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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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Krüger A, Frunzke J. A pseudokinase version of the histidine kinase ChrS promotes high heme tolerance of Corynebacterium glutamicum. Front Microbiol 2022; 13:997448. [PMID: 36160252 PMCID: PMC9491836 DOI: 10.3389/fmicb.2022.997448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
Heme is an essential cofactor for almost all living cells by acting as prosthetic group for various proteins or serving as alternative iron source. However, elevated levels are highly toxic for cells. Several corynebacterial species employ two paralogous, heme-responsive two-component systems (TCS), ChrSA and HrrSA, to cope with heme stress and to maintain intracellular heme homeostasis. Significant cross-talk at the level of phosphorylation between these systems was previously demonstrated. In this study, we have performed a laboratory evolution experiment to adapt Corynebacterium glutamicum to increasing heme levels. Isolated strains showed a highly increased tolerance to heme growing at concentrations of up to 100 μM. The strain featuring the highest heme tolerance harbored a frameshift mutation in the catalytical and ATPase-domain (CA-domain) of the chrS gene, converting it into a catalytically-inactive pseudokinase (ChrS_CA-fs). Reintroduction of the respective mutation in the parental C. glutamicum strain confirmed high heme tolerance and showed a drastic upregulation of hrtBA encoding a heme export system, conserved in Firmicutes and Actinobacteria. The strain encoding the ChrS pseudokinase variant showed significantly higher heme tolerance than a strain lacking chrS. Mutational analysis revealed that induction of hrtBA in the evolved strain is solely mediated via the cross-phosphorylation of the response regulator (RR) ChrA by the kinase HrrS and BACTH assays revealed the formation of heterodimers between HrrS and ChrS. Overall, our results emphasize an important role of the ChrS pseudokinase in high heme tolerance of the evolved C. glutamicum and demonstrate the promiscuity in heme-dependent signaling of the paralogous two-component systems facilitating fast adaptation to changing environmental conditions.
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Direct Inhibition of RetS Synthesis by RsmA Contributes to Homeostasis of the Pseudomonas aeruginosa Gac/Rsm Signaling System. J Bacteriol 2022; 204:e0058021. [PMID: 35041497 PMCID: PMC8923221 DOI: 10.1128/jb.00580-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gac/Rsm system is a global regulator of Pseudomonas aeruginosa gene expression. The primary effectors are RsmA and RsmF. Both are RNA-binding proteins that interact with target mRNAs to modulate protein synthesis. RsmA/RsmF recognize GGA sequences presented in the loop portion of stem-loop structures. For repressed targets, the GGA sites usually overlap the ribosome binding site (RBS) and RsmA/RsmF binding inhibits translation initiation. RsmA/RsmF activity is controlled by several small non-coding RNAs (sRNA) that sequester RsmA/RsmF from target mRNAs. The most important sequestering sRNAs are RsmY and RsmZ. Transcription of rsmY/rsmZ is directly controlled by the GacSA two-component regulatory system. GacSA activity is antagonized by RetS, a hybrid sensor kinase. In the absence of retS, rsmY/rsmZ transcription is derepressed and RsmA/RsmF are sequestered by RsmY/RsmZ. Gac/Rsm system homeostasis is tightly controlled by at least two mechanisms. First, direct binding of RsmA to the rsmA and rsmF mRNAs inhibits further synthesis of both proteins. Second, RsmA stimulates rsmY/rsmZ transcription through an undefined mechanism. In this study we demonstrate that RsmA stimulates rsmY/rsmZ transcription by directly inhibiting RetS synthesis. RetS protein levels are elevated 2.5-fold in an rsmA mutant. Epistasis experiments demonstrate that the rsmA requirement for rsmY/rsmZ transcription is entirely suppressed in an rsmA, retS double mutant. RsmA directly interacts with the retS mRNA and requires two distinct GGA sites, one of which overlaps the RBS. We propose a model wherein RsmA inhibits RetS synthesis to promote rsmY/rsmZ transcription and that this acts as a checkpoint to limit RsmA/RsmF availability. IMPORTANCE The Pseudomonas aeruginosa Gac/Rsm system controls ∼500 genes and governs a critical lifestyle switch by inversely regulating factors that favor acute or chronic colonization. Control of gene expression by the Gac/Rsm system is mediated through RsmA and RsmF, small RNA-binding proteins that interact with target mRNAs to inhibit or promote protein synthesis and/or mRNA stability. RsmA/RsmF activity is governed by two small non-coding RNAs (RsmY and RsmZ) that sequester RsmA/RsmF from target mRNAs. The GacSA two-component regulatory system plays a pivotal role in the Gac/Rsm system by controlling rsmYZ transcription. This study provides insight into the control of homeostasis by demonstrating that RsmA directly targets and inhibits expression of RetS, an orphan sensor kinase critical for rsmYZ transcription.
