Affiliation(s)
- Ronit Vogt Sionov
- The Biofilm Research Laboratory, The Institute of Biomedical and Oral Research, The Faculty of Dental Medicine, Hadassah Medical School, The Hebrew University, Jerusalem 9112102, Israel;
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28
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Khera R, Mehdipour AR, Bolla JR, Kahnt J, Welsch S, Ermler U, Muenke C, Robinson CV, Hummer G, Xie H, Michel H. Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. EMBO J 2022; 41:e109990. [PMID: 35698912 PMCID: PMC9475539 DOI: 10.15252/embj.2021109990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/16/2022] Open
Abstract
Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis, and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from Escherichia coli, which belongs to the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism.
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Affiliation(s)
- Radhika Khera
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ahmad R Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Centre for molecular modelling, Ghent University, Zwijnaarde, Belgium
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Joerg Kahnt
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ulrich Ermler
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Cornelia Muenke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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29
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Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors. Sci Rep 2022; 12:8788. [PMID: 35610252 PMCID: PMC9130244 DOI: 10.1038/s41598-022-12463-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In this paper, we study the response mechanisms of E. coli when exposed to different environmental stressors via differential expression and co-expression analysis. Gene co-expression networks were generated and analyzed via Weighted Gene Co-expression Network Analysis (WGCNA). Based on the gene co-expression networks, genes with similar expression profiles were clustered into modules. The modules were analysed for identification of hub genes, enrichment of biological processes and transcription factors. In addition, we also studied the link between transcription factors and their differentially regulated targets to understand the regulatory mechanisms involved. These networks validate known gene interactions and provide new insights into genes mediating transcriptional regulation in specific stress environments, thus allowing for in silico hypothesis generation.
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30
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Li Y, Feng T, Wang Y. The role of bacterial signaling networks in antibiotics response and resistance regulation. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:163-178. [PMID: 37073223 PMCID: PMC10077285 DOI: 10.1007/s42995-022-00126-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/07/2022] [Indexed: 05/03/2023]
Abstract
Excessive use of antibiotics poses a threat to public health and the environment. In ecosystems, such as the marine environment, antibiotic contamination has led to an increase in bacterial resistance. Therefore, the study of bacterial response to antibiotics and the regulation of resistance formation have become an important research field. Traditionally, the processes related to antibiotic responses and resistance regulation have mainly included the activation of efflux pumps, mutation of antibiotic targets, production of biofilms, and production of inactivated or passivation enzymes. In recent years, studies have shown that bacterial signaling networks can affect antibiotic responses and resistance regulation. Signaling systems mostly alter resistance by regulating biofilms, efflux pumps, and mobile genetic elements. Here we provide an overview of how bacterial intraspecific and interspecific signaling networks affect the response to environmental antibiotics. In doing so, this review provides theoretical support for inhibiting bacterial antibiotic resistance and alleviating health and ecological problems caused by antibiotic contamination.
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Affiliation(s)
- Yuying Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Tao Feng
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Yan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071 China
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31
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Worthan SB, Franklin EA, Pham C, Yap MNF, Cruz-Vera LR. The Identity of the Constriction Region of the Ribosomal Exit Tunnel Is Important to Maintain Gene Expression in Escherichia coli. Microbiol Spectr 2022; 10:e0226121. [PMID: 35311583 PMCID: PMC9045200 DOI: 10.1128/spectrum.02261-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
Mutational changes in bacterial ribosomes often affect gene expression and consequently cellular fitness. Understanding how mutant ribosomes disrupt global gene expression is critical to determining key genetic factors that affect bacterial survival. Here, we describe gene expression and phenotypic changes presented in Escherichia coli cells carrying an uL22(K90D) mutant ribosomal protein, which displayed alterations during growth. Ribosome profiling analyses revealed reduced expression of operons involved in catabolism, indole production, and lysine-dependent acid resistance. In general, translation initiation of proximal genes in several of these affected operons was substantially reduced. These reductions in expression were accompanied by increases in the expression of acid-induced membrane proteins and chaperones, the glutamate-decarboxylase regulon, and the autoinducer-2 metabolic regulon. In agreement with these changes, uL22(K90D) mutant cells had higher glutamate decarboxylase activity, survived better in extremely acidic conditions, and generated more biofilm in static cultures compared to their parental strain. Our work demonstrates that a single mutation in a non-conserved residue of a ribosomal protein affects a substantial number of genes to alter pH resistance and the formation of biofilms. IMPORTANCE All newly synthesized proteins must pass through a channel in the ribosome named the exit tunnel before emerging into the cytoplasm, membrane, and other compartments. The structural characteristics of the tunnel could govern protein folding and gene expression in a species-specific manner but how the identity of tunnel elements influences gene expression is less well-understood. Our global transcriptomics and translatome profiling demonstrate that a single substitution in a non-conserved amino acid of the E. coli tunnel protein uL22 has a profound impact on catabolism, cellular signaling, and acid resistance systems. Consequently, cells bearing the uL22 mutant ribosomes had an increased ability to survive acidic conditions and form biofilms. This work reveals a previously unrecognized link between tunnel identity and bacterial stress adaptation involving pH response and biofilm formation.
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Affiliation(s)
- Sarah B. Worthan
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Elizabeth A. Franklin
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Chi Pham
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Mee-Ngan F. Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Luis R. Cruz-Vera
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama, USA
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32
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Lourenço M, Chaffringeon L, Lamy-Besnier Q, Titécat M, Pédron T, Sismeiro O, Legendre R, Varet H, Coppée JY, Bérard M, De Sordi L, Debarbieux L. The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection. Cell Host Microbe 2022; 30:556-569.e5. [PMID: 35421351 DOI: 10.1016/j.chom.2022.03.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/14/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022]
Abstract
Abundance and diversity of bacteria and their viral predators, bacteriophages (phages), in the digestive tract are associated with human health. Particularly intriguing is the long-term coexistence of these two antagonistic populations. We performed genome-wide RNA sequencing on a human enteroaggregative Escherichia coli isolate to identify genes differentially expressed between in vitro conditions and in murine intestines. We experimentally demonstrated that four of these differentially expressed genes modified the interactions between E. coli and three virulent phages by either increasing or decreasing its susceptibility/resistance pattern and also by interfering with biofilm formation. Therefore, the regulation of bacterial genes expression during the colonization of the digestive tract influences the coexistence of phages and bacteria, highlighting the intricacy of tripartite relationships between phages, bacteria, and the animal host in intestinal homeostasis.
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Affiliation(s)
- Marta Lourenço
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Lorenzo Chaffringeon
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, Ile-de-France, France
| | - Quentin Lamy-Besnier
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France
| | - Marie Titécat
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Université de Lille, INSERM, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, 59000 Lille, France
| | - Thierry Pédron
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Rachel Legendre
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France; Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Hugo Varet
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France; Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Jean-Yves Coppée
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Marion Bérard
- Institut Pasteur, Université Paris Cité, DT, Animalerie Centrale, Centre de Gnotobiologie, 75724 Paris, France
| | - Luisa De Sordi
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, Ile-de-France, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France.
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. PLANT COMMUNICATIONS 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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Meng F, Zhang F, Chen Q, Yang M, Yang Y, Li X, Gu W, Yu J. Virtual screening and in vitro experimental verification of LuxS inhibitors from natural products for Lactobacillus reuteri. Biomed Pharmacother 2022; 147:112521. [PMID: 35149360 DOI: 10.1016/j.biopha.2021.112521] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/02/2022] Open
Abstract
The rapid proliferation and colonization of probiotics in the intestines are essential for human health. Quorum sensing (QS) is a communication mechanism among bacteria, which can regulate various bacterial crowd behavior. This study aimed to enhance the viability of Lactobacillus reuteri 1-12 by regulating QS. Herein, we built a database containing 72 natural products (previously reported) that can improve intestinal flora. Virtual screening (VS) was subsequently conducted to screen four potential active compounds. After that, molecular docking was conducted to analyze the binding mode of the four natural products to S-Ribosylhomocysteinase (LuxS). The results showed that norathyriol, mangiferin, baicalein, and kaempferol had good binding ability to LuxS. The validation experiment showed that norathyriol, mangiferin, baicalein, and kaempferol could inhibit the production of autoinducer-2 (AI-2). Moreover, mangiferin significantly increased L. reuteri 1-12 biomass and promoted L. reuteri 1-12 biofilm formation and structure. Besides, only mangiferin inhibited luxS expression, thus increasing L. reuteri 1-12 biomass. This research indicated that mangiferin may be a potential inhibitor of LuxS, promoting the probiotic properties of L. reuteri and human health.
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Affiliation(s)
- Fanying Meng
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Fan Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Qiuding Chen
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Min Yang
- Kunming Third People's Hospital, 319 Wujing Road, Guandu District, Kunming, Yunnan, China
| | - Yaqin Yang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Xue Li
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China
| | - Wen Gu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China.
| | - Jie Yu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Chenggong District, Kunming, Yunnan, China.
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Li H, Xie R, Xu X, Liao X, Guo J, Fang Y, Fang Z, Huang J. Static Magnetic Field Inhibits Growth of Escherichia coli Colonies via Restriction of Carbon Source Utilization. Cells 2022; 11:cells11050827. [PMID: 35269449 PMCID: PMC8909705 DOI: 10.3390/cells11050827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Magnetobiological effects on growth and virulence have been widely reported in Escherichia coli (E. coli). However, published results are quite varied and sometimes conflicting because the underlying mechanism remains unknown. Here, we reported that the application of 250 mT static magnetic field (SMF) significantly reduces the diameter of E. coli colony-forming units (CFUs) but has no impact on the number of CFUs. Transcriptomic analysis revealed that the inhibitory effect of SMF is attributed to differentially expressed genes (DEGs) primarily involved in carbon source utilization. Consistently, the addition of glycolate or glyoxylate to the culture media successfully restores the bacterial phenotype in SMF, and knockout mutants lacking glycolate oxidase are no longer sensitive to SMF. These results suggest that SMF treatment results in a decrease in glycolate oxidase activity. In addition, metabolomic assay showed that long-chain fatty acids (LCFA) accumulate while phosphatidylglycerol and middle-chain fatty acids decrease in the SMF-treated bacteria, suggesting that SMF inhibits LCFA degradation. Based on the published evidence together with ours derived from this study, we propose a model showing that free radicals generated by LCFA degradation are the primary target of SMF action, which triggers the bacterial oxidative stress response and ultimately leads to growth inhibition.
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Affiliation(s)
- Haodong Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Runnan Xie
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xiang Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xingru Liao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Jiaxin Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Yanwen Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Zhicai Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
- Correspondence:
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Keizers M, Dobrindt U, Berger M. A Simple Biosensor-Based Assay for Quantitative Autoinducer-2 Analysis. ACS Synth Biol 2022; 11:747-759. [PMID: 35090122 DOI: 10.1021/acssynbio.1c00459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteria produce and react to interspecies signaling molecules in order to control the expression of genes that are particularly beneficial when they are expressed by a bacterial community. In addition to intraspecies communication, the signaling molecule autoinducer-2 (AI-2) can also serve for interspecies communication between Gram-positive and Gram-negative bacteria and is therefore of particular interest. The analysis and quantification of AI-2 are essential for understanding population density-dependent changes in bacterial behavior and pathogenicity. However, currently available bioassays for AI-2 quantification are rather complex, have narrow detection ranges, and are very sensitive to trace components of, for example, growth media. To facilitate and improve the detection of AI-2, we have developed an Escherichia coli biosensor-based assay that is sensitive, cheap, fast, robust, and reliable in the quantification of biologically active AI-2. The bioassay is based on an lsr promoter-fluorescent reporter gene fusion cassette that we chromosomally integrated in a biosensor strain, but the cassette can also be used in a low-copy number plasmid for the application in other Gram-negative bacterial species. We show here that AI-2 quantification was possible in a concentration range from 400 nM to 100 μM and that a critical interpretation of the kinetics of the measurements can reveal sugar interference. With the help of our biosensor strain, coculture experiments were done to test the capability and kinetics of AI-2 secretion by various Gram-negative bacteria in real time. Finally, calibration curves were used to calculate the absolute AI-2 concentration in cell-free bacterial samples.
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Affiliation(s)
- Marla Keizers
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Michael Berger
- Institute of Hygiene, University of Münster, Münster 48149, Germany
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Chen X, Tian J, Luo C, Wang X, Li X, Wang M. Cell Membrane Remodeling Mediates Polymyxin B Resistance in Klebsiella pneumoniae: An Integrated Proteomics and Metabolomics Study. Front Microbiol 2022; 13:810403. [PMID: 35222333 PMCID: PMC8866958 DOI: 10.3389/fmicb.2022.810403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022] Open
Abstract
Polymyxin B (PB) is introduced into the clinic as the last-line therapy against carbapenem-resistant Klebsiella pneumoniae (CRKP). Unfortunately, increased resistance to PB in Klebsiella pneumoniae (K. pneumoniae) has threatened global health. Resistance of K. pneumoniae to PB was induced by passaging in serial concentrations of PB and determined by microbroth dilution method. Growth characteristics of induced strains including growth curve, reversibility of resistance, and biofilm formation (crystal violet staining method) were measured. This study employed TMT-labeled quantitative proteomics and LC-MS/MS metabolomics analysis to investigate the key biological processes associated with PB resistance in K. pneumoniae. A total of 315 differentially expressed proteins (DEPs) were identified, of which 133 were upregulated and 182 were downregulated in the PB-resistant K. pneumoniae. KEGG enrichment analysis revealed that the DEPs were mainly involved in ATP-binding cassette (ABC) transporters and cationic antimicrobial peptide (CAMP) resistance. Proteins related to central carbon metabolism were inhibited in the PB-resistant K. pneumoniae, but proteins mediating LPS modification were activated. Transcriptional levels of CAMP resistance-related proteins were significantly different between PB-susceptible and -resistant K. pneumoniae. PB treatment led to an increase in reactive oxygen species (ROS) levels of K. pneumoniae. Metabolomics data demonstrated that 23 metabolites were significantly upregulated in PB-resistant K. pneumoniae and 5 were downregulated. The differential metabolites were mainly lipids, including glycerophospholipids, sphingolipids, and fatty acids. Exposure to PB resulted in increased level of phospholipid transport gene mlaF in K. pneumoniae. Our study suggested that membrane remodeling and inhibited central carbon metabolism are conducive to the development of PB resistance in K. pneumoniae.
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Affiliation(s)
| | | | | | | | | | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
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Ruiz CH, Osorio-Llanes E, Trespalacios MH, Mendoza-Torres E, Rosales W, Gómez CMM. Quorum Sensing Regulation as a Target for Antimicrobial Therapy. Mini Rev Med Chem 2021; 22:848-864. [PMID: 34856897 DOI: 10.2174/1389557521666211202115259] [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: 10/04/2020] [Revised: 05/20/2021] [Accepted: 09/04/2021] [Indexed: 11/22/2022]
Abstract
Some bacterial species use a cell-to-cell communication mechanism called Quorum Sensing (QS). Bacteria release small diffusible molecules, usually termed signals which allow the activation of beneficial phenotypes that guarantee bacterial survival and the expression of a diversity of virulence genes in response to an increase in population density. The study of the molecular mechanisms that relate signal molecules with bacterial pathogenesis is an area of growing interest due to its use as a possible therapeutic alternative through the development of synthetic analogues of autoinducers as a strategy to regulate bacterial communication as well as the study of bacterial resistance phenomena, the study of these relationships is based on the structural diversity of natural or synthetic autoinducers and their ability to inhibit bacterial QS, which can be approached with a molecular perspective from the following topics: i) Molecular signals and their role in QS regulation; ii) Strategies in the modulation of Quorum Sensing; iii) Analysis of Bacterial QS circuit regulation strategies; iv) Structural evolution of natural and synthetic autoinducers as QS regulators. This mini-review allows a molecular view of the QS systems, showing a perspective on the importance of the molecular diversity of autoinducer analogs as a strategy for the design of new antimicrobial agents.
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Affiliation(s)
- Caterine Henríquez Ruiz
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
| | - Estefanie Osorio-Llanes
- Faculty of Exact and Natural sciences. Grupo de Investigación Avanzada en Biomedicina. Universidad Libre. Barranquilla. Colombia
| | - Mayra Hernández Trespalacios
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
| | - Evelyn Mendoza-Torres
- Faculty of Health Sciences. Grupo de Investigación Avanzada en Biomedicina-Universidad Libre. Barranquilla. Colombia
| | - Wendy Rosales
- Faculty of Exact and Natural sciences. Grupo de Investigación Avanzada en Biomedicina. Universidad Libre. Barranquilla. Colombia
| | - Carlos Mario Meléndez Gómez
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
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Shang F, Wang H, Zhang D, Wang W, Yu J, Xue T. Construction of an AI-2 quorum sensing induced heterologous protein expression system in Escherichia coli. PeerJ 2021; 9:e12497. [PMID: 34820206 PMCID: PMC8603832 DOI: 10.7717/peerj.12497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
Background The pET expression system based on T7 promoter which is induced by isopropyl-β-D-1-thiogalactopyranoside (IPTG) is by far the most commonly used system for production of heterogeneous proteins in Escherichia coli. However, this system was limited by obvious drawbacks including the host toxicity and metabolic burden imposed by the presence of IPTG. Methods In this study, we incorporated the autoinducer-2 (AI-2) quorum sensing system to realize autoinduction of the pET expression system. The autoinduction expression vector pXWZ1 was constructed by inserting the lsr promoter regions into the pET28a(+) vector. The expression efficiency of the reporter genes gfpuv and lacZ by the pXWZ1 and pET28a(+) vectors were compared. Results The results showed that the expression levels of the both report genes in the cells transformed with pXWZ1 without any addition of exogenous inducer were higher than that transformed with pET28a(+) vectors by the induction of IPTG. Conclusion This new auto-induction system will exclude the limitations of the IPTG induction including toxic to host and increasing formation of inclusion body and will become a more economical and convenient tool for recombinant protein expression.
