451
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Denega I, d'Enfert C, Bachellier-Bassi S. Candida albicans Biofilms Are Generally Devoid of Persister Cells. Antimicrob Agents Chemother 2019; 63:e01979-18. [PMID: 30783002 PMCID: PMC6496073 DOI: 10.1128/aac.01979-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/10/2019] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is known for its ability to form biofilms, which are communities of microorganisms embedded in an extracellular matrix developing on different surfaces. Biofilms are highly tolerant to antifungal therapy. This phenomenon has been partially explained by the appearance of so-called persister cells, phenotypic variants of wild-type cells, capable of surviving very high concentrations of antimicrobial agents. Persister cells in C. albicans were found exceptionally in biofilms, while none were detected in planktonic cultures of this fungus. Yet, this topic remains controversial, as others could not observe persister cells in biofilms formed by the C. albicans SC5314 laboratory strain. Due to ambiguous data in the literature, this work aimed to reevaluate the presence of persister cells in C. albicans biofilms. We demonstrated that the isolation of C. albicans "persister cells" as described previously was likely to be the result of the survival of biofilm cells that were not reached by the antifungal. We tested biofilms of SC5314 and its derivatives, as well as 95 clinical isolates, using an improved protocol, demonstrating that persister cells are not a characteristic trait of C. albicans biofilms. Although some clinical isolates are able to yield survivors upon the antifungal treatment of biofilms, this phenomenon is rather stochastic and inconsistent.
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Affiliation(s)
- Iryna Denega
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Christophe d'Enfert
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, Paris, France
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452
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Zhang YE, Bærentsen RL, Fuhrer T, Sauer U, Gerdes K, Brodersen DE. (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch. Mol Cell 2019; 74:1239-1249.e4. [PMID: 31023582 DOI: 10.1016/j.molcel.2019.03.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/07/2019] [Accepted: 03/27/2019] [Indexed: 01/17/2023]
Abstract
The stringent response alarmones pppGpp and ppGpp are essential for rapid adaption of bacterial physiology to changes in the environment. In Escherichia coli, the nucleosidase PpnN (YgdH) regulates purine homeostasis by cleaving nucleoside monophosphates and specifically binds (p)ppGpp. Here, we show that (p)ppGpp stimulates the catalytic activity of PpnN both in vitro and in vivo causing accumulation of several types of nucleobases during stress. The structure of PpnN reveals a tetramer with allosteric (p)ppGpp binding sites located between subunits. pppGpp binding triggers a large conformational change that shifts the two terminal domains to expose the active site, providing a structural rationale for the stimulatory effect. We find that PpnN increases fitness and adjusts cellular tolerance to antibiotics and propose a model in which nucleotide levels can rapidly be adjusted during stress by simultaneous inhibition of biosynthesis and stimulation of degradation, thus achieving a balanced physiological response to constantly changing environments.
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Affiliation(s)
- Yong Everett Zhang
- Department of Biology, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, 2200 Copenhagen, Denmark.
| | - René Lysdal Bærentsen
- Department of Molecular Biology and Genetics, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), Aarhus University, 8000 Aarhus C, Denmark
| | - Tobias Fuhrer
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland
| | - Kenn Gerdes
- Department of Biology, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ditlev Egeskov Brodersen
- Department of Molecular Biology and Genetics, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), Aarhus University, 8000 Aarhus C, Denmark.
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453
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Svenningsen MS, Veress A, Harms A, Mitarai N, Semsey S. Birth and Resuscitation of (p)ppGpp Induced Antibiotic Tolerant Persister Cells. Sci Rep 2019; 9:6056. [PMID: 30988388 PMCID: PMC6465370 DOI: 10.1038/s41598-019-42403-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
Transient antibiotic treatment typically eradicates most sensitive bacteria except a few survivors called persisters. The second messenger (p)ppGpp plays a key role in persister formation in Escherichia coli populations but the underlying mechanisms have remained elusive. In this study we induced (p)ppGpp synthesis by modulating tRNA charging and then directly observed the stochastic appearance, antibiotic tolerance, and resuscitation of persister cells using live microscopy. Different physiological parameters of persister cells as well as their regularly growing ancestors and sisters were continuously monitored using fluorescent reporters. Our results confirmed previous findings that high (p)ppGpp levels are critical for persister formation, but the phenomenon remained strikingly stochastic without any correlation between (p)ppGpp levels and antibiotic tolerance on the single-cell level. We could not confirm previous notions that persisters exhibit markedly low concentrations of intracellular ATP or were linked to post-transcriptional effects of (p)ppGpp through the activation of small genetic elements known as toxin-antitoxin (TA) modules. Instead, we suggest that persister cell formation under regular conditions is driven by the transcriptional response to increased (p)ppGpp levels.
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Affiliation(s)
| | - Alexandra Veress
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 København N, København, Denmark
| | - Alexander Harms
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 København N, København, Denmark
| | - Namiko Mitarai
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 København Ø, København, Denmark.
| | - Szabolcs Semsey
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 København N, København, Denmark.
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454
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Interaction studies on bacterial stringent response protein RelA with uncharged tRNA provide evidence for its prerequisite complex for ribosome binding. Curr Genet 2019; 65:1173-1184. [PMID: 30968189 DOI: 10.1007/s00294-019-00966-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
The bacterial stringent response is regulated by the synthesis of (p)ppGpp which is mediated by RelA in a complex with uncharged tRNA and ribosome. We intended to probe RelA-uncharged tRNA interactions off the ribosome to understand the sequential activation mechanism of RelA. Stringent response is a key regulatory pleiotropic mechanism which allows bacteria to survive in unfavorable conditions. Since the discovery of RelA, it has been believed that it is activated upon binding to ribosomes which already have uncharged tRNA on acceptor site (A-site). However, uncharged tRNA occupied in the A-site of the ribosome prior to RelA binding could not be observed; therefore, recently an alternate model for RelA activation has been proposed in which RelA first binds to uncharged tRNA and then RelA-uncharged tRNA complex is loaded on to the ribosome to synthesize (p)ppGpp. To explore the alternate hypothesis, we report here the in vitro binding of uncharged tRNA to RelA in the absence of ribosome using formaldehyde cross-linking, fluorescence spectroscopy, surface plasmon resonance, size-exclusion chromatography, and hydrogen-deuterium exchange mass spectrometry. Altogether, our results clearly indicate binding between RelA and uncharged tRNA without the involvement of ribosome. Moreover, we have analyzed their binding kinetics and mapping of tRNA-interacting regions of RelA structure. We have also co-purified TGS domain in complex with tRNA to further establish in vivo RelA-tRNA binding. We have observed that TGS domain recognizes all types of uncharged tRNA similar to EF-Tu and tRNA interactions. Altogether, our results demonstrate the complex formation between RelA and uncharged tRNA that may be loaded to the ribosome for (p)ppGpp synthesis.
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455
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Prasetyoputri A, Jarrad AM, Cooper MA, Blaskovich MA. The Eagle Effect and Antibiotic-Induced Persistence: Two Sides of the Same Coin? Trends Microbiol 2019; 27:339-354. [DOI: 10.1016/j.tim.2018.10.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/21/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022]
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456
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Zheng G, Lu Y, Wang D, Zhou L. Importance of sludge conditioning in attenuating antibiotic resistance: Removal of antibiotic resistance genes by bioleaching and chemical conditioning with Fe[III]/CaO. WATER RESEARCH 2019; 152:61-73. [PMID: 30660902 DOI: 10.1016/j.watres.2018.12.053] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/14/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Conditioning can drastically improve the dewaterability of sewage sludge and thus it is widely practiced in most wastewater treatment plants (WWTPs). In WWTPs, various antibiotic resistance genes (ARGs) present in sewage are concentrated in the sewage sludge, but the effect of sludge conditioning on ARGs in sewage sludge remains unclear. Here, we evaluated and compared the effectiveness of four sludge conditioning methods (namely chemical conditioning with polyacrylamide (PAM), chemical conditioning with Fe[III]/CaO, bioleaching conditioning, and chemical acidification conditioning) and an aerobic incubation control in removing 46 target ARGs and intI1 from a municipal sewage sludge. The damage of sludge microbial cells and the change in the sludge bacterial community during the various sludge conditioning treatments were also characterized. The results suggested that the chemical conditioning with PAM and aerobic incubation treatment did not remove ARGs and intI1 from the sewage sludge. The chemical acidification reduced the absolute abundances of most ARGs and intI1, but increased their relative abundances. However, the chemical conditioning with Fe[III]/CaO and bioleaching conditioning reduced both the absolute and relative abundances of most ARGs and removed a majority of extracellular ARGs in the sludge. During sludge conditioning treatments, the sludge microbial cells were severely damaged to decrease the total bacterial biomass in sludge, and accordingly the bacterial hosts carrying ARGs and intI were effectively damaged to reduce the absolute abundances of most ARGs and intI1. In addition, the sludge bacterial community in conditioned sludge determined the relative abundances of residual ARGs. Our findings suggest that sludge conditioning can be an important sludge treatment process in attenuating antibiotic resistance in sewage sludge, and bioleaching and chemical conditioning with Fe[III]/CaO can be employed as effective conditioning ways to reduce ARGs in sewage sludge, potentially limiting their release to the environment.
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Affiliation(s)
- Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Lu
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dianzhan Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
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457
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Lag Phase Is a Dynamic, Organized, Adaptive, and Evolvable Period That Prepares Bacteria for Cell Division. J Bacteriol 2019; 201:JB.00697-18. [PMID: 30642990 DOI: 10.1128/jb.00697-18] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Lag is a temporary period of nonreplication seen in bacteria that are introduced to new media. Despite latency being described by Müller in 1895, only recently have we gained insights into the cellular processes characterizing lag phase. This review covers literature to date on the transcriptomic, proteomic, metabolomic, physiological, biochemical, and evolutionary features of prokaryotic lag. Though lag is commonly described as a preparative phase that allows bacteria to harvest nutrients and adapt to new environments, the implications of recent studies indicate that a refinement of this view is well deserved. As shown, lag is a dynamic, organized, adaptive, and evolvable process that protects bacteria from threats, promotes reproductive fitness, and is broadly relevant to the study of bacterial evolution, host-pathogen interactions, antibiotic tolerance, environmental biology, molecular microbiology, and food safety.
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458
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Barrett TC, Mok WWK, Murawski AM, Brynildsen MP. Enhanced antibiotic resistance development from fluoroquinolone persisters after a single exposure to antibiotic. Nat Commun 2019; 10:1177. [PMID: 30862812 PMCID: PMC6414640 DOI: 10.1038/s41467-019-09058-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial persisters are able to tolerate high levels of antibiotics and give rise to new populations. Persister tolerance is generally attributed to minimally active cellular processes that prevent antibiotic-induced damage, which has led to the supposition that persister offspring give rise to antibiotic-resistant mutants at comparable rates to normal cells. Using time-lapse microscopy to monitor Escherichia coli populations following ofloxacin treatment, we find that persisters filament extensively and induce impressive SOS responses before returning to a normal appearance. Further, populations derived from fluoroquinolone persisters contain significantly greater quantities of antibiotic-resistant mutants than those from untreated controls. We confirm that resistance is heritable and that the enhancement requires RecA, SOS induction, an opportunity to recover from treatment, and the involvement of error-prone DNA polymerase V (UmuDC). These findings show that fluoroquinolones damage DNA in persisters and that the ensuing SOS response accelerates the development of antibiotic resistance from these survivors. Fluoroquinolone (FQ)-induced DNA damage in persisters could promote antibiotic resistance. Here, using time-lapse microscopy and genetic analyses, the authors show that after a single round of FQ treatment, SOS response in persisters accelerates the development of resistance to unrelated antibiotics.
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Affiliation(s)
- Theresa C Barrett
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Wendy W K Mok
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, 06032-3305, USA
| | - Allison M Murawski
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
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459
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Bioprospecting of Native Efflux Pumps To Enhance Furfural Tolerance in Ethanologenic Escherichia coli. Appl Environ Microbiol 2019; 85:AEM.02985-18. [PMID: 30635383 DOI: 10.1128/aem.02985-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/04/2019] [Indexed: 02/03/2023] Open
Abstract
Efficient microbial conversion of lignocellulose into valuable products is often hindered by the presence of furfural, a dehydration product of pentoses in hemicellulose sugar syrups derived from woody biomass. For a cost-effective lignocellulose microbial conversion, robust biocatalysts are needed that can tolerate toxic inhibitors while maintaining optimal metabolic activities. A comprehensive plasmid-based library encoding native multidrug resistance (MDR) efflux pumps, porins, and select exporters from Escherichia coli was screened for furfural tolerance in an ethanologenic E. coli strain. Small multidrug resistance (SMR) pumps, such as SugE and MdtJI, as well as a lactate/glycolate:H+ symporter, LldP, conferred furfural tolerance in liquid culture tests. Expression of the SMR pump potentially increased furfural efflux and cellular viability upon furfural assault, suggesting novel activities for SMR pumps as furfural efflux proteins. Furthermore, induced expression of mdtJI enhanced ethanol fermentative production of LY180 in the presence of furfural or 5-hydroxymethylfurfural, further demonstrating the applications of SMR pumps. This work describes an effective approach to identify useful efflux systems with desired activities for nonnative toxic chemicals and provides a platform to further enhance furfural efflux by protein engineering and mutagenesis.IMPORTANCE Lignocellulosic biomass, especially agricultural residues, represents an important potential feedstock for microbial production of renewable fuels and chemicals. During the deconstruction of hemicellulose by thermochemical processes, side products that inhibit cell growth and production, such as furan aldehydes, are generated, limiting cost-effective lignocellulose conversion. Here, we developed a new approach to increase cellular tolerance by expressing multidrug resistance (MDR) pumps with putative efflux activities for furan aldehydes. The developed plasmid library and screening methods may facilitate new discoveries of MDR pumps for diverse toxic chemicals important for microbial conversion.
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460
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Khitun A, Ness TJ, Slavoff SA. Small open reading frames and cellular stress responses. Mol Omics 2019; 15:108-116. [PMID: 30810554 DOI: 10.1039/c8mo00283e] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small open reading frames (smORFs) encoding polypeptides of less than 100 amino acids in eukaryotes (50 amino acids in prokaryotes) were historically excluded from genome annotation. However, recent advances in genomics, ribosome footprinting, and proteomics have revealed thousands of translated smORFs in genomes spanning evolutionary space. These smORFs can encode functional polypeptides, or act as cis-translational regulators. Herein we review evidence that some smORF-encoded polypeptides (SEPs) participate in stress responses in both prokaryotes and eukaryotes, and that some upstream ORFs (uORFs) regulate stress-responsive translation of downstream cistrons in eukaryotic cells. These studies provide insight into a regulated subclass of smORFs and suggest that at least some SEPs may participate in maintenance of cellular homeostasis under stress.
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Affiliation(s)
- Alexandra Khitun
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Travis J Ness
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Sarah A Slavoff
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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461
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Wood TK, Song S, Yamasaki R. Ribosome dependence of persister cell formation and resuscitation. J Microbiol 2019; 57:213-219. [PMID: 30806978 DOI: 10.1007/s12275-019-8629-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/13/2018] [Accepted: 12/26/2018] [Indexed: 01/05/2023]
Abstract
Since most bacterial cells are starving, they must enter a resting stage. Persister is the term used for metabolically-dormant cells that are not spores, and these cells arise from stress such as that from antibiotics as well as that from starvation. Because of their lack of metabolism, persister cells survive exposure to multiple stresses without undergoing genetic change; i.e., they have no inherited phenotype and behave as wild-type cells once the stress is removed and nutrients are presented. In contrast, mutations allow resistant bacteria to grow in the presence of antibiotics and slow growth allows tolerant cells to withstand higher concentrations of antibiotics; hence, there are three closely-related phenotypes: persistent, resistant, and tolerant. In addition, since dormancy is so prevalent, persister cells must have a means for resuscitating (since so many cells should obtain this resting state). In this review, we focus on what is known about the formation and resuscitation of persister cells.
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Affiliation(s)
- Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400, USA.
| | - Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400, USA
| | - Ryota Yamasaki
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802-4400, USA
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462
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Brunati C, Thomsen TT, Gaspari E, Maffioli S, Sosio M, Jabes D, Løbner-Olesen A, Donadio S. Expanding the potential of NAI-107 for treating serious ESKAPE pathogens: synergistic combinations against Gram-negatives and bactericidal activity against non-dividing cells. J Antimicrob Chemother 2019; 73:414-424. [PMID: 29092042 PMCID: PMC5890740 DOI: 10.1093/jac/dkx395] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/27/2017] [Indexed: 11/12/2022] Open
Abstract
Objectives To characterize NAI-107 and related lantibiotics for their in vitro activity against Gram-negative pathogens, alone or in combination with polymyxin, and against non-dividing cells or biofilms of Staphylococcus aureus. NAI-107 was also evaluated for its propensity to select or induce self-resistance in Gram-positive bacteria. Methods We used MIC determinations and chequerboard experiments to establish the antibacterial activity of the examined compounds against target microorganisms. Time-kill assays were used to evaluate killing of exponential and stationary-phase cells. The effects on biofilms (growth inhibition and biofilm eradication) were evaluated using biofilm-coated pegs. The frequency of spontaneous resistant mutants was evaluated by either direct plating or by continuous sub-culturing at 0.5 × MIC levels, followed by population analysis profiles. Results The results showed that NAI-107 and its brominated variant are highly active against Neisseria gonorrhoeae and some other fastidious Gram-negative pathogens. Furthermore, all compounds strongly synergized with polymyxin against Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa, and showed bactericidal activity. Surprisingly, NAI-107 alone was bactericidal against non-dividing A. baumannii cells. Against S. aureus, NAI-107 and related lantibiotics showed strong bactericidal activity against dividing and non-dividing cells. Activity was also observed against S. aureus biofilms. As expected for a lipid II binder, no significant resistance to NAI-107 was observed by direct plating or serial passages. Conclusions Overall, the results of the current work, along with previously published results on the efficacy of NAI-107 in experimental models of infection, indicate that this lantibiotic represents a promising option in addressing the serious threat of antibiotic resistance.
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Affiliation(s)
- Cristina Brunati
- NAICONS Srl, Viale Ortles 22/4, 20139 Milano, Italy.,KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | - Thomas T Thomsen
- Department of Biology, University of Copenhagen, Ole Maaløe's Vej 5, 2200 Copenhagen, Denmark
| | | | | | - Margherita Sosio
- NAICONS Srl, Viale Ortles 22/4, 20139 Milano, Italy.,KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | | | - Anders Løbner-Olesen
- Department of Biology, University of Copenhagen, Ole Maaløe's Vej 5, 2200 Copenhagen, Denmark
| | - Stefano Donadio
- NAICONS Srl, Viale Ortles 22/4, 20139 Milano, Italy.,KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
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463
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Zhang J, Wang J, Feng T, Du R, Tian X, Wang Y, Zhang XH. Heterologous Expression of the Marine-Derived Quorum Quenching Enzyme MomL Can Expand the Antibacterial Spectrum of Bacillus brevis. Mar Drugs 2019; 17:E128. [PMID: 30795579 PMCID: PMC6409708 DOI: 10.3390/md17020128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 12/28/2022] Open
Abstract
Quorum sensing (QS) is closely associated with the production of multiple virulence factors in bacterial pathogens. N-acyl homoserine lactones (AHLs) are important QS signal molecules that modulate the virulence of gram-negative pathogenic bacteria. Enzymatic degradation of AHLs to interrupt QS, termed quorum quenching (QQ), has been considered a novel strategy for reduction of pathogenicity and prevention of bacterial disease. However, the low expression levels of QQ proteins in the original host bacteria has affected the applications of these proteins. Previously, we identified a novel marine QQ enzyme, named MomL, with high activity and promising biocontrol function. In this study, we linked the target fragment momL to pNCMO2, which provided a basis for the first heterologous expression of MomL in the antifungal and anti-gram-positive-bacteria biocontrol strain Bacillus brevis, and obtaining the recombinant strain named BbMomL. The QQ activity of BbMomL was confirmed using a series of bioassays. BbMomL could not only degrade the exogenous signal molecule C6-HSL, but also the AHL signal molecules produced by the gram-negative pathogens Pectobacterium carotovorum subsp. carotovorum (Pcc) and Pseudomonas aeruginosa PAO1. In addition, BbMomL significantly reduced the secretion of pathogenic factors and the pathogenicity of Pcc and P. aeruginosa PAO1. We tested the biocontrol function of BbMomL for prevention of plant diseases in vitro. The result indicates that BbMomL has a broad antibacterial spectrum. Compared with wild-type B. brevis, BbMomL not only inhibited fungi and gram-positive bacterial pathogens but also considerably inhibited gram-negative bacterial pathogens. Moreover, the Bacillus brevis expression system has good application prospects and is an ideal host for expression and secretion of foreign proteins.
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Affiliation(s)
- Jingjing Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jiayi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Tao Feng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Rui Du
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xiaorong Tian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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464
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Mandal S, Njikan S, Kumar A, Early JV, Parish T. The relevance of persisters in tuberculosis drug discovery. MICROBIOLOGY-SGM 2019; 165:492-499. [PMID: 30775961 DOI: 10.1099/mic.0.000760] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacterial persisters are a subpopulation of cells that exhibit phenotypic resistance during exposure to a lethal dose of antibiotics. They are difficult to target and thought to contribute to the long treatment duration required for tuberculosis. Understanding the molecular and cellular biology of persisters is critical to finding new tuberculosis drugs that shorten treatment. This review focuses on mycobacterial persisters and describes the challenges they pose in tuberculosis therapy, their characteristics and formation, how persistence leads to resistance, and the current approaches being used to target persisters within mycobacterial drug discovery.
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Affiliation(s)
- Soma Mandal
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Samuel Njikan
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Anuradha Kumar
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Julie V Early
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave. E, Suite 400, Seattle, WA 98102, USA
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465
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Sulaiman JE, Lam H. Application of proteomics in studying bacterial persistence. Expert Rev Proteomics 2019; 16:227-239. [DOI: 10.1080/14789450.2019.1575207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Kowloon, Hong Kong
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466
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Tandon H, Sharma A, Sandhya S, Srinivasan N, Singh R. Mycobacterium tuberculosis Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. Sci Rep 2019; 9:1163. [PMID: 30718534 PMCID: PMC6362051 DOI: 10.1038/s41598-018-37473-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitously existing addiction modules with essential roles in bacterial persistence and virulence. The genome of Mycobacterium tuberculosis encodes approximately 79 TA systems. Through computational and experimental investigations, we report for the first time that Rv0366c-Rv0367c is a non-canonical PezAT-like toxin-antitoxin system in M. tuberculosis. Homology searches with known PezT homologues revealed that residues implicated in nucleotide, antitoxin-binding and catalysis are conserved in Rv0366c. Unlike canonical PezA antitoxins, the N-terminal of Rv0367c is predicted to adopt the ribbon-helix-helix (RHH) motif for deoxyribonucleic acid (DNA) recognition. Further, the modelled complex predicts that the interactions between PezT and PezA involve conserved residues. We performed a large-scale search in sequences encoded in 101 mycobacterial and 4500 prokaryotic genomes and show that such an atypical PezAT organization is conserved in 20 other mycobacterial organisms and in families of class Actinobacteria. We also demonstrate that overexpression of Rv0366c induces bacteriostasis and this growth defect could be restored upon co-expression of cognate antitoxin, Rv0367c. Further, we also observed that inducible expression of Rv0366c in Mycobacterium smegmatis results in decreased cell-length and enhanced tolerance against a front-line tuberculosis (TB) drug, ethambutol. Taken together, we have identified and functionally characterized a novel non-canonical TA system from M. tuberculosis.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Arun Sharma
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO Box #4, Faridabad, Haryana, 121001, India
| | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | | | - Ramandeep Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO Box #4, Faridabad, Haryana, 121001, India.
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467
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Moriarty TF, Harris LG, Mooney RA, Wenke JC, Riool M, Zaat SAJ, Moter A, Schaer TP, Khanna N, Kuehl R, Alt V, Montali A, Liu J, Zeiter S, Busscher HJ, Grainger DW, Richards RG. Recommendations for design and conduct of preclinical in vivo studies of orthopedic device-related infection. J Orthop Res 2019; 37:271-287. [PMID: 30667561 DOI: 10.1002/jor.24230] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/06/2018] [Indexed: 02/04/2023]
Abstract
Orthopedic device-related infection (ODRI), including both fracture-related infection (FRI) and periprosthetic joint infection (PJI), remain among the most challenging complications in orthopedic and musculoskeletal trauma surgery. ODRI has been convincingly shown to delay healing, worsen functional outcome and incur significant socio-economic costs. To address this clinical problem, ever more sophisticated technologies targeting the prevention and/or treatment of ODRI are being developed and tested in vitro and in vivo. Among the most commonly described innovations are antimicrobial-coated orthopedic devices, antimicrobial-loaded bone cements and void fillers, and dual osteo-inductive/antimicrobial biomaterials. Unfortunately, translation of these technologies to the clinic has been limited, at least partially due to the challenging and still evolving regulatory environment for antimicrobial drug-device combination products, and a lack of clarity in the burden of proof required in preclinical studies. Preclinical in vivo testing (i.e. animal studies) represents a critical phase of the multidisciplinary effort to design, produce and reliably test both safety and efficacy of any new antimicrobial device. Nonetheless, current in vivo testing protocols, procedures, models, and assessments are highly disparate, irregularly conducted and reported, and without standardization and validation. The purpose of the present opinion piece is to discuss best practices in preclinical in vivo testing of antimicrobial interventions targeting ODRI. By sharing these experience-driven views, we aim to aid others in conducting such studies both for fundamental biomedical research, but also for regulatory and clinical evaluation. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:271-287, 2019.