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Jing X, Hou Y, Hallett W, Sahajwalla CG, Ji P. Key Physicochemical Characteristics Influencing ADME Properties of Therapeutic Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:115-129. [PMID: 31482497 DOI: 10.1007/978-981-13-7709-9_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Therapeutic proteins are a rapidly growing class of drugs in clinical settings. The pharmacokinetics (PK) of therapeutic proteins relies on their absorption, distribution, metabolism, and excretion (ADME) properties. Moreover, the ADME properties of therapeutic proteins are impacted by their physicochemical characteristics. Comprehensive evaluation of these characteristics and their impact on ADME properties are critical to successful drug development. This chapter summarizes all relevant physicochemical characteristics and their effect on ADME properties of therapeutic proteins.
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Affiliation(s)
- Xing Jing
- U.S. Food and Drug Administration, Office of Clinical Pharmacology, DV II, Silver Spring, MD, USA.
| | - Yan Hou
- U.S. Food and Drug Administration, Office of Clinical Pharmacology, DV II, Silver Spring, MD, USA
| | - William Hallett
- U.S. Food and Drug Administration, Office of Clinical Pharmacology, DV II, Silver Spring, MD, USA
| | - Chandrahas G Sahajwalla
- U.S. Food and Drug Administration, Office of Clinical Pharmacology, DV II, Silver Spring, MD, USA
| | - Ping Ji
- U.S. Food and Drug Administration, Office of Clinical Pharmacology, DV II, Silver Spring, MD, USA
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Francis VI, Waters EM, Finton-James SE, Gori A, Kadioglu A, Brown AR, Porter SL. Multiple communication mechanisms between sensor kinases are crucial for virulence in Pseudomonas aeruginosa. Nat Commun 2018; 9:2219. [PMID: 29880803 PMCID: PMC5992135 DOI: 10.1038/s41467-018-04640-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
Bacteria and many non-metazoan Eukaryotes respond to stresses and threats using two-component systems (TCSs) comprising sensor kinases (SKs) and response regulators (RRs). Multikinase networks, where multiple SKs work together, detect and integrate different signals to control important lifestyle decisions such as sporulation and virulence. Here, we study interactions between two SKs from Pseudomonas aeruginosa, GacS and RetS, which control the switch between acute and chronic virulence. We demonstrate three mechanisms by which RetS attenuates GacS signalling: RetS takes phosphoryl groups from GacS-P; RetS has transmitter phosphatase activity against the receiver domain of GacS-P; and RetS inhibits GacS autophosphorylation. These mechanisms play important roles in vivo and during infection, and exemplify an unprecedented degree of signal processing by SKs that may be exploited in other multikinase networks.
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Affiliation(s)
- Vanessa I Francis
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Elaine M Waters
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Sutharsan E Finton-James
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Andrea Gori
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Alan R Brown
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Steven L Porter
- Biosciences, Geoffrey Pope Building, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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6
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Bhagirath AY, Pydi SP, Li Y, Lin C, Kong W, Chelikani P, Duan K. Characterization of the Direct Interaction between Hybrid Sensor Kinases PA1611 and RetS That Controls Biofilm Formation and the Type III Secretion System in Pseudomonas aeruginosa. ACS Infect Dis 2017; 3:162-175. [PMID: 27957853 DOI: 10.1021/acsinfecdis.6b00153] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the leading causes of morbidity and mortality in cystic fibrosis (CF) patients is pulmonary infection with Pseudomonas aeruginosa, and the pathophysiology of pulmonary infection in CF is affected by the lifestyle of this micro-organism. RetS-GacS/A-RsmA is a key regulatory pathway in P. aeruginosa that determines the bacterium's lifestyle choice. Previously, we identified PA1611, a hybrid sensor kinase, as a new player in this pathway that interacts with RetS and influences biofilm formation and type III secretion system. In this study, we explored the structural and mechanistic basis of the interaction between PA1611 and RetS. We identified the amino acid residues critical for PA1611-RetS interactions by molecular modeling. These residues were then targeted for site-directed mutagenesis. Amino acid substitutions were carried out at seven key positions in PA1611 and at six corresponding key positions in RetS. The influence of such substitutions in PA1611 on the interaction was analyzed by bacterial two-hybrid assays. We carried out functional analysis of these mutants in P. aeruginosa for their effect on specific phenotypes. Two residues, F269 and E276, located within the histidine kinