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Brink KR, Hunt MG, Mu AM, Groszman K, Hoang KV, Lorch KP, Pogostin BH, Gunn JS, Tabor JJ. An E. coli display method for characterization of peptide-sensor kinase interactions. Nat Chem Biol 2023; 19:451-459. [PMID: 36482094 PMCID: PMC10065900 DOI: 10.1038/s41589-022-01207-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/10/2022] [Indexed: 12/13/2022]
Abstract
Bacteria use two-component system (TCS) signaling pathways to sense and respond to peptides involved in host defense, quorum sensing and inter-bacterial warfare. However, little is known about the broad peptide-sensing capabilities of TCSs. In this study, we developed an Escherichia coli display method to characterize the effects of human antimicrobial peptides (AMPs) on the pathogenesis-regulating TCS PhoPQ of Salmonella Typhimurium with much higher throughput than previously possible. We found that PhoPQ senses AMPs with diverse sequences, structures and biological functions. We further combined thousands of displayed AMP variants with machine learning to identify peptide sub-domains and biophysical features linked to PhoPQ activation. Most of the newfound AMP activators induce PhoPQ in S. Typhimurium, suggesting possible roles in virulence regulation. Finally, we present evidence that PhoPQ peptide-sensing specificity has evolved across commensal and pathogenic bacteria. Our method enables new insights into the specificities, mechanisms and evolutionary dynamics of TCS-mediated peptide sensing in bacteria.
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Affiliation(s)
- Kathryn R Brink
- Ph.D. Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Maxwell G Hunt
- Ph.D. Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Andrew M Mu
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Ken Groszman
- Operations Research Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ky V Hoang
- Center for Microbial Pathogenesis, Nationwide Children's Hospital, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Kevin P Lorch
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - John S Gunn
- Center for Microbial Pathogenesis, Nationwide Children's Hospital, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Jeffrey J Tabor
- Ph.D. Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.
- Department of Biosciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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2
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Pat- and Pta-mediated protein acetylation is required for horizontally-acquired virulence gene expression in Salmonella Typhimurium. J Microbiol 2022; 60:823-831. [DOI: 10.1007/s12275-022-2095-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
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3
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Li J, Claudi B, Fanous J, Chicherova N, Cianfanelli FR, Campbell RAA, Bumann D. Tissue compartmentalization enables Salmonella persistence during chemotherapy. Proc Natl Acad Sci U S A 2021; 118:e2113951118. [PMID: 34911764 PMCID: PMC8713819 DOI: 10.1073/pnas.2113951118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial chemotherapy can fail to eradicate the pathogen, even in the absence of antimicrobial resistance. Persisting pathogens can subsequently cause relapsing diseases. In vitro studies suggest various mechanisms of antibiotic persistence, but their in vivo relevance remains unclear because of the difficulty of studying scarce pathogen survivors in complex host tissues. Here, we localized and characterized rare surviving Salmonella in mouse spleen using high-resolution whole-organ tomography. Chemotherapy cleared >99.5% of the Salmonella but was inefficient against a small Salmonella subset in the white pulp. Previous models could not explain these findings: drug exposure was adequate, Salmonella continued to replicate, and host stresses induced only limited Salmonella drug tolerance. Instead, antimicrobial clearance required support of Salmonella-killing neutrophils and monocytes, and the density of such cells was lower in the white pulp than in other spleen compartments containing higher Salmonella loads. Neutrophil densities declined further during treatment in response to receding Salmonella loads, resulting in insufficient support for Salmonella clearance from the white pulp and eradication failure. However, adjunctive therapies sustaining inflammatory support enabled effective clearance. These results identify uneven Salmonella tissue colonization and spatiotemporal inflammation dynamics as main causes of Salmonella persistence and establish a powerful approach to investigate scarce but impactful pathogen subsets in complex host environments.
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Affiliation(s)
- Jiagui Li
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | | | - Joseph Fanous
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | | | | | | | - Dirk Bumann
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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4
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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5
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Groisman EA, Duprey A, Choi J. How the PhoP/PhoQ System Controls Virulence and Mg 2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution. Microbiol Mol Biol Rev 2021; 85:e0017620. [PMID: 34191587 PMCID: PMC8483708 DOI: 10.1128/mmbr.00176-20] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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6
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Cianfanelli FR, Cunrath O, Bumann D. Efficient dual-negative selection for bacterial genome editing. BMC Microbiol 2020; 20:129. [PMID: 32448155 PMCID: PMC7245781 DOI: 10.1186/s12866-020-01819-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Gene editing is key for elucidating gene function. Traditional methods, such as consecutive single-crossovers, have been widely used to modify bacterial genomes. However, cumbersome cloning and limited efficiency of negative selection often make this method slower than other methods such as recombineering. Results Here, we established a time-effective variant of consecutive single-crossovers. This method exploits rapid plasmid construction using Gibson assembly, a convenient E. coli donor strain, and efficient dual-negative selection for improved suicide vector resolution. We used this method to generate in-frame deletions, insertions and point mutations in Salmonella enterica with limited hands-on time. Adapted versions enabled efficient gene editing also in Pseudomonas aeruginosa and multi-drug resistant (MDR) Escherichia coli clinical isolates. Conclusions Our method is time-effective and allows facile manipulation of multiple bacterial species including MDR clinical isolates. We anticipate that this method might be broadly applicable to additional bacterial species, including those for which recombineering has been difficult to implement.
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Affiliation(s)
| | - Olivier Cunrath
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland.
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7
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Nanomolar Responsiveness of an Anaerobic Degradation Specialist to Alkylphenol Pollutants. J Bacteriol 2020; 202:JB.00595-19. [PMID: 31843798 DOI: 10.1128/jb.00595-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Anaerobic degradation of p-cresol (4-methylphenol) by the denitrifying betaproteobacterium Aromatoleum aromaticum EbN1 is regulated with high substrate specificity, presumed to be mediated by the predicted σ54-dependent two-component system PcrSR. An unmarked, in-frame ΔpcrSR deletion mutant showed reduced expression of the genes cmh (21-fold) and hbd (8-fold) that encode the two enzymes for initial oxidation of p-cresol to p-hydroxybenzoate compared to their expression in the wild type. The expression of cmh and hbd was restored by in trans complementation with pcrSR in the ΔpcrSR background to even higher levels than in the wild type. This is likely due to ∼200-/∼30-fold more transcripts of pcrSR in the complemented mutant. The in vivo responsiveness of A. aromaticum EbN1 to p-cresol was studied in benzoate-limited anaerobic cultures by the addition of p-cresol at various concentrations (from 100 μM down to 0.1 nM). Time-resolved transcript profiling by quantitative reverse transcription-PCR (qRT-PCR) revealed that the lowest p-cresol concentrations just affording cmh and hbd expression (response threshold) ranged between 1 and 10 nM, which is even more sensitive than the respective odor receptors of insects. A similar response threshold was determined for another alkylphenol, p-ethylphenol, which strain EbN1 anaerobically degrades via a different route and senses by the σ54-dependent one-component system EtpR. Based on these data and theoretical considerations, p-cresol or p-ethylphenol added as a single pulse (10 nM) requires less than a fraction of a second to reach equilibrium between intra- and extracellular space (∼20 molecules per cell), with an estimated Kd (dissociation constant) of <100 nM alkylphenol (p-cresol or p-ethylphenol) for its respective sensory protein (PcrS or EtpR).IMPORTANCE Alkylphenols (like p-cresol and p-ethylphenol) represent bulk chemicals for industrial syntheses. Besides massive local damage events, large-scale micropollution is likewise of environmental and health concern. Next to understanding how such pollutants can be degraded by microorganisms, it is also relevant to determine the microorganisms' lower threshold of responsiveness. Aromatoleum aromaticum EbN1 is a specialist in anaerobic degradation of aromatic compounds, employing a complex and substrate-specifically regulated catabolic network. The present study aims at verifying the predicted role of the PcrSR system in sensing p-cresol and at determining the threshold of responsiveness for alkylphenols. The findings have implications for the enigmatic persistence of dissolved organic matter (escape from biodegradation) and for the lower limits of aromatic compounds required for bacterial growth.
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8
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Choi J, Groisman EA. Activation of master virulence regulator PhoP in acidic pH requires the Salmonella-specific protein UgtL. Sci Signal 2017; 10:10/494/eaan6284. [PMID: 28851823 DOI: 10.1126/scisignal.aan6284] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Acidic conditions, such as those inside phagosomes, stimulate the intracellular pathogen Salmonella enterica to activate virulence genes. The sensor PhoQ responds to a mildly acidic pH by phosphorylating, and thereby activating, the virulence regulator PhoP. This PhoP/PhoQ two-component system is conserved in a subset of Gram-negative bacteria. PhoQ is thought to be sufficient to activate PhoP in mildly acidic pH. However, we found that the Salmonella-specific protein UgtL, which was horizontally acquired by Salmonella before the divergence of S. enterica and Salmonella bongori, was also necessary for PhoQ to activate PhoP under mildly acidic pH conditions but not for PhoQ to activate PhoP in response to low Mg2+ or the antimicrobial peptide C18G. UgtL increased the abundance of phosphorylated PhoP by stimulating autophosphorylation of PhoQ, thereby increasing the amount of the phosphodonor for PhoP. Deletion of ugtL attenuated Salmonella virulence and further reduced PhoP activation in a strain bearing a form of PhoQ that is not responsive to acidic pH. These data suggest that when Salmonella experiences mildly acidic pH, PhoP activation requires PhoQ to detect pH and UgtL to amplify the PhoQ response. Our findings reveal how acquisition of a foreign gene can strengthen signal responsiveness in an ancestral regulatory system.
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Affiliation(s)
- Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA. .,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
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9
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Clayton AL, Enomoto S, Su Y, Dale C. The regulation of antimicrobial peptide resistance in the transition to insect symbiosis. Mol Microbiol 2017; 103:958-972. [PMID: 27987256 DOI: 10.1111/mmi.13598] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2016] [Indexed: 01/02/2023]
Abstract
Many bacteria utilize two-component systems consisting of a sensor kinase and a transcriptional response regulator to detect environmental signals and modulate gene expression for adaptation. The response regulator PhoP and its cognate sensor kinase PhoQ compose a two-component system known for its role in responding to low levels of Mg2+ , Ca2+ , pH and to the presence of antimicrobial peptides and activating the expression of genes involved in adaptation to host association. Compared with their free-living relatives, mutualistic insect symbiotic bacteria inhabit a static environment where the requirement for sensory functions is expected to be relaxed. The insect symbiont, Sodalis glossinidius, requires PhoP to resist killing by host derived antimicrobial peptides. However, the S. glossinidius PhoQ was found to be insensitive to Mg2+ , Ca2+ and pH. Here they show that Sodalis praecaptivus, a close non host-associated relative of S. glossinidius, utilizes a magnesium sensing PhoP-PhoQ and an uncharacterized MarR-like transcriptional regulator (Sant_4061) to control antimicrobial peptide resistance in vitro. While the inactivation of phoP, phoQ or Sant_4061 completely retards the growth of S. praecaptivus in the presence of an antimicrobial peptide in vitro, inactivation of both phoP and Sant_4061 is necessary to abrogate growth of this bacterium in an insect host.
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Affiliation(s)
- Adam L Clayton
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | | | - Yinghua Su
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Colin Dale
- Department of Biology, University of Utah, Salt Lake City, UT, USA
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10
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Abstract
Antimicrobial peptides (AMPs), also known as host defense peptides, are small naturally occurring microbicidal molecules produced by the host innate immune response that function as a first line of defense to kill pathogenic microorganisms by inducing deleterious cell membrane damage. AMPs also possess signaling and chemoattractant activities and can modulate the innate immune response to enhance protective immunity or suppress inflammation. Human pathogens have evolved defense molecules and strategies to counter and survive the AMPs released by host immune cells such as neutrophils and macrophages. Here, we review the various mechanisms used by human bacterial pathogens to resist AMP-mediated killing, including surface charge modification, active efflux, alteration of membrane fluidity, inactivation by proteolytic digestion, and entrapment by surface proteins and polysaccharides. Enhanced understanding of AMP resistance at the molecular level may offer insight into the mechanisms of bacterial pathogenesis and augment the discovery of novel therapeutic targets and drug design for the treatment of recalcitrant multidrug-resistant bacterial infections.
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11
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MgtC as a Host-Induced Factor and Vaccine Candidate against Mycobacterium abscessus Infection. Infect Immun 2016; 84:2895-903. [PMID: 27481243 DOI: 10.1128/iai.00359-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/18/2016] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus is an emerging pathogenic mycobacterium involved in pulmonary and mucocutaneous infections, presenting a serious threat for patients with cystic fibrosis (CF). The lack of an efficient treatment regimen and the emergence of multidrug resistance in clinical isolates require the development of new therapeutic strategies against this pathogen. Reverse genetics has revealed genes that are present in M. abscessus but absent from saprophytic mycobacteria and that are potentially involved in pathogenicity. Among them, MAB_3593 encodes MgtC, a known virulence factor involved in intramacrophage survival and adaptation to Mg(2+) deprivation in several major bacterial pathogens. Here, we demonstrated a strong induction of M. abscessus MgtC at both the transcriptional and translational levels when bacteria reside inside macrophages or upon Mg(2+) deprivation. Moreover, we showed that M. abscessus MgtC was recognized by sera from M. abscessus-infected CF patients. The intramacrophage growth (J774 or THP1 cells) of a M. abscessus knockout mgtC mutant was, however, not significantly impeded. Importantly, our results indicated that inhibition of MgtC in vivo through immunization with M. abscessus mgtC DNA, formulated with a tetrafunctional amphiphilic block copolymer, exerted a protective effect against an aerosolized M. abscessus challenge in CF (ΔF508 FVB) mice. The formulated DNA immunization was likely associated with the production of specific MgtC antibodies, which may stimulate a protective effect by counteracting MgtC activity during M. abscessus infection. These results emphasize the importance of M. abscessus MgtC in vivo and provide a basis for the development of novel therapeutic tools against pulmonary M. abscessus infections in CF patients.
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12
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Choi J, Groisman EA. Acidic pH sensing in the bacterial cytoplasm is required for Salmonella virulence. Mol Microbiol 2016; 101:1024-38. [PMID: 27282333 PMCID: PMC5015592 DOI: 10.1111/mmi.13439] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 01/12/2023]
Abstract
pH regulates gene expression, biochemical activities and cellular behaviors. A mildly acidic pH activates the master virulence regulatory system PhoP/PhoQ in the facultative intracellular pathogen Salmonella enterica serovar Typhimurium. The sensor PhoQ harbors an extracytoplasmic domain implicated in signal sensing, and a cytoplasmic domain controlling activation of the regulator PhoP. We now report that, surprisingly, a decrease in Salmonella's own cytoplasmic pH induces transcription of PhoP-activated genes even when the extracytoplasmic pH remains neutral. Amino acid substitutions in PhoQ's cytoplasmic domain hindered activation by acidic pH and attenuated virulence in mice, but did not abolish activation by low Mg(2+) or the antimicrobial peptide C18G. Conversely, removal of PhoQ's extracytoplasmic domains prevented the response to the latter PhoQ-activating signals but not to acidic pH. PhoP-dependent genes were minimally induced by acidic pH in the non-pathogenic species Salmonella bongori but were activated by low Mg(2+) and C18G as in pathogenic S. enterica. Our findings indicate that the sensor PhoQ enables S. enterica to respond to both host- and bacterial-derived signals that alter its cytoplasmic pH.
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Affiliation(s)
- Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, 06536, USA.
- Yale Microbial Sciences Institute, West Haven, CT, 06516, USA.
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13
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Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions. Nature 2016; 529:496-501. [PMID: 26789254 DOI: 10.1038/nature16547] [Citation(s) in RCA: 338] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.
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Affiliation(s)
- Alexander J Westermann
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Konrad U Förstner
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany.,University of Würzburg, Core Unit Systems Medicine, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Fabian Amman
- University of Leipzig, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, D-04107 Leipzig, Germany.,University of Vienna, Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria
| | - Lars Barquist
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Yanjie Chao
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Leon N Schulte
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany
| | - Lydia Müller
- University of Leipzig, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Peter F Stadler
- University of Leipzig, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, D-04107 Leipzig, Germany.,University of Vienna, Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.,Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, New Mexico 87501, USA
| | - Jörg Vogel
- University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany.,Research Centre for Infectious Diseases (ZINF), University of Würzburg, D-97070 Würzburg, Germany
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14
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Abstract
The outcome of an infection depends on host recognition of the pathogen, hence leading to the activation of signaling pathways controlling defense responses. A long-held belief is that the modification of the lipid A moiety of the lipopolysaccharide could help Gram-negative pathogens to evade innate immunity. However, direct evidence that this happens in vivo is lacking. Here we report the lipid A expressed in the tissues of infected mice by the human pathogen Klebsiella pneumoniae. Our findings demonstrate that Klebsiella remodels its lipid A in a tissue-dependent manner. Lipid A species found in the lungs are consistent with a 2-hydroxyacyl-modified lipid A dependent on the PhoPQ-regulated oxygenase LpxO. The in vivo lipid A pattern is lost in minimally passaged bacteria isolated from the tissues. LpxO-dependent modification reduces the activation of inflammatory responses and mediates resistance to antimicrobial peptides. An lpxO mutant is attenuated in vivo thereby highlighting the importance of this lipid A modification in Klebsiella infection biology. Colistin, one of the last options to treat multidrug-resistant Klebsiella infections, triggers the in vivo lipid A pattern. Moreover, colistin-resistant isolates already express the in vivo lipid A pattern. In these isolates, LpxO-dependent lipid A modification mediates resistance to colistin. Deciphering the lipid A expressed in vivo opens the possibility of designing novel therapeutics targeting the enzymes responsible for the in vivo lipid A pattern.
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15
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HAMP Domain Rotation and Tilting Movements Associated with Signal Transduction in the PhoQ Sensor Kinase. mBio 2015; 6:e00616-15. [PMID: 26015499 PMCID: PMC4447245 DOI: 10.1128/mbio.00616-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
HAMP domains are α-helical coiled coils that often transduce signals from extracytoplasmic sensing domains to cytoplasmic domains. Limited structural information has resulted in hypotheses that specific HAMP helix movement changes downstream enzymatic activity. These hypotheses were tested by mutagenesis and cysteine cross-linking analysis of the PhoQ histidine kinase, essential for resistance to antimicrobial peptides in a variety of enteric pathogens. These results support a mechanistic model in which periplasmic signals which induce an activation state generate a rotational movement accompanied by a tilt in α-helix 1 which activates kinase activity. Biochemical data and a high-confidence model of the PhoQ cytoplasmic domain indicate a possible physical interaction of the HAMP domain with the catalytic domain as necessary for kinase repression. These results support a model of PhoQ activation in which changes in the periplasmic domain lead to conformational movements in the HAMP domain helices which disrupt interaction between the HAMP and the catalytic domains, thus promoting increased kinase activity. Most studies on the HAMP domain signaling states have been performed with chemoreceptors or the HAMP domain of Af1503. Full-length structures of the HAMP-containing histidine kinases VicK and CpxA or a hybrid between the HAMP domain of Af1503 and the EnvZ histidine kinase agree with the parallel four-helix bundle structure identified in Af1503 and provide snapshots of structural conformations experienced by HAMP domains. We took advantage of the fact that we can easily regulate the activation state of PhoQ histidine kinase to study its HAMP domain in the context of the full-length protein in living cells and provide biochemical evidence for different conformational states experienced by Salmonella enterica serovar Typhimurium PhoQ HAMP domain upon signaling.
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Hicks KG, Delbecq SP, Sancho-Vaello E, Blanc MP, Dove KK, Prost LR, Daley ME, Zeth K, Klevit RE, Miller SI. Acidic pH and divalent cation sensing by PhoQ are dispensable for systemic salmonellae virulence. eLife 2015; 4:e06792. [PMID: 26002083 PMCID: PMC4473727 DOI: 10.7554/elife.06792] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/22/2015] [Indexed: 12/30/2022] Open
Abstract
Salmonella PhoQ is a histidine kinase with a periplasmic sensor domain (PD) that promotes virulence by detecting the macrophage phagosome. PhoQ activity is repressed by divalent cations and induced in environments of acidic pH, limited divalent cations, and cationic antimicrobial peptides (CAMP). Previously, it was unclear which signals are sensed by salmonellae to promote PhoQ-mediated virulence. We defined conformational changes produced in the PhoQ PD on exposure to acidic pH that indicate structural flexibility is induced in α-helices 4 and 5, suggesting this region contributes to pH sensing. Therefore, we engineered a disulfide bond between W104C and A128C in the PhoQ PD that restrains conformational flexibility in α-helices 4 and 5. PhoQW104C-A128C is responsive to CAMP, but is inhibited for activation by acidic pH and divalent cation limitation. phoQW104C-A128CSalmonella enterica Typhimurium is virulent in mice, indicating that acidic pH and divalent cation sensing by PhoQ are dispensable for virulence. DOI:http://dx.doi.org/10.7554/eLife.06792.001 Salmonella bacteria cause illnesses in humans, such as food poisoning and typhoid fever. In response to a Salmonella infection, immune cells known as macrophages detect and engulf the bacteria. The conditions inside the macrophage (which include an acidic pH and high levels of antimicrobial molecules) can destroy some bacteria. However, Salmonella bacteria (which are also called salmonellae) can sense and counteract these hostile conditions; this allows them to remodel their surface to survive and reproduce inside macrophages and continue to cause disease. A protein known as PhoQ, which is found on the surface of Salmonella bacteria, is a sensor that detects when the bacterium is inside a macrophage and so needs to boost its defenses. The PhoQ sensor is able to respond to acidity, the absence of divalent cations—such as magnesium and calcium ions—and certain antimicrobial peptide molecules. These conditions and components are used inside macrophages to try and kill the bacteria, but it was not known which of these signals PhoQ actually senses during an infection. Hicks et al. established how the sensor region of PhoQ changes when it is exposed to acid. This knowledge enabled variants of this protein to be constructed that do not respond when exposed to acidic conditions or low levels of divalent cations. Salmonellae that have these modified PhoQ sensors were still able to infect macrophages and cause disease in mice. These findings suggest that antimicrobial peptide sensing alone is sufficient to trigger the bacteria's defenses inside host organisms. Understanding how salmonellae detect antimicrobial factors could help with the development of new treatments for the diseases caused by these bacteria. Furthermore, the new tools developed by Hicks et al. could be applied to other systems to characterize how bacteria interact with their host environment during infection. DOI:http://dx.doi.org/10.7554/eLife.06792.002
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Affiliation(s)
- Kevin G Hicks
- Department of Microbiology, University of Washington Medical School, Seattle, United States
| | - Scott P Delbecq
- Department of Biochemistry, University of Washington Medical School, Seattle, United States
| | - Enea Sancho-Vaello
- Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Leioa, Bizkaia, Spain
| | - Marie-Pierre Blanc
- Department of Microbiology, University of Washington Medical School, Seattle, United States
| | - Katja K Dove
- Department of Biochemistry, University of Washington Medical School, Seattle, United States
| | - Lynne R Prost
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Margaret E Daley
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, United States
| | - Kornelius Zeth
- Department of Biochemistry and Molecular Biology, University of Basque Country, Leioa, Spain
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington Medical School, Seattle, United States
| | - Samuel I Miller
- Department of Microbiology, University of Washington Medical School, Seattle, United States
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Mucosal physical and chemical innate barriers: Lessons from microbial evasion strategies. Semin Immunol 2015; 27:111-8. [PMID: 25936225 DOI: 10.1016/j.smim.2015.03.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/13/2015] [Indexed: 12/24/2022]
Abstract
The innate immune system has evolved since millions of years under a selective pressure. Among the different host mechanisms selected and conserved as a first line of defense, the gastrointestinal mucus layer constitutes an efficient physical and chemical barrier against invading microbes. Mucin glycoproteins and antimicrobial peptides are the major components of the mucus barrier, and evidences prove that they form an effective protection against most microbes. However, successful pathogens have evolved evasion strategies to circumvent this defense barrier. Here, we discuss the interactions between pathogens, mucins, and antimicrobial peptides, and the mechanisms that pathogens have developed to evade the innate defense systems of the intestinal mucosal barrier.
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Heimlich DR, Harrison A, Mason KM. Host Antimicrobial Peptides in Bacterial Homeostasis and Pathogenesis of Disease. Antibiotics (Basel) 2014; 3:645-76. [PMID: 26029470 PMCID: PMC4448142 DOI: 10.3390/antibiotics3040645] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/05/2014] [Accepted: 11/05/2014] [Indexed: 01/10/2023] Open
Abstract
Innate immune responses function as a first line of host defense against the development of bacterial infection, and in some cases to preserve the sterility of privileged sites in the human host. Bacteria that enter these sites must counter host responses for colonization. From the host's perspective, the innate immune system works expeditiously to minimize the bacterial threat before colonization and subsequent dysbiosis. The multifactorial nature of disease further challenges predictions of how each independent variable influences bacterial pathogenesis. From bacterial colonization to infection and through disease, the microenvironments of the host are in constant flux as bacterial and host factors contribute to changes at the host-pathogen interface, with the host attempting to eradicate bacteria and the bacteria fighting to maintain residency. A key component of this innate host response towards bacterial infection is the production of antimicrobial peptides (AMPs). As an early component of the host response, AMPs modulate bacterial load and prevent establishment of infection. Under quiescent conditions, some AMPs are constitutively expressed by the epithelium. Bacterial infection can subsequently induce production of other AMPs in an effort to maintain sterility, or to restrict colonization. As demonstrated in various studies, the absence of a single AMP can influence pathogenesis, highlighting the importance of AMP concentration in maintaining homeostasis. Yet, AMPs can increase bacterial virulence through the co-opting of the peptides or alteration of bacterial virulence gene expression. Further, bacterial factors used to subvert AMPs can modify host microenvironments and alter colonization of the residential flora that principally maintain homeostasis. Thus, the dynamic interplay between host defense peptides and bacterial factors produced to quell peptide activity play a critical role in the progression and outcome of disease.
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Affiliation(s)
- Derek R. Heimlich
- The Research Institute at Nationwide Children’s Center for Microbial Pathogenesis, Columbus, OH 43205, USA; E-Mails: (D.R.H.); (A.H.)
| | - Alistair Harrison
- The Research Institute at Nationwide Children’s Center for Microbial Pathogenesis, Columbus, OH 43205, USA; E-Mails: (D.R.H.); (A.H.)
| | - Kevin M. Mason
- The Research Institute at Nationwide Children’s Center for Microbial Pathogenesis, Columbus, OH 43205, USA; E-Mails: (D.R.H.); (A.H.)
- The Ohio State University College of Medicine, Department of Pediatrics, Columbus, OH 43205, USA
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Groisman EA, Hollands K, Kriner MA, Lee EJ, Park SY, Pontes MH. Bacterial Mg2+ homeostasis, transport, and virulence. Annu Rev Genet 2013; 47:625-46. [PMID: 24079267 DOI: 10.1146/annurev-genet-051313-051025] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Organisms must maintain physiological levels of Mg(2+) because this divalent cation is critical for the stabilization of membranes and ribosomes, for the neutralization of nucleic acids, and as a cofactor in a variety of enzymatic reactions. In this review, we describe the mechanisms that bacteria utilize to sense the levels of Mg(2+) both outside and inside the cytoplasm. We examine how bacteria achieve Mg(2+) homeostasis by adjusting the expression and activity of Mg(2+) transporters and by changing the composition of their cell envelope. We discuss the connections that exist between Mg(2+) sensing, Mg(2+) transport, and bacterial virulence. Additionally, we explore the logic behind the fact that bacterial genomes encode multiple Mg(2+) transporters and distinct sensing systems for cytoplasmic and extracytoplasmic Mg(2+). These analyses may be applicable to the homeostatic control of other cations.
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Affiliation(s)
- Eduardo A Groisman
- Department of Microbial Pathogenesis, Boyer Center for Molecular Medicine, Yale School of Medicine, New Haven, Connecticut 06536; , , , , ,
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20
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Seref O, Brooks JP, Fong SS. Decomposition of flux distributions into metabolic pathways. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:984-993. [PMID: 24334391 DOI: 10.1109/tcbb.2013.115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genome-scale reconstructions are often used for studying relationships between fundamental components of a metabolic system. In this study, we develop a novel computational method for analyzing predicted flux distributions for metabolic reconstructions. Because chemical reactions may have multiple reactants and products, a directed hypergraph where hyperarcs may have multiple tail vertices and head vertices is a more appropriate representation of the metabolic network than a conventional network. We use this view to represent predicted flux distributions by maximum generalized flows on hypergraphs. We then demonstrate that the generalized hyperflow problem may be transformed to an equivalent network flow problem with side constraints. This transformation allows a flux to be decomposed into chains of reactions. Subsequent analysis of these chains helps to characterize active pathways in a flux distribution. Such characterizations facilitate comparisons of flux distributions for different environmental conditions. The proposed method is applied to compare predicted flux distributions for Salmonella typhimurium to study changes in metabolism that cause enhanced virulence during a space flight. The differences between flux distributions corresponding to normal and enhanced virulence states confirm previous observations concerning infection mechanisms and suggest new pathways for exploration.
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Affiliation(s)
- Onur Seref
- Virginia Polytechnic Institute and State University, Blacksburg
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21
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Lu JX, Xu YS, Shaw WJ. Phosphorylation and ionic strength alter the LRAP-HAP interface in the N-terminus. Biochemistry 2013; 52:2196-205. [PMID: 23477367 PMCID: PMC3626292 DOI: 10.1021/bi400071a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The conditions present during enamel crystallite development change dramatically as a function of time, including the pH, protein concentration, surface type, and ionic strength. In this work, we investigate the role that two of these changing conditions, pH and ionic strength, have in modulating the interaction of the amelogenin, LRAP, with hydroxyapatite (HAP). Using solid-state NMR dipolar recoupling and chemical shift data, we investigate the structure, orientation, and dynamics of three regions in the N-terminus of the protein: L(15) to V(19), V(19) to L(23), and K(24) to S(28). These regions are also near the only phosphorylated residue in the protein pS(16); therefore, changes in the LRAP-HAP interaction as a function of phosphorylation (LRAP(-P) vs LRAP(+P)) were also investigated. All of the regions and conditions studied for the surface immobilized proteins showed restricted motion, with indications of slightly more mobility under all conditions for L(15)(+P) and K(24)(-P). The structure and orientation of the LRAP-HAP interaction in the N-terminus of the phosphorylated protein is very stable to changing solution conditions. From REDOR dipolar recoupling data, the structure and orientation in the region L(15)V(19)(+P) did not change significantly as a function of pH or ionic strength. The structure and orientation of the region V(19)L(23)(+P) were also stable to changes in pH, with the only significant change observed at high ionic strength, where the region becomes extended, suggesting this may be an important region in regulating mineral development. Chemical shift studies also suggest minimal changes in all three regions studied for both LRAP(-P) and LRAP(+P) as a function of pH or ionic strength, and also reveal that K(24) has multiple resolvable resonances, suggestive of two coexisting structures. Phosphorylation also alters the LRAP-HAP interface. All of the three residues investigated (L(15), V(19), and K(24)) are closer to the surface in LRAP(+P), but only K(24)S(28) changes structure as a result of phosphorylation, from a random coil to a largely helical structure, and V(19)L(23) becomes more extended at high ionic strength when phosphorylated. These observations suggest that ionic strength and dephosphorylation may provide switching mechanisms to trigger a change in the function of the N-terminus during enamel development.
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Affiliation(s)
- Jun-xia Lu
- Pacific Northwest National Laboratory, Richland, WA 99354
| | | | - Wendy J. Shaw
- Pacific Northwest National Laboratory, Richland, WA 99354
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22
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Beceiro A, Tomás M, Bou G. Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? Clin Microbiol Rev 2013; 26:185-230. [PMID: 23554414 PMCID: PMC3623377 DOI: 10.1128/cmr.00059-12] [Citation(s) in RCA: 630] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Hosts and bacteria have coevolved over millions of years, during which pathogenic bacteria have modified their virulence mechanisms to adapt to host defense systems. Although the spread of pathogens has been hindered by the discovery and widespread use of antimicrobial agents, antimicrobial resistance has increased globally. The emergence of resistant bacteria has accelerated in recent years, mainly as a result of increased selective pressure. However, although antimicrobial resistance and bacterial virulence have developed on different timescales, they share some common characteristics. This review considers how bacterial virulence and fitness are affected by antibiotic resistance and also how the relationship between virulence and resistance is affected by different genetic mechanisms (e.g., coselection and compensatory mutations) and by the most prevalent global responses. The interplay between these factors and the associated biological costs depend on four main factors: the bacterial species involved, virulence and resistance mechanisms, the ecological niche, and the host. The development of new strategies involving new antimicrobials or nonantimicrobial compounds and of novel diagnostic methods that focus on high-risk clones and rapid tests to detect virulence markers may help to resolve the increasing problem of the association between virulence and resistance, which is becoming more beneficial for pathogenic bacteria.
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23
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Transcriptome of Dickeya dadantii infecting Acyrthosiphon pisum reveals a strong defense against antimicrobial peptides. PLoS One 2013; 8:e54118. [PMID: 23342088 PMCID: PMC3544676 DOI: 10.1371/journal.pone.0054118] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/05/2012] [Indexed: 01/01/2023] Open
Abstract
The plant pathogenic bacterium Dickeya dadantii has recently been shown to be able to kill the aphid Acyrthosiphon pisum. While the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. To identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. More than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. No homologue to known toxin genes could be identified in the upregulated genes. The upregulated genes reflect the response of the bacteria to the conditions encountered inside aphids. While only a few genes involved in the response to oxidative stress were induced, a strong defense against antimicrobial peptides (AMP) was induced. Expression of a great number of efflux proteins and transporters was increased. Besides the genes involved in LPS modification by addition of 4-aminoarabinose (the arnBCADTEF operon) and phosphoethanolamine (pmrC, eptB) usually induced in Gram negative bacteria in response to AMPs, dltBAC and pbpG genes, which confer Gram positive bacteria resistance to AMPs by adding alanine to teichoic acids, were also induced. Both types of modification confer D. dadantii resistance to the AMP polymyxin. A. pisum harbors symbiotic bacteria and it is thought that it has a very limited immune system to maintain these populations and do not synthesize AMPs. The arnB mutant was less pathogenic to A. pisum, which suggests that, in contrast to what has been supposed, aphids do synthesize AMP.
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24
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de Oca EPM. Antimicrobial peptide elicitors: New hope for the post-antibiotic era. Innate Immun 2012; 19:227-41. [DOI: 10.1177/1753425912460708] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial peptides or host defense peptides are fundamental components of human innate immunity. Recent and growing evidence suggests they have a role in a broad range of diseases, including cancer, allergies and susceptibility to infection, including HIV/AIDS. Antimicrobial peptide elicitors (APEs) are physical, biological or chemical agents that boost human antimicrobial peptide expression. The current knowledge of APEs and their potential use in the treatment of human infectious diseases are reviewed, and a classification system for APEs is proposed. The efficient use of APEs in clinical practice could mark the beginning of the urgently needed post-antibiotic era, but further trials assessing their efficacy and safety are required.
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Affiliation(s)
- Ernesto Prado Montes de Oca
- Molecular Biology Laboratory, Biosecurity Area, CIATEJ – National Council of Science and Technology, Guadalajara, Jalisco, Mexico
- In silico Laboratory, Pharmaceutical and Medical Biotechnology Unit, CIATEJ – National Council of Science and Technology, Guadalajara, Jalisco, Mexico
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25
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Gruenheid S, Le Moual H. Resistance to antimicrobial peptides in Gram-negative bacteria. FEMS Microbiol Lett 2012; 330:81-9. [PMID: 22339775 DOI: 10.1111/j.1574-6968.2012.02528.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/30/2012] [Accepted: 02/11/2012] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are present in virtually all organisms and are an ancient and critical component of innate immunity. In mammals, AMPs are present in phagocytic cells, on body surfaces such as skin and mucosa, and in secretions and body fluids such as sweat, saliva, urine, and breast milk, consistent with their role as part of the first line of defense against a wide range of pathogenic microorganisms including bacteria, viruses, and fungi. AMPs are microbicidal and have also been shown to act as immunomodulators with chemoattractant and signaling activities. During the co-evolution of hosts and bacterial pathogens, bacteria have developed the ability to sense and initiate an adaptive response to AMPs to resist their bactericidal activity. Here, we review the various mechanisms used by Gram-negative bacteria to sense and resist AMP-mediated killing. These mechanisms play an important role in bacterial resistance to host-derived AMPs that are encountered during the course of infection. Bacterial resistance to AMPs should also be taken into consideration in the development and use of AMPs as anti-infective agents, for which there is currently a great deal of academic and commercial interest.