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Affiliation(s)
- T Fintan Moriarty
- AO Research Institute Davos, Clavadelerstrasse 8, 7270, Davos Platz, Switzerland
| | - Llinos G Harris
- Microbiology and Infectious Diseases, Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | - Robert A Mooney
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York
| | - Joseph C Wenke
- Extremity Trauma and Regenerative Medicine Task Area, US Army Institute of Surgical Research, JBSA-Fort Sam Houston, Texas
| | - Martijn Riool
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam, The Netherlands
| | - Sebastian A J Zaat
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam, The Netherlands
| | - Annette Moter
- Institute of Microbiology and Infection Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas P Schaer
- Department of Clinical Studies New Bolton Center, University of Pennsylvania, Kennett Square, Pennsylvania
| | - Nina Khanna
- Infection Biology Laboratory, Department of Biomedicine, University Hospital of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Basel, Basel, Switzerland
| | - Richard Kuehl
- Infection Biology Laboratory, Department of Biomedicine, University Hospital of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Basel, Basel, Switzerland
| | - Volker Alt
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Giessen-Marburg, GmbH, Campus Giessen, Germany
| | | | - Jianfeng Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, P.R. China
| | - Stephan Zeiter
- AO Research Institute Davos, Clavadelerstrasse 8, 7270, Davos Platz, Switzerland
| | - Henk J Busscher
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - David W Grainger
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA.,Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - R Geoff Richards
- AO Research Institute Davos, Clavadelerstrasse 8, 7270, Davos Platz, Switzerland
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468
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Gene Expression Changes with Minor Effects on the Population Average Have Major Effects on the Occurrence of Cells with Extreme Protein Concentrations. mSphere 2019; 4:4/1/e00575-18. [PMID: 30700510 PMCID: PMC6354807 DOI: 10.1128/msphere.00575-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cell-to-cell heterogeneity in a bacterial population provides a rich response to environmental changes and robust survival of an isogenic population. Especially, the rare, extreme phenotypes can be important for survival under transient lethal conditions. The cell-to-cell heterogeneity in a bacterial population provides a rich response to environmental changes and robust survival of an isogenic population. Especially, the rare, extreme phenotypes can be important for survival under transient lethal conditions. We analyze the probability of having an extremely high or low protein level in a stochastic model of gene expression. The fraction of rare state cells defined as the cells in the tails of distributions is found to be highly sensitive to small changes of the mean protein level. The result highlights the importance of relatively weak changes to the mean for the occurrence of rare phenotypes.
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469
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Windels EM, Michiels JE, Fauvart M, Wenseleers T, Van den Bergh B, Michiels J. Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates. ISME JOURNAL 2019; 13:1239-1251. [PMID: 30647458 DOI: 10.1038/s41396-019-0344-9] [Citation(s) in RCA: 230] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/09/2018] [Accepted: 12/23/2018] [Indexed: 02/08/2023]
Abstract
Persisters are transiently antibiotic-tolerant cells that complicate the treatment of bacterial infections. Both theory and experiments have suggested that persisters facilitate genetic resistance by constituting an evolutionary reservoir of viable cells. Here, we provide evidence for a strong positive correlation between persistence and the likelihood to become genetically resistant in natural and lab strains of E. coli. This correlation can be partly attributed to the increased availability of viable cells associated with persistence. However, our data additionally show that persistence is pleiotropically linked with mutation rates. Our theoretical model further demonstrates that increased survival and mutation rates jointly affect the likelihood of evolving clinical resistance. Overall, these results suggest that the battle against antibiotic resistance will benefit from incorporating anti-persister therapies.
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Affiliation(s)
- Etthel Martha Windels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Joran Elie Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,imec, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Douglas lab, Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.
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470
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Nitrogen Starvation Induces Persister Cell Formation in Escherichia coli. J Bacteriol 2019; 201:JB.00622-18. [PMID: 30420451 DOI: 10.1128/jb.00622-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/02/2018] [Indexed: 01/23/2023] Open
Abstract
To cope with fluctuations in their environment, bacteria have evolved multiple adaptive stress responses. One such response is the nitrogen regulation stress response, which allows bacteria, such as Escherichia coli, to cope with and overcome conditions of nitrogen limitation. This response is directed by the two-component system NtrBC, where NtrC acts as the major transcriptional regulator to activate the expression of genes to mount the response. Recently, my colleagues and I showed that NtrC directly regulates the expression of the relA gene, the major (p)ppGpp synthetase in E. coli, coupling the nitrogen regulation stress and stringent responses. As elevated levels of (p)ppGpp have been implicated in the formation of persister cells, here, I investigated whether nitrogen starvation promotes their formation and whether the NtrC-RelA regulatory cascade plays a role. The results reveal that nitrogen-starved E. coli synthesizes (p)ppGpp and forms a higher percentage of persister cells than nonstarved cells and that both NtrC and RelA are important for these processes. This study provides novel insights into how the formation of persisters can be promoted in response to a nutritional stress.IMPORTANCE Bacteria often reside in environments where nutrient availability is scarce; therefore, they have evolved adaptive responses to rapidly cope with conditions of feast and famine. Understanding the mechanisms that underpin the regulation of how bacteria cope with this stress is a fundamentally important question in the wider context of understanding the biology of the bacterial cell and bacterial pathogenesis. Two major adaptive mechanisms to cope with starvation are the nitrogen regulation (ntr) stress and stringent responses. Here, I describe how these bacterial stress responses are coordinated under conditions of nitrogen starvation to promote the formation of antibiotic-tolerant persister cells by elevating levels of the secondary messenger (p)ppGpp.
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471
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Chen X, Li G, Liao X, Fang J, Li B, Yu S, Sun M, Wu J, Zhang L, Hu Y, Jiao J, Liu T, Xu L, Chen X, Liu M, Li H, Hu F, Sun K. A switch in the poly(dC)/RmlB complex regulates bacterial persister formation. Nat Commun 2019; 10:27. [PMID: 30604752 PMCID: PMC6318315 DOI: 10.1038/s41467-018-07861-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/27/2018] [Indexed: 01/16/2023] Open
Abstract
Bacterial persisters are phenotypic variants that tolerate exposure to lethal antibiotics. These dormant cells are responsible for chronic and recurrent infections. Multiple mechanisms have been linked to persister formation. Here, we report that a complex, consisting of an extracellular poly(dC) and its membrane-associated binding protein RmlB, appears to be associated with persistence of the opportunistic pathogen Pseudomonas aeruginosa. Environmental stimuli triggers a switch in the complex physiological state (from poly(dC)/RmlB to P-poly(dC)/RmlB or RmlB). In response to the switch, bacteria decrease proton motive force and intracellular ATP levels, forming dormant cells. This alteration in complex status is linked to a (p)ppGpp-controlled signaling pathway that includes inorganic polyphosphate, Lon protease, exonuclease VII (XseA/XseB), and the type III secretion system. The persistence might be also an adaptive response to the lethal action of the dTDP-l-rhamnose pathway shutdown, which occurs due to switching of poly(dC)/RmlB. The mechanisms underlying bacterial persisters formation remain poorly understood. Here, Chen et al. identify a complex formed by extracellular poly(dC) and the binding protein RmlB that controls Pseudomonas aeruginosa persister formation in response to environmental stimuli.
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Affiliation(s)
- Xu Chen
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Gen Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xuewei Liao
- Center for Analysis and Testing, Nanjing Normal University, Nanjing, China
| | - Jie Fang
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bo Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shanshan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Lihao Zhang
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yi Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiaguo Jiao
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ting Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Li Xu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyun Chen
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China.,Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, China
| | - Huixin Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kouhong Sun
- Zoonbio Biotechnology Co., Ltd, Nanjing, China
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472
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Yashiro Y, Yamashita S, Tomita K. Crystal Structure of the Enterohemorrhagic Escherichia coli AtaT-AtaR Toxin-Antitoxin Complex. Structure 2019; 27:476-484.e3. [PMID: 30612860 DOI: 10.1016/j.str.2018.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/24/2018] [Accepted: 11/06/2018] [Indexed: 11/29/2022]
Abstract
AtaT-AtaR is an enterohemorrhagic Escherichia coli toxin-antitoxin system that modulates cellular growth under stress conditions. AtaT and AtaR act as a toxin and its repressor, respectively. AtaT is a member of the GNAT family, and the dimeric AtaT acetylates the α-amino group of the aminoacyl moiety of methionyl initiator tRNAfMet, thereby inhibiting translation initiation. The crystallographic analysis of the AtaT-AtaR complex revealed that the AtaT-AtaR proteins form a heterohexameric [AtaT-(AtaR4)-AtaT] complex, where two V-shaped AtaR dimers bridge two AtaT molecules. The N-terminal region of AtaR is required for its dimerization, and the C-terminal region of AtaR interacts with AtaT. The two AtaT molecules are spatially separated in the AtaT-AtaR complex. AtaT alone forms a dimer in solution, which is enzymatically active. The present structure, in which AtaR prevents AtaT from forming an active dimer, reveals the molecular basis of the AtaT toxicity repression by the antitoxin AtaR.
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Affiliation(s)
- Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Seisuke Yamashita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
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473
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Xu ML, Guan LY, Li SK, Chen L, Chen Z. Stable gold graphitic nanocapsule doped hydrogels for efficient photothermal antibacterial applications. Chem Commun (Camb) 2019; 55:5359-5362. [DOI: 10.1039/c9cc01933b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have fabricated gold nanorod graphitic nanocapsule (AuNR@G) doped poly(vinyl alcohol) (PVA)/chitosan (CS) hydrogels, which possessed highly efficient and stable photothermal antibacterial properties under the irradiation of a near-infrared laser.
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Affiliation(s)
- Ming-Lu Xu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University
- Changsha
- China
| | - Lu-Yao Guan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University
- Changsha
- China
| | - Sheng-Kai Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University
- Changsha
- China
| | - Long Chen
- Faculty of Science and Technology, University of Macau
- Macau
- China
| | - Zhuo Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University
- Changsha
- China
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474
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Shahrour H, Ferrer-Espada R, Dandache I, Bárcena-Varela S, Sánchez-Gómez S, Chokr A, Martinez-de-Tejada G. AMPs as Anti-biofilm Agents for Human Therapy and Prophylaxis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:257-279. [PMID: 30980362 DOI: 10.1007/978-981-13-3588-4_14] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microbial cells show a strong natural tendency to adhere to surfaces and to colonize them by forming complex communities called biofilms. In this growth mode, biofilm-forming cells encase themselves inside a dense matrix which efficiently protects them against antimicrobial agents and effectors of the immune system. Moreover, at the physiological level, biofilms contain a very heterogeneous cell population including metabolically inactive organisms and persisters, which are highly tolerant to antibiotics. The majority of human infectious diseases are caused by biofilm-forming microorganisms which are responsible for pathologies such as cystic fibrosis, infective endocarditis, pneumonia, wound infections, dental caries, infections of indwelling devices, etc. AMPs are well suited to combat biofilms because of their potent bactericidal activity of broad spectrum (including resting cells and persisters) and their ability to first penetrate and then to disorganize these structures. In addition, AMPs frequently synergize with antimicrobial compounds and were recently reported to repress the molecular pathways leading to biofilm formation. Finally, there is a very active research to develop AMP-containing coatings that can prevent biofilm formation by killing microbial cells on contact or by locally releasing their active principle. In this chapter we will describe these strategies and discuss the perspectives of the use of AMPs as anti-biofilm agents for human therapy and prophylaxis.
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Affiliation(s)
- Hawraa Shahrour
- Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain.,Laboratory of Microbiology, Department of Life & Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat campus, Beirut, Lebanon.,Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon
| | - Raquel Ferrer-Espada
- Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain.,Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Israa Dandache
- Laboratory of Microbiology, Department of Life & Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat campus, Beirut, Lebanon.,Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon
| | | | | | - Ali Chokr
- Laboratory of Microbiology, Department of Life & Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat campus, Beirut, Lebanon.,Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon
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475
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Fontaine BM, Duggal Y, Weinert EE. Exploring the Links between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial Virulence. ACS Infect Dis 2018; 4:1645-1655. [PMID: 30381948 DOI: 10.1021/acsinfecdis.8b00255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The survival of all organisms depends on implementation of appropriate phenotypic responses upon perception of relevant environmental stimuli. Sensory inputs are propagated via interconnected biochemical and/or electrical cascades mediated by diverse signaling molecules, including gases, metal cations, lipids, peptides, and nucleotides. These networks often comprise second messenger signaling systems in which a ligand (the primary messenger) binds to an extracellular receptor, thereby altering the intracellular concentration of a second messenger molecule which ultimately modulates gene expression through interaction with various effectors. The identification of intersections of these signaling pathways, such as nucleotide second messengers and quorum sensing, provides new insights into the mechanisms by which bacteria use multiple inputs to regulate cellular metabolism and phenotypes. Further investigations of the overlap between bacterial signaling pathways may yield new targets and methods to control bacterial behavior, such as biofilm formation and virulence.
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Affiliation(s)
- Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Yashasvika Duggal
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
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476
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Zou W, Chen Y, Zhang X, Li J, Sun L, Gui Z, Du B, Chen S. Cytocompatible chitosan based multi-network hydrogels with antimicrobial, cell anti-adhesive and mechanical properties. Carbohydr Polym 2018; 202:246-257. [DOI: 10.1016/j.carbpol.2018.08.124] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 01/04/2023]
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477
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Abstract
P. aeruginosa is a soil dwelling bacterium and a plant pathogen, and it also causes life-threatening infections in humans. Thus, P. aeruginosa thrives in diverse environments and over a broad range of temperatures. Some P. aeruginosa strains rely on the CRISPR-Cas adaptive immune system as a phage defense mechanism. Our discovery that low temperatures increase CRISPR adaptation suggests that the rarely occurring but crucial naive adaptation events may take place predominantly under conditions of slow growth, e.g., during the bacterium’s soil dwelling existence and during slow growth in biofilms. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) systems are adaptive defense systems that protect bacteria and archaea from invading genetic elements. In Pseudomonas aeruginosa, quorum sensing (QS) induces the CRISPR-Cas defense system at high cell density when the risk of bacteriophage infection is high. Here, we show that another cue, temperature, modulates P. aeruginosa CRISPR-Cas. Increased CRISPR adaptation occurs at environmental (i.e., low) temperatures compared to that at body (i.e., high) temperature. This increase is a consequence of the accumulation of CRISPR-Cas complexes, coupled with reduced P. aeruginosa growth rate at the lower temperature, the latter of which provides additional time prior to cell division for CRISPR-Cas to patrol the cell and successfully eliminate and/or acquire immunity to foreign DNA. Analyses of a QS mutant and synthetic QS compounds show that the QS and temperature cues act synergistically. The diversity and level of phage encountered by P. aeruginosa in the environment exceed that in the human body, presumably warranting increased reliance on CRISPR-Cas at environmental temperatures.
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478
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Genotoxic, Metabolic, and Oxidative Stresses Regulate the RNA Repair Operon of Salmonella enterica Serovar Typhimurium. J Bacteriol 2018; 200:JB.00476-18. [PMID: 30201777 DOI: 10.1128/jb.00476-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
The σ54 regulon in Salmonella enterica serovar Typhimurium includes a predicted RNA repair operon encoding homologs of the metazoan Ro60 protein (Rsr), Y RNAs (YrlBA), RNA ligase (RtcB), and RNA 3'-phosphate cyclase (RtcA). Transcription from σ54-dependent promoters requires that a cognate bacterial enhancer binding protein (bEBP) be activated by a specific environmental or cellular signal; the cognate bEBP for the σ54-dependent promoter of the rsr-yrlBA-rtcBA operon is RtcR. To identify conditions that generate the signal for RtcR activation in S Typhimurium, transcription of the RNA repair operon was assayed under multiple stress conditions that result in nucleic acid damage. RtcR-dependent transcription was highly induced by the nucleic acid cross-linking agents mitomycin C (MMC) and cisplatin, and this activation was dependent on RecA. Deletion of rtcR or rtcB resulted in decreased cell viability relative to that of the wild type following treatment with MMC. Oxidative stress from peroxide exposure also induced RtcR-dependent transcription of the operon. Nitrogen limitation resulted in RtcR-independent increased expression of the operon; the effect of nitrogen limitation required NtrC. The adjacent toxin-antitoxin module, dinJ-yafQ, was cotranscribed with the RNA repair operon but was not required for RtcR activation, although YafQ endoribonuclease activated RtcR-dependent transcription. Stress conditions shown to induce expression the RNA repair operon of Escherichia coli (rtcBA) did not stimulate expression of the S Typhimurium RNA repair operon. Similarly, MMC did not induce expression of the E. coli rtcBA operon, although when expressed in S Typhimurium, E. coli RtcR responds effectively to the unknown signal(s) generated there by MMC exposure.IMPORTANCE Homologs of the metazoan RNA repair enzymes RtcB and RtcA occur widely in eubacteria, suggesting a selective advantage. Although the enzymatic activities of the eubacterial RtcB and RtcA have been well characterized, the physiological roles remain largely unresolved. Here we report stress responses that activate expression of the σ54-dependent RNA repair operon (rsr-yrlBA-rtcBA) of S Typhimurium and demonstrate that expression of the operon impacts cell survival under MMC-induced stress. Characterization of the requirements for activation of this tightly regulated operon provides clues to the possible functions of operon components in vivo, enhancing our understanding of how this human pathogen copes with environmental stressors.
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479
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Morgan J, Smith M, Mc Auley MT, Enrique Salcedo-Sora J. Disrupting folate metabolism reduces the capacity of bacteria in exponential growth to develop persisters to antibiotics. Microbiology (Reading) 2018; 164:1432-1445. [DOI: 10.1099/mic.0.000722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jasmine Morgan
- 1Department of Biology, Edge Hill University, St. Helens Road, Ormskirk, Lancashire, L39 4QP, UK
| | - Matthew Smith
- 2School of Health Sciences, Liverpool Hope University, Hope Park, L16 9JD, Liverpool, UK
| | - Mark T. Mc Auley
- 3Chemical Engineering Department, University of Chester, Thronton Science Park, CH2 4NU, Chester, UK
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480
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Jin M, Lu J, Chen Z, Nguyen SH, Mao L, Li J, Yuan Z, Guo J. Antidepressant fluoxetine induces multiple antibiotics resistance in Escherichia coli via ROS-mediated mutagenesis. ENVIRONMENT INTERNATIONAL 2018; 120:421-430. [PMID: 30125859 DOI: 10.1016/j.envint.2018.07.046] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/28/2018] [Accepted: 07/29/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Antibiotic resistance poses a great threat to global public health. Overuse of antibiotics is generally considered as the major factor contributing to it. However, little is known about whether non-antibiotic drugs could play potential roles in the emergence of antibiotic resistance. OBJECTIVE We aimed to investigate whether antidepressant fluoxetine induces multiple antibiotic resistances and reveal underlying mechanisms. METHODOLOGY Escherichia coli K12 was exposed to different concentrations of fluoxetine (0, 0.5, 5, 50 and 100 mg/L) and the resistant strains were isolated by plating on antibiotic containing plates. Resistant strains were randomly selected to determine the increase of minimum inhibition concentration (MIC) of multiple antibiotics. Genome-wide DNA sequencing was performed on cells cultured in lysogeny broth (LB) without any fluoxetine or antibiotics exposure. RNA sequencing and proteomic profiling of isolated mutants grown in LB with 100 mg/L fluoxetine were analyzed to reveal the underlying mechanisms. RESULTS Exposure of Escherichia coli to fluoxetine at 5-100 mg/L after repeated subculture in LB for 30 days promoted its mutation frequency resulting in increased resistance against the antibiotics chloramphenicol, amoxicillin and tetracycline. This increase was up to 5.0 × 107 fold in a dose-time pattern. Isolated mutants with resistance to one of these antibiotics also exhibited multiple resistances against fluoroquinolone, aminoglycoside, β-lactams, tetracycline and chloramphenicol. According to global transcriptional and proteomic analyses, the AcrAB-TolC pump together with the YadG/YadH transporter, a Tsx channel and the MdtEF-TolC pump have been triggered to export the antibiotics to the exterior of the cell. Whole-genome DNA analysis of the mutants further revealed that ROS-mediated mutagenesis (e.g., deletion, insertion, and substitution) of DNA-binding transcriptional regulators (e.g., marR, rob, sdiA, cytR and crp) to up-regulate the expression of efflux pumps, may further enhance the antibiotic efflux. CONCLUSIONS Our findings for the first time demonstrated that the exposure to antidepressant fluoxetine induces multiple antibiotic resistance in E. coli via the ROS-mediated mutagenesis.
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Affiliation(s)
- Min Jin
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Ji Lu
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Zhaoyu Chen
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Son Hoang Nguyen
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Likai Mao
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Junwen Li
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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481
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Winter AJ, Williams C, Isupov MN, Crocker H, Gromova M, Marsh P, Wilkinson OJ, Dillingham MS, Harmer NJ, Titball RW, Crump MP. The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA. J Biol Chem 2018; 293:19429-19440. [PMID: 30337369 DOI: 10.1074/jbc.ra118.005173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/16/2018] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of hicAB in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.
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Affiliation(s)
- Ashley J Winter
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Christopher Williams
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Michail N Isupov
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Hannah Crocker
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Mariya Gromova
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Philip Marsh
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Oliver J Wilkinson
- the School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD United Kingdom
| | - Mark S Dillingham
- the School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD United Kingdom
| | - Nicholas J Harmer
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Richard W Titball
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom,
| | - Matthew P Crump
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom,
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482
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Slayden RA, Dawson CC, Cummings JE. Toxin-antitoxin systems and regulatory mechanisms in Mycobacterium tuberculosis. Pathog Dis 2018; 76:4969681. [PMID: 29788125 DOI: 10.1093/femspd/fty039] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/01/2018] [Indexed: 11/14/2022] Open
Abstract
There has been a significant reduction in annual tuberculosis incidence since the World Health Organization declared tuberculosis a global health threat. However, treatment of M. tuberculosis infections requires lengthy multidrug therapeutic regimens to achieve a durable cure. The development of new drugs that are active against resistant strains and phenotypically diverse organisms continues to present the greatest challenge in the future. Numerous phylogenomic analyses have revealed that the Mtb genome encodes a significantly expanded repertoire of toxin-antitoxin (TA) loci that makes up the Mtb TA system. A TA loci is a two-gene operon encoding a 'toxin' protein that inhibits bacterial growth and an interacting 'antitoxin' partner that neutralizes the inhibitory activity of the toxin. The presence of multiple chromosomally encoded TA loci in Mtb raises important questions in regard to expansion, regulation and function. Thus, the functional roles of TA loci in Mtb pathogenesis have received considerable attention over the last decade. The cumulative results indicate that they are involved in regulating adaptive responses to stresses associated with the host environment and drug treatment. Here we review the TA families encoded in Mtb, discuss the duplication of TA loci in Mtb, regulatory mechanism of TA loci, and phenotypic heterogeneity and pathogenesis.
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Affiliation(s)
- Richard A Slayden
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-0922, USA
| | - Clinton C Dawson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-0922, USA
| | - Jason E Cummings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-0922, USA
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483
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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484
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Kidd TJ, Canton R, Ekkelenkamp M, Johansen HK, Gilligan P, LiPuma JJ, Bell SC, Elborn JS, Flume PA, VanDevanter DR, Waters VJ. Defining antimicrobial resistance in cystic fibrosis. J Cyst Fibros 2018; 17:696-704. [PMID: 30266518 DOI: 10.1016/j.jcf.2018.08.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/21/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022]
Abstract
Antimicrobial resistance (AMR) can present significant challenges in the treatment of cystic fibrosis (CF) lung infections. In CF and other chronic diseases, AMR has a different profile and clinical consequences compared to acute infections and this requires different diagnostic and treatment approaches. This review defines AMR, explains how it occurs, describes the methods used to measure AMR as well as their limitations, and concludes with future directions for research and development in the area of AMR in CF.
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Affiliation(s)
- Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Peter Gilligan
- Clinical Microbiology-Immunology Laboratories, UNC HealthCare, Chapel Hill, NC, USA.
| | - John J LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital and QIMR Berghofer Medical Researhc Institute, Brisbane, Australia.
| | - J Stuart Elborn
- Imperial College and Royal Brompton Hospital, London, Queen's University Belfast, United Kingdom.
| | - Patrick A Flume
- Departments of Medicine and Pediatrics, Medical University of South Carolina, Charleston, SC, USA.
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, USA.