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Affiliation(s)
- Fei Shang
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Hui Wang
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Dan Zhang
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Wenhui Wang
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Jiangliu Yu
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Ting Xue
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
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40
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Fang Y, Visvalingam J, Zhang P, Yang X. Biofilm formation by Non-O157 Shiga toxin-producing Escherichia coli in monocultures and co-cultures with meat processing surface bacteria. Food Microbiol 2021; 102:103902. [PMID: 34809934 DOI: 10.1016/j.fm.2021.103902] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/10/2021] [Accepted: 09/10/2021] [Indexed: 11/04/2022]
Abstract
This study investigated the impact of meat processing surface bacteria (MPB) on biofilm formation by non-O157 Shiga toxin-producing Escherichia coli (STEC), and potential links between biofilm formation by STEC and biofilm-related genes in their genomes. Biofilm development by 50 MPB and 6 STEC strains in mono- and co-cultures was assessed by the crystal violet staining method, and their expression of curli and cellulose was determined using the Congo red agar method. Genes (n = 141) associated with biofilm formation in the STEC strains were profiled. Biofilm formation in general correlated with cellulose and curli expression in both mono- and co-cultures. Most MPB strains had antagonistic effects on the biofilm formation of the STEC strains. Of the genes investigated, 81% were common among the STEC strains and there seems to be a gene-redundancy in biofilm formation. The inability of the O26 strain to form biofilms could be due to mutations in the rpoS gene. Truncation in the mlrA gene in the O145 strain seems not affecting its biofilm formation alone or with MPB. The O45 strain, despite having the greatest number of biofilm-related genes, did not form measurable biofilms. Overall, biofilm formation of STEC was affected by curli-cellulose expression and companion strains.
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Affiliation(s)
- Yuan Fang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada
| | - Jeyachchandran Visvalingam
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada
| | - Peipei Zhang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada.
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Interplay between Sublethal Aminoglycosides and Quorum Sensing: Consequences on Survival in V. cholerae. Cells 2021; 10:cells10113227. [PMID: 34831448 PMCID: PMC8621022 DOI: 10.3390/cells10113227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/01/2023] Open
Abstract
Antibiotics are well known drugs which, when present above certain concentrations, are able to inhibit the growth of certain bacteria. However, a growing body of evidence shows that even when present at lower doses (subMIC, for sub-minimal inhibitory concentration), unable to inhibit or affect microbial growth, antibiotics work as signaling molecules, affect gene expression and trigger important bacterial stress responses. However, how subMIC antibiotic signaling interplays with other well-known signaling networks in bacteria (and the consequences of such interplay) is not well understood. In this work, through transcriptomic and genetic approaches, we have explored how quorum-sensing (QS) proficiency of V. cholerae affects this pathogen’s response to subMIC doses of the aminoglycoside tobramycin (TOB). We show that the transcriptomic signature of V. cholerae in response to subMIC TOB depends highly on the presence of QS master regulator HapR. In parallel, we show that subMIC doses of TOB are able to negatively interfere with the AI-2/LuxS QS network of V. cholerae, which seems critical for survival to aminoglycoside treatment and TOB-mediated induction of SOS response in this species. This interplay between QS and aminoglycosides suggests that targeting QS signaling may be a strategy to enhance aminoglycoside efficacy in V. cholerae.
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42
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Šoltysová M, Sieglová I, Fábry M, Brynda J, Škerlová J, Řezáčová P. Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1411-1424. [PMID: 34726169 DOI: 10.1107/s2059798321009633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/16/2021] [Indexed: 11/11/2022]
Abstract
The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and bsCggR in complex with DNA duplexes representing the minimal operator sequence at resolutions of 2.3 and 2.1 Å, respectively. While bsDeoRDBD contains a homeodomain-like HTH-type domain, bsCggRDBD contains a winged helix-turn-helix-type motif. Both proteins form C2-symmetric dimers that recognize two consecutive major grooves, and the protein-DNA interactions have been analyzed in detail. The crystal structures were used to model the interactions of the proteins with the full DNA operators, and a common mode of DNA recognition is proposed that is most likely to be shared by other members of the SorC/DeoR family.
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Affiliation(s)
- Markéta Šoltysová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Irena Sieglová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Brynda
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jana Škerlová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Pavlína Řezáčová
- Structural Biology, Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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Wang N, Jin Y, He G, Yuan L. Intraspecific and interspecific extracellular metabolites remodel biofilms formed by thermophilic spoilage bacteria. J Appl Microbiol 2021; 133:2096-2106. [PMID: 34689405 DOI: 10.1111/jam.15338] [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: 07/14/2021] [Revised: 09/24/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022]
Abstract
AIMS Thermophilic spoilage bacteria and their biofilms formed during milk powder processing posed threats to safety and quality of dairy products. This research aims to understand more about the bacterial behaviours and their social models in biofilms. METHODS AND RESULTS Interactional effects from both extracellular metabolites and co-culture on biofilms formation of the contaminating thermophilic bacteria were determined. The results showed that strong biofilm formers always had high AI-2 activities, including Geobacillus stearothermophilus gs1, Bacillus licheniformis bl1 and Thermoactinomyces vulgaris tv1. Metabolites from themself or other species altered their biofilm biomass detected by crystal violet staining. Dual-species cultures observed by confocal laser scanning microscope indicated either synergistic or inhibitory effects between B. circulans bc1 and G. stearothermophilus gs1, as well as B. licheniformis bl1 and G. stearothermophilus gs1. Fourier transform infrared spectrometry results revealed the significant diversities in polysaccharides of the biofilm matrix. CONCLUSIONS Cell communication played an important role on biofilm formation in the complex microbial community. Intraspecific and interspecific extracellular metabolites influenced collective bacterial behaviours under mixed circumstances. SIGNIFICANCE AND IMPACT OF STUDY This research provided evidences on cell communication and biofilm formation of thermophilic bacteria in dairy industry.
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Affiliation(s)
- Ni Wang
- School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, China
| | - Yujie Jin
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Guoqing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
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Joudeh N, Saragliadis A, Schulz C, Voigt A, Almaas E, Linke D. Transcriptomic Response Analysis of Escherichia coli to Palladium Stress. Front Microbiol 2021; 12:741836. [PMID: 34690987 PMCID: PMC8533678 DOI: 10.3389/fmicb.2021.741836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Palladium (Pd), due to its unique catalytic properties, is an industrially important heavy metal especially in the form of nanoparticles. It has a wide range of applications from automobile catalytic converters to the pharmaceutical production of morphine. Bacteria have been used to biologically produce Pd nanoparticles as a new environmentally friendly alternative to the currently used energy-intensive and toxic physicochemical methods. Heavy metals, including Pd, are toxic to bacterial cells and cause general and oxidative stress that hinders the use of bacteria to produce Pd nanoparticles efficiently. In this study, we show in detail the Pd stress-related effects on E. coli. Pd stress effects were measured as changes in the transcriptome through RNA-Seq after 10 min of exposure to 100 μM sodium tetrachloropalladate (II). We found that 709 out of 3,898 genes were differentially expressed, with 58% of them being up-regulated and 42% of them being down-regulated. Pd was found to induce several common heavy metal stress-related effects but interestingly, Pd causes unique effects too. Our data suggests that Pd disrupts the homeostasis of Fe, Zn, and Cu cellular pools. In addition, the expression of inorganic ion transporters in E. coli was found to be massively modulated due to Pd intoxication, with 17 out of 31 systems being affected. Moreover, the expression of several carbohydrate, amino acid, and nucleotide transport and metabolism genes was vastly changed. These results bring us one step closer to the generation of genetically engineered E. coli strains with enhanced capabilities for Pd nanoparticles synthesis.