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Affiliation(s)
- Samantha Gruenheid
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
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26
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Kawasaki K. Complexity of lipopolysaccharide modifications in Salmonella enterica: Its effects on endotoxin activity, membrane permeability, and resistance to antimicrobial peptides. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.01.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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27
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Mulcahy H, Lewenza S. Magnesium limitation is an environmental trigger of the Pseudomonas aeruginosa biofilm lifestyle. PLoS One 2011; 6:e23307. [PMID: 21858064 PMCID: PMC3156716 DOI: 10.1371/journal.pone.0023307] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 07/15/2011] [Indexed: 11/30/2022] Open
Abstract
Biofilm formation is a conserved strategy for long-term bacterial survival in nature and during infections. Biofilms are multicellular aggregates of cells enmeshed in an extracellular matrix. The RetS, GacS and LadS sensors control the switch from a planktonic to a biofilm mode of growth in Pseudomonas aeruginosa. Here we detail our approach to identify environmental triggers of biofilm formation by investigating environmental conditions that repress expression of the biofilm repressor RetS. Mg2+ limitation repressed the expression of retS leading to increased aggregation, exopolysaccharide (EPS) production and biofilm formation. Repression of retS expression under Mg2+ limitation corresponded with induced expression of the GacA-controlled small regulatory RNAs rsmZ and rsmY and the EPS biosynthesis operons pel and psl. We recently demonstrated that extracellular DNA sequesters Mg2+ cations and activates the cation-sensing PhoPQ two-component system, which leads to increased antimicrobial peptide resistance in biofilms. Here we show that exogenous DNA and EDTA, through their ability to chelate Mg2+, promoted biofilm formation. The repression of retS in low Mg2+ was directly controlled by PhoPQ. PhoP also directly controlled expression of rsmZ but not rsmY suggesting that PhoPQ controls the equilibrium of the small regulatory RNAs and thus fine-tunes the expression of genes in the RetS pathway. In summary, Mg2+ limitation is a biologically relevant environmental condition and the first bonafide environmental signal identified that results in transcriptional repression of retS and promotes P. aeruginosa biofilm formation.
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Affiliation(s)
- Heidi Mulcahy
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Shawn Lewenza
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- * E-mail:
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28
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Koprivnjak T, Peschel A. Bacterial resistance mechanisms against host defense peptides. Cell Mol Life Sci 2011; 68:2243-54. [PMID: 21560069 PMCID: PMC11115334 DOI: 10.1007/s00018-011-0716-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 12/30/2022]
Abstract
Host defense peptides and proteins are important components of the innate host defense against pathogenic microorganisms. They target negatively charged bacterial surfaces and disrupt microbial cytoplasmic membranes, which ultimately leads to bacterial destruction. Throughout evolution, pathogens devised several mechanisms to protect themselves from deleterious damage of host defense peptides. These strategies include (a) inactivation and cleavage of host defense peptides by production of host defense binding proteins and proteases, (b) repulsion of the peptides by alteration of pathogen's surface charge employing modifications by amino acids or amino sugars of anionic molecules (e.g., teichoic acids, lipid A and phospholipids), (c) alteration of bacterial membrane fluidity, and (d) expulsion of the peptides using multi drug pumps. Together with bacterial regulatory network(s) that regulate expression and activity of these mechanisms, they represent attractive targets for development of novel antibacterials.
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Affiliation(s)
- Tomaz Koprivnjak
- Department of Biotechnology, National Institute of Chemistry Slovenia, Hajdrihova 19, 1000, Ljubljana, Slovenia,
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29
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Analysis of the networks controlling the antimicrobial-peptide-dependent induction of Klebsiella pneumoniae virulence factors. Infect Immun 2011; 79:3718-32. [PMID: 21708987 DOI: 10.1128/iai.05226-11] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial peptides (APs) impose a threat to the survival of pathogens, and it is reasonable to postulate that bacteria have developed strategies to counteract them. Polymyxins are becoming the last resort to treat infections caused by multidrug-resistant Gram-negative bacteria and, similar to APs, they interact with the anionic lipopolysaccharide. Given that polymyxins and APs share the initial target, it is possible that bacterial defense mechanisms against polymyxins will be also effective against host APs. We sought to determine whether exposure to polymyxin will increase Klebsiella pneumoniae resistance to host APs. Indeed, exposure of K. pneumoniae to polymyxin induces cross-resistance not only to polymyxin itself but also to APs present in the airways. Polymyxin treatment upregulates the expression of the capsule polysaccharide operon and the loci required to modify the lipid A with aminoarabinose and palmitate with a concomitant increase in capsule and lipid A species containing such modifications. Moreover, these surface changes contribute to APs resistance and also to polymyxin-induced cross-resistance to APs. Bacterial loads of lipid A mutants in trachea and lungs of intranasally infected mice were lower than those of wild-type strain. PhoPQ, PmrAB, and the Rcs system govern polymyxin-induced transcriptional changes, and there is a cross talk between PhoPQ and the Rcs system. Our findings support the notion that Klebsiella activates a defense program against APs that is controlled by three signaling systems. Therapeutic strategies directed to prevent the activation of this program could be a new approach worth exploring to facilitate the clearance of the pathogen from the airways.
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30
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Chakraborty S, Li M, Chatterjee C, Sivaraman J, Leung KY, Mok YK. Temperature and Mg2+ sensing by a novel PhoP-PhoQ two-component system for regulation of virulence in Edwardsiella tarda. J Biol Chem 2010; 285:38876-88. [PMID: 20937832 DOI: 10.1074/jbc.m110.179150] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The PhoP-PhoQ two-component system is commonly used by bacteria to sense environmental factors. Here we show that the PhoP-PhoQ system of Edwardsiella tarda detects changes in environmental temperature and Mg(2+) concentration as well as regulates the type III and VI secretion systems through direct activation of esrB. Protein secretion is activated from 23 to 35 °C or at low Mg(2+) concentrations, but it is suppressed at or below 20 °C, at or above 37 °C, or at high Mg(2+) concentrations. The effects of temperature and Mg(2+) concentration are additive. The PhoQ sensor domain has a low T(m) of 37.9 °C, and it detects temperatures through a conformational change of its secondary structure. Mutation of specific Pro or Thr residues increased the stability of the PhoQ sensor drastically, altering its temperature-sensing ability. The PhoQ sensor detects Mg(2+) concentration through the direct binding of Mg(2+) to a cluster of acidic residues (DDDSAD) and through changes that likely affect its tertiary structure. Here, we describe for the first time the use of PhoP-PhoQ as a temperature sensor for bacterial virulence control.