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485
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Sultan I, Rahman S, Jan AT, Siddiqui MT, Mondal AH, Haq QMR. Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective. Front Microbiol 2018; 9:2066. [PMID: 30298054 PMCID: PMC6160567 DOI: 10.3389/fmicb.2018.02066] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022] Open
Abstract
History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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486
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Adaptive Metabolism in Staphylococci: Survival and Persistence in Environmental and Clinical Settings. J Pathog 2018; 2018:1092632. [PMID: 30327733 PMCID: PMC6171259 DOI: 10.1155/2018/1092632] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/28/2018] [Accepted: 08/12/2018] [Indexed: 01/04/2023] Open
Abstract
Staphylococci are highly successful at colonizing a variety of dynamic environments, both nonpathogenic and those of clinical importance, and comprise the list of pathogens of global public health significance. Their remarkable survival and persistence can be attributed to a host of strategies, one of which is metabolic versatility—their ability to rapidly alter their metabolism in the presence of transient or long-term bacteriostatic and bactericidal conditions and facilitate cellular homeostasis. These attributes contribute to their widespread dissemination and challenging eradication particularly from clinical settings. The study of microbial behaviour at the metabolite level provides insight into mechanisms of survival and persistence under defined environmental and clinical conditions. This paper reviews the range of metabolic modulations that facilitate staphylococcal acclimatization and persistence in varying terrestrial and host conditions, and their public health ramifications in these settings.
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487
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Walling LR, Butler JS. Toxins targeting transfer RNAs: Translation inhibition by bacterial toxin-antitoxin systems. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1506. [PMID: 30296016 DOI: 10.1002/wrna.1506] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/07/2018] [Accepted: 08/13/2018] [Indexed: 01/09/2023]
Abstract
Prokaryotic toxin-antitoxin (TA) systems are composed of a protein toxin and its cognate antitoxin. These systems are abundant in bacteria and archaea and play an important role in growth regulation. During favorable growth conditions, the antitoxin neutralizes the toxin's activity. However, during conditions of stress or starvation, the antitoxin is inactivated, freeing the toxin to inhibit growth and resulting in dormancy. One mechanism of growth inhibition used by several TA systems results from targeting transfer RNAs (tRNAs), either through preventing aminoacylation, acetylating the primary amino group, or endonucleolytic cleavage. All of these mechanisms inhibit translation and result in growth arrest. Many of these toxins only act on a specific tRNA or a specific subset of tRNAs; however, more work is necessary to understand the specificity determinants of these toxins. For the toxins whose specificity has been characterized, both sequence and structural components of the tRNA appear important for recognition by the toxin. Questions also remain regarding the mechanisms used by dormant bacteria to resume growth after toxin induction. Rescue of stalled ribosomes by transfer-messenger RNAs, removal of acetylated amino groups from tRNAs, or ligation of cleaved RNA fragments have all been implicated as mechanisms for reversing toxin-induced dormancy. However, the mechanisms of resuming growth after induction of the majority of tRNA targeting toxins are not yet understood. This article is categorized under: Translation > Translation Regulation RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Lauren R Walling
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York
| | - J Scott Butler
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York.,Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.,Center for RNA Biology, University of Rochester Medical Center, Rochester, New York
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488
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Semanjski M, Germain E, Bratl K, Kiessling A, Gerdes K, Macek B. The kinases HipA and HipA7 phosphorylate different substrate pools in
Escherichia coli
to promote multidrug tolerance. Sci Signal 2018; 11. [DOI: 10.1126/scisignal.aat5750] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Differences in the targets of HipA and its variant HipA7 may explain why these kinases have different effects on bacterial persistence.
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Affiliation(s)
- Maja Semanjski
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Elsa Germain
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Ole Maaloesvej 5, DK-2200 Copenhagen, Denmark
| | - Katrin Bratl
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Andreas Kiessling
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Kenn Gerdes
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Ole Maaloesvej 5, DK-2200 Copenhagen, Denmark
| | - Boris Macek
- Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
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489
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Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat Microbiol 2018; 3:1115-1121. [PMID: 30177741 DOI: 10.1038/s41564-018-0237-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/01/2018] [Indexed: 01/22/2023]
Abstract
To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles1. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF)2-4. Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria5-8, and reveals a unique role for bS1 in translation regulation.
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490
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Akkaya Ö, Pérez-Pantoja DR, Calles B, Nikel PI, de Lorenzo V. The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates. mBio 2018; 9:e01512-18. [PMID: 30154264 PMCID: PMC6113623 DOI: 10.1128/mbio.01512-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the background metabolic network by an environmental bacterium may either foster or curtail the still-evolving pathway for 2,4-dinitrotoluene (2,4-DNT) catabolism. To this end, the genetically tractable strain Pseudomonas putida EM173 was implanted with the whole genetic complement necessary for the complete biodegradation of 2,4-DNT (recruited from the environmental isolate Burkholderia sp. R34). By using reporter technology and direct measurements of ROS formation, we observed that the engineered P. putida strain experienced oxidative stress when catabolizing the nitroaromatic substrate. However, the formation of ROS was neither translated into significant activation of the SOS response to DNA damage nor did it result in a mutagenic regime (unlike what has been observed in Burkholderia sp. R34, the original host of the pathway). To inspect whether the tolerance of P. putida to oxidative challenges could be traced to its characteristic reductive redox regime, we artificially altered the NAD(P)H pool by means of a water-forming, NADH-specific oxidase. Under the resulting low-NAD(P)H status, catabolism of 2,4-DNT triggered a conspicuous mutagenic and genomic diversification scenario. These results indicate that the background biochemical network of environmental bacteria ultimately determines the evolvability of metabolic pathways. Moreover, the data explain the efficacy of some bacteria (e.g., pseudomonads) to host and evolve with new catabolic routes.IMPORTANCE Some environmental bacteria evolve with new capacities for the aerobic biodegradation of chemical pollutants by adapting preexisting redox reactions to novel compounds. The process typically starts by cooption of enzymes from an available route to act on the chemical structure of the substrate-to-be. The critical bottleneck is generally the first biochemical step, and most of the selective pressure operates on reshaping the initial reaction. The interim uncoupling of the novel substrate to preexisting Rieske nonheme iron oxygenases usually results in formation of highly mutagenic ROS. In this work, we demonstrate that the background metabolic regime of the bacterium that hosts an evolving catabolic pathway (e.g., biodegradation of the xenobiotic 2,4-DNT) determines whether the cells either adopt a genetic diversification regime or a robust ROS-tolerant status. Furthermore, our results offer new perspectives to the rational design of efficient whole-cell biocatalysts, which are pursued in contemporary metabolic engineering.
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Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics, Faculty of Sciences, Gebze Technical University, Kocaeli, Turkey
| | - Danilo R Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago de Chile, Chile
| | - Belén Calles
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Madrid, Spain
| | - Pablo I Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Madrid, Spain
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491
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Horn N, Bhunia AK. Food-Associated Stress Primes Foodborne Pathogens for the Gastrointestinal Phase of Infection. Front Microbiol 2018; 9:1962. [PMID: 30190712 PMCID: PMC6115488 DOI: 10.3389/fmicb.2018.01962] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022] Open
Abstract
The incidence of foodborne outbreaks and product recalls is on the rise. The ability of the pathogen to adapt and survive under stressful environments of food processing and the host gastrointestinal tract may contribute to increasing foodborne illnesses. In the host, multiple factors such as bacteriolytic enzymes, acidic pH, bile, resident microflora, antimicrobial peptides, and innate and adaptive immune responses are essential in eliminating pathogens. Likewise, food processing and preservation techniques are employed to eliminate or reduce human pathogens load in food. However, sub-lethal processing or preservation treatments may evoke bacterial coping mechanisms that alter gene expression, specifically and broadly, resulting in resistance to the bactericidal insults. Furthermore, environmentally cued changes in gene expression can lead to changes in bacterial adhesion, colonization, invasion, and toxin production that contribute to pathogen virulence. The shared microenvironment between the food preservation techniques and the host gastrointestinal tract drives microbes to adapt to the stressful environment, resulting in enhanced virulence and infectivity during a foodborne illness episode.
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Affiliation(s)
- Nathan Horn
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
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492
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Matilla MA. Shedding light into the mechanisms of formation and resuscitation of persistent bacterial cells. Environ Microbiol 2018; 20:3129-3131. [PMID: 30051562 DOI: 10.1111/1462-2920.14334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, 18008, Granada, Spain
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493
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Bar-Yaacov D, Pilpel Y, Dahan O. RNA editing in bacteria: occurrence, regulation and significance. RNA Biol 2018; 15:863-867. [PMID: 30071181 DOI: 10.1080/15476286.2018.1481698] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA harbors the blueprint for life. However, the instructions stored in the DNA could be altered at the RNA level before they are executed. One of these processes is RNA editing, which was shown to modify RNA sequences in many organisms. The most abundant modification is the deamination of adenosine (A) into inosine (I). In turn, inosine can be identified as a guanosine (G) by the ribosome and other cellular machineries such as reverse transcriptase. In multicellular organisms, enzymes from the ADAR (adenosine deaminase acting on RNA) family mediate RNA editing in mRNA, whereas enzymes from the ADAT family mediate A-to-I editing on tRNAs. In bacteria however, until recently, only one editing site was described, in tRNAArg, but never in mRNA. The tRNA site was shown to be modified by tadA (tRNA specific adenosine deaminase) which is believed to be the ancestral enzyme for the RNA editing family of enzymes. In our recent work, we have shown for the first time, editing on multiple sites in bacterial mRNAs and identified tadA as the enzyme responsible for this editing activity. Focusing on one of the identified targets - the self-killing toxin hokB, we found that editing is physiologically regulated and that it increases protein activity. Here we discuss possible modes of regulation on hokB editing, potential roles of RNA editing in bacteria, possible implications, and future research directions.
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Affiliation(s)
- Dan Bar-Yaacov
- a Morgridge Institute for Research , Madison , WI , USA.,b Department of Integrative Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - Yitzhak Pilpel
- c Department of Molecular Genetics , Weizmann Institute of Science , Rehovot , Israel
| | - Orna Dahan
- c Department of Molecular Genetics , Weizmann Institute of Science , Rehovot , Israel
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494
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Kochanowski K, Morinishi L, Altschuler S, Wu L. Drug persistence - from antibiotics to cancer therapies. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 10:1-8. [PMID: 30740553 PMCID: PMC6366840 DOI: 10.1016/j.coisb.2018.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Drug-insensitive tumor subpopulations remain a significant barrier to effective cancer treatment. Recent works suggest that within isogenic drug-sensitive cancer populations, subsets of cells can enter a 'persister' state allowing them to survive prolonged drug treatment. Such persisters are well-described in antibiotic-treated bacterial populations. In this review, we compare mechanisms of drug persistence in bacteria and cancer. Both bacterial and cancer persisters are associated with slow-growing phenotypes, are metabolically distinct from non-persisters, and depend on the activation of specific regulatory programs. Moreover, evidence suggests that bacterial and cancer persisters are an important reservoir for the emergence of drug-resistant mutants. The emerging parallels between persistence in bacteria and cancer can guide efforts to untangle mechanistic links between growth, metabolism, and cellular regulation, and reveal exploitable therapeutic vulnerabilities.
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Affiliation(s)
| | - Leanna Morinishi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Steven Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Lani Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
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495
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Kell DB, Pretorius E. No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. Biol Rev Camb Philos Soc 2018; 93:1518-1557. [PMID: 29575574 PMCID: PMC6055827 DOI: 10.1111/brv.12407] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 12/11/2022]
Abstract
Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.
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Affiliation(s)
- Douglas B. Kell
- School of ChemistryThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- The Manchester Institute of BiotechnologyThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
| | - Etheresia Pretorius
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
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496
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Mechanisms of Bacterial Tolerance and Persistence in the Gastrointestinal and Respiratory Environments. Clin Microbiol Rev 2018; 31:31/4/e00023-18. [PMID: 30068737 DOI: 10.1128/cmr.00023-18] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Pathogens that infect the gastrointestinal and respiratory tracts are subjected to intense pressure due to the environmental conditions of the surroundings. This pressure has led to the development of mechanisms of bacterial tolerance or persistence which enable microorganisms to survive in these locations. In this review, we analyze the general stress response (RpoS mediated), reactive oxygen species (ROS) tolerance, energy metabolism, drug efflux pumps, SOS response, quorum sensing (QS) bacterial communication, (p)ppGpp signaling, and toxin-antitoxin (TA) systems of pathogens, such as Escherichia coli, Salmonella spp., Vibrio spp., Helicobacter spp., Campylobacter jejuni, Enterococcus spp., Shigella spp., Yersinia spp., and Clostridium difficile, all of which inhabit the gastrointestinal tract. The following respiratory tract pathogens are also considered: Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Burkholderia cenocepacia, and Mycobacterium tuberculosis Knowledge of the molecular mechanisms regulating the bacterial tolerance and persistence phenotypes is essential in the fight against multiresistant pathogens, as it will enable the identification of new targets for developing innovative anti-infective treatments.
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497
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Antibiotic Scars Left on the Gut Microbiota from the Stringent Response. Trends Microbiol 2018; 26:735-737. [PMID: 30025977 DOI: 10.1016/j.tim.2018.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/05/2018] [Accepted: 06/20/2018] [Indexed: 02/08/2023]
Abstract
Current research is primarily focused on compositional shifts and alterations in the metabolic status of the gut microbiota to elucidate the damage caused by antibiotics. However, the impact of the stringent response, which is governed by a global gene regulatory system conserved in most gut bacteria, should not be overlooked.
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498
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Nyström L, Strömstedt AA, Schmidtchen A, Malmsten M. Peptide-Loaded Microgels as Antimicrobial and Anti-Inflammatory Surface Coatings. Biomacromolecules 2018; 19:3456-3466. [DOI: 10.1021/acs.biomac.8b00776] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-22184 Lund, Sweden
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499
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Miyaue S, Suzuki E, Komiyama Y, Kondo Y, Morikawa M, Maeda S. Bacterial Memory of Persisters: Bacterial Persister Cells Can Retain Their Phenotype for Days or Weeks After Withdrawal From Colony-Biofilm Culture. Front Microbiol 2018; 9:1396. [PMID: 29997606 PMCID: PMC6028600 DOI: 10.3389/fmicb.2018.01396] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/07/2018] [Indexed: 01/07/2023] Open
Abstract
Persister cells, or persisters, are a specific subpopulation of bacterial cells that have acquired temporary antibiotic-resistant phenotypes. In this study, we showed that Escherichia coli produces many more persister cells in colony-biofilm culture than in the usual liquid culture and that these persisters can be maintained in higher numbers than those from liquid culture for up to 4 weeks at 37°C in a fresh, nutrient-rich, antibiotic-containing medium, even after complete withdrawal from the colony-biofilm culture. This suggests the presence of a long-retention effect, or "memory effect", in the persister cell state of E. coli cells. We also discovered that such increases in persisters during colony-biofilm culture and their memory effects are common, to a greater or lesser degree, in other bacterial species. This is true not only for gram-negative bacteria (Acinetobacter and Salmonella) but also for gram-positive bacteria (Staphylococcus and Bacillus). This is the first report to suggest the presence of a common memory mechanism for the persister cell state, which is inscribed during colony-biofilm culture, in a wide variety of bacteria.
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Affiliation(s)
- Saki Miyaue
- Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
| | - Erika Suzuki
- Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
| | - Yoko Komiyama
- Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
| | - Yu Kondo
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
| | - Miki Morikawa
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
| | - Sumio Maeda
- Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan.,Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
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500
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Wu S, Yu PL, Wheeler D, Flint S. Transcriptomic study on persistence and survival of Listeria monocytogenes following lethal treatment with nisin. J Glob Antimicrob Resist 2018; 15:25-31. [PMID: 29933119 DOI: 10.1016/j.jgar.2018.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES The aim of this study was to determine gene expression associated with the persistence of a Listeria monocytogenes stationary-phase population when facing lethal nisin treatment. METHODS RNA-Seq analysis was used for gene expression profiling of persister cells in nutrient-rich medium (persister TN) compared with untreated cells (non-persister). The results were confirmed using reverse transcription quantitative PCR (RT-qPCR). RESULTS Functional genes associated with the persister population were identified in multiple systems, such as heat-shock-related stress response, cell wall synthesis, ATP-binding cassette (ABC) transport system, phosphotransferase system (PTS) and SOS/DNA repair. CONCLUSIONS This study pointed to genetic regulation of persister cells exposed to lethal nisin concentrations and provides some insight into possible mechanisms of impeding bacterial persistence.
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Affiliation(s)
- Shuyan Wu
- Massey Institute of Food Science and Technology, Massey University, Riddet Road, 4442 Palmerston North, New Zealand
| | - Pak-Lam Yu
- School of Engineering & Advanced Technology, Massey University, Riddet Road, 4442 Palmerston North, New Zealand
| | - Dave Wheeler
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Steve Flint
- Massey Institute of Food Science and Technology, Massey University, Riddet Road, 4442 Palmerston North, New Zealand.
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