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Affiliation(s)
- Nadeem Joudeh
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Christian Schulz
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - André Voigt
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway
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45
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Hoke AK, Reynoso G, Smith MR, Gardner MI, Lockwood DJ, Gilbert NE, Wilhelm SW, Becker IR, Brennan GJ, Crider KE, Farnan SR, Mendoza V, Poole AC, Zimmerman ZP, Utz LK, Wurch LL, Steffen MM. Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere. PLoS One 2021; 16:e0257017. [PMID: 34550975 PMCID: PMC8457463 DOI: 10.1371/journal.pone.0257017] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.
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Affiliation(s)
- Alexa K. Hoke
- James Madison University, Harrisonburg, VA, United States of America
| | - Guadalupe Reynoso
- James Madison University, Harrisonburg, VA, United States of America
- Virginia Tech, Blacksburg, VA, United States of America
| | - Morgan R. Smith
- James Madison University, Harrisonburg, VA, United States of America
- Texas A&M University, College Station, TX, United States of America
| | - Malia I. Gardner
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Naomi E. Gilbert
- James Madison University, Harrisonburg, VA, United States of America
- University of Tennessee, Knoxville, TN, United States of America
| | | | | | - Grant J. Brennan
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Shannon R. Farnan
- James Madison University, Harrisonburg, VA, United States of America
| | - Victoria Mendoza
- James Madison University, Harrisonburg, VA, United States of America
| | - Alison C. Poole
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Lucy K. Utz
- James Madison University, Harrisonburg, VA, United States of America
| | - Louie L. Wurch
- James Madison University, Harrisonburg, VA, United States of America
| | - Morgan M. Steffen
- James Madison University, Harrisonburg, VA, United States of America
- * E-mail:
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46
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Meza-Torres J, Auria E, Dupuy B, Tremblay YDN. Wolf in Sheep's Clothing: Clostridioides difficile Biofilm as a Reservoir for Recurrent Infections. Microorganisms 2021; 9:1922. [PMID: 34576818 PMCID: PMC8470499 DOI: 10.3390/microorganisms9091922] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/21/2022] Open
Abstract
The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission.
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Affiliation(s)
- Jazmin Meza-Torres
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Emile Auria
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Yannick D. N. Tremblay
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
- Health Sciences Building, Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK S7N 5E5, Canada
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Li E, Wu J, Zhang D. Exogenous autoinducer-2 inhibits biofilm development of Desulfovibrio sp. Huiquan2017. World J Microbiol Biotechnol 2021; 37:124. [PMID: 34170406 DOI: 10.1007/s11274-021-03071-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 05/16/2021] [Indexed: 11/28/2022]
Abstract
Sulfate-reducing bacteria (SRB) are culprits for microbiologically influenced corrosion, and biofilms are believed to play essential roles in the corrosion induced by SRB. However, little is known about the regulation of SRB biofilms. Quorum sensing signal molecules acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) regulate biofilm formation of many bacteria. In this study, the production of AHLs and AI-2 by one SRB strain, Desulfovibrio sp. Huiquan2017, was detected, and the effect of exogenous AI-2 on bacterial biofilm formation was discussed. It was found that the cell-free supernatants of Desulfovibrio sp. Huiquan2017 induced luminescence in a ∆luxS mutant strain Vibrio harveyi BB170, indicating the production of functional AI-2 by the bacterium. In the presence of exogenous AI-2, the growth of Desulfovibrio sp. Huiquan2017 and early biofilm formation were not affected, but the later stage of biofilm development was inhibited significantly. The biofilms became looser, smaller, and thinner, and contained less bacteria and extracellular polymeric substances (EPS). The inhibition effect of AI-2 on the biofilm development of Desulfovibrio sp. Huiquan2017 was mainly achieved through reducing the amount of EPS in biofilms. These findings shed light on the biofilm regulation of SRB.