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Affiliation(s)
- Smarajit Chakraborty
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543
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31
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Le Sage V, Zhu L, Lepage C, Portt A, Viau C, Daigle F, Gruenheid S, Le Moual H. An outer membrane protease of the omptin family prevents activation of the Citrobacter rodentium PhoPQ two-component system by antimicrobial peptides. Mol Microbiol 2009; 74:98-111. [PMID: 19708916 DOI: 10.1111/j.1365-2958.2009.06854.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The PhoPQ two-component system of the intracellular pathogen Salmonella enterica senses and controls resistance to alpha-helical antimicrobial peptides (AMPs) by regulating covalent modifications of lipid A. A homologue of the phoPQ operon was found in the genome of the murine enteric extracellular pathogen, Citrobacter rodentium. Here we report that C. rodentium PhoPQ was apparently unable to mediate activation of target genes in the presence of alpha-helical AMPs. However, these AMPs activated C. rodentium PhoPQ expressed in a S. entericaDeltaphoPQ mutant. Analysis of the outer membrane (OM) fractions of the C. rodentium wild-type and DeltaphoPQ strains led to the identification of an omptin family protease (CroP) that was absent in DeltaphoPQ. Deletion of croP in C. rodentium resulted in higher susceptibility to alpha-helical AMPs, indicating a direct role of CroP in AMP resistance. CroP greatly contributed to the protection of the OM from AMP damage by actively degrading alpha-helical AMPs before they reach the periplasmic space. Accordingly, transcriptional activation of PhoP-regulated genes by alpha-helical AMPs was restored in the DeltacroP mutant. This study shows that resistance to alpha-helical AMPs by the extracellular pathogen C. rodentium relies primarily on the CroP OM protease.
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Affiliation(s)
- Valerie Le Sage
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Lei Zhu
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Christine Lepage
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Andrea Portt
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Charles Viau
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - France Daigle
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Samantha Gruenheid
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Hervé Le Moual
- Department of Microbiology and Immunology andFaculty of Dentistry, McGill University, Montreal, QC, H3A 2B4, Canada.Department of Microbiology and Immunology, University of Montreal, Montreal, QC, H3C 3J7, Canada
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The sensor kinase PhoQ mediates virulence in Pseudomonas aeruginosa. Microbiology (Reading) 2009; 155:699-711. [DOI: 10.1099/mic.0.024554-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous environmental Gram-negative bacterium that is also a major opportunistic human pathogen in nosocomial infections and cystic fibrosis chronic lung infections. PhoP-PhoQ is a two-component regulatory system that has been identified as essential for virulence and cationic antimicrobial peptide resistance in several other Gram-negative bacteria. This study demonstrated that mutation of phoQ caused reduced twitching motility, biofilm formation and rapid attachment to surfaces, 2.2-fold reduced cytotoxicity to human lung epithelial cells, substantially reduced lettuce leaf virulence, and a major, 10 000-fold reduction in competitiveness in chronic rat lung infections. Microarray analysis revealed that PhoQ controlled the expression of many genes consistent with these phenotypes and with its known role in polymyxin B resistance. It was also demonstrated that PhoQ controls the expression of many genes outside the known PhoP regulon.
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Transcription factor function and promoter architecture govern the evolution of bacterial regulons. Proc Natl Acad Sci U S A 2009; 106:4319-24. [PMID: 19251636 DOI: 10.1073/pnas.0810343106] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Evolutionary changes in ancestral regulatory circuits can bring about phenotypic differences between related organisms. Studies of regulatory circuits in eukaryotes suggest that these modifications result primarily from changes in cis-regulatory elements (as opposed to alterations in the transcription factors that act upon these sequences). It is presently unclear how the evolution of gene regulatory circuits has proceeded in bacteria, given the rampant effects of horizontal gene transfer, which has significantly altered the composition of bacterial regulons. We now demonstrate that the evolution of the regulons governed by the regulatory protein PhoP in the related human pathogens Salmonella enterica and Yersinia pestis has entailed functional changes in the PhoP protein as well as in the architecture of PhoP-dependent promoters. These changes have resulted in orthologous PhoP proteins that differ both in their ability to promote transcription and in their role as virulence regulators. We posit that these changes allow bacterial transcription factors to incorporate newly acquired genes into ancestral regulatory circuits and yet retain control of the core members of a regulon.
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The Salmonella pathogenicity island 2-encoded type III secretion system is essential for the survival of Salmonella enterica serovar Typhimurium in free-living amoebae. Appl Environ Microbiol 2009; 75:1793-5. [PMID: 19168655 DOI: 10.1128/aem.02033-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Free-living amoebae represent a potential reservoir and predator of Salmonella enterica. Through the use of type III secretion system (T3SS) mutants and analysis of transcription of selected T3SS genes, we demonstrated that the Salmonella pathogenicity island 2 is highly induced during S. enterica serovar Typhimurium infection of Acanthamoeba polyphaga and is essential for survival within amoebae.
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Bogel G, Schrempf H, Ortiz de Orué Lucana D. The heme-binding protein HbpS regulates the activity of the Streptomyces reticuli iron-sensing histidine kinase SenS in a redox-dependent manner. Amino Acids 2008; 37:681-91. [PMID: 18931968 DOI: 10.1007/s00726-008-0188-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 10/01/2008] [Indexed: 12/18/2022]
Abstract
The SenS/SenR system of Streptomyces reticuli regulates the expression of the redox regulator FurS, the catalase-peroxidase CpeB and the heme-binding protein HbpS. SenS/SenR is also proposed to participate in sensing redox changes, mediated by HbpS. Here, we show in vitro that heme-free HbpS represses the autokinase activity of SenS; whereas hemin-treated HbpS considerably enhances SenS autophosphorylation under redox conditions using either H(2)O(2) or DTT. The presence of iron ions alone or in combination with H(2)O(2) or DTT also leads to significantly increased phosphorylation levels of SenS. Further comparative physiological studies using the S. reticuli WT, a S. reticuli hbpS mutant and a S. reticuli senS-senR mutant corroborates the importance of HbpS and the SenS/SenR system for resistance against high concentrations of iron ions and hemin in vivo. Hence SenS/SenR and HbpS act in concert as a novel three-component system which detects redox stress, mediated by iron ions and heme.
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Affiliation(s)
- Gabriele Bogel
- FB Biologie/Chemie, Angewandte Genetik der Mikroorganismen, Universität Osnabrück, Barbarastr. 13, 49069, Osnabrück, Germany
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