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Affiliation(s)
- Ee Li
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China
| | - Jiajia Wu
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
| | - Dun Zhang
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
- Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
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Pacheco T, Gomes AÉI, Siqueira NMG, Assoni L, Darrieux M, Venter H, Ferraz LFC. SdiA, a Quorum-Sensing Regulator, Suppresses Fimbriae Expression, Biofilm Formation, and Quorum-Sensing Signaling Molecules Production in Klebsiella pneumoniae. Front Microbiol 2021; 12:597735. [PMID: 34234747 PMCID: PMC8255378 DOI: 10.3389/fmicb.2021.597735] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has become a worldwide concern due to the emergence of multidrug-resistant isolates responsible for various invasive infectious diseases. Biofilm formation constitutes a major virulence factor for K. pneumoniae and relies on the expression of fimbrial adhesins and aggregation of bacterial cells on biotic or abiotic surfaces in a coordinated manner. During biofilm aggregation, bacterial cells communicate with each other through inter- or intra-species interactions mediated by signallng molecules, called autoinducers, in a mechanism known as quorum sensing (QS). In most Gram-negative bacteria, intra-species communication typically involves the LuxI/LuxR system: LuxI synthase produces N-acyl homoserine lactones (AHLs) as autoinducers and the LuxR transcription factor is their cognate receptor. However, K. pneumoniae does not produce AHL but encodes SdiA, an orphan LuxR-type receptor that responds to exogenous AHL molecules produced by other bacterial species. While SdiA regulates several cellular processes and the expression of virulence factors in many pathogens, the role of this regulator in K. pneumoniae remains unknown. In this study, we describe the characterization of sdiA mutant strain of K. pneumoniae. The sdiA mutant strain has increased biofilm formation, which correlates with the increased expression of type 1 fimbriae, thus revealing a repressive role of SdiA in fimbriae expression and bacterial cell adherence and aggregation. On the other hand, SdiA acts as a transcriptional activator of cell division machinery assembly in the septum, since cells lacking SdiA regulator exhibited a filamentary shape rather than the typical rod shape. We also show that K. pneumoniae cells lacking SdiA regulator present constant production of QS autoinducers at maximum levels, suggesting a putative role for SdiA in the regulation of AI-2 production. Taken together, our results demonstrate that SdiA regulates cell division and the expression of virulence factors such as fimbriae expression, biofilm formation, and production of QS autoinducers in K. pneumoniae.
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Affiliation(s)
- Thaisy Pacheco
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Ana Érika Inácio Gomes
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | | | - Lucas Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Michelle Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
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Wang S, Tsao CY, Motabar D, Li J, Payne GF, Bentley WE. A Redox-Based Autoinduction Strategy to Facilitate Expression of 5xCys-Tagged Proteins for Electrobiofabrication. Front Microbiol 2021; 12:675729. [PMID: 34220759 PMCID: PMC8250426 DOI: 10.3389/fmicb.2021.675729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 01/17/2023] Open
Abstract
Biofabrication utilizes biological materials and biological means, or mimics thereof, for assembly. When interfaced with microelectronics, electrobiofabricated assemblies enable exquisite sensing and reporting capabilities. We recently demonstrated that thiolated polyethylene glycol (PEG-SH) could be oxidatively assembled into a thin disulfide crosslinked hydrogel at an electrode surface; with sufficient oxidation, extra sulfenic acid groups are made available for covalent, disulfide coupling to sulfhydryl groups of proteins or peptides. We intentionally introduced a polycysteine tag (5xCys-tag) consisting of five consecutive cysteine residues at the C-terminus of a Streptococcal protein G to enable its covalent coupling to an electroassembled PEG-SH film. We found, however, that its expression and purification from E. coli was difficult, owing to the extra cysteine residues. We developed a redox-based autoinduction methodology that greatly enhanced the yield, especially in the soluble fraction of E. coli extracts. The redox component involved the deletion of oxyRS, a global regulator of the oxidative stress response and the autoinduction component integrated a quorum sensing (QS) switch that keys the secreted QS autoinducer-2 to induction. Interestingly, both methods helped when independently employed and further, when used in combination (i.e., autodinduced oxyRS mutant) the results were best—we found the highest total yield and highest yield in the soluble fraction. We hypothesize that the production host was less prone to severe metabolic perturbations that might reduce yield or drive sequestration of the -tagged protein into inclusion bodies. We expect this methodology will be useful for the expression of many such Cys-tagged proteins, ultimately enabling a diverse array of functionalized devices.
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Affiliation(s)
- Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Chen-Yu Tsao
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Dana Motabar
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Jinyang Li
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Gregory F Payne
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
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50
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Friends or Foes-Microbial Interactions in Nature. BIOLOGY 2021; 10:biology10060496. [PMID: 34199553 PMCID: PMC8229319 DOI: 10.3390/biology10060496] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability. Abstract Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.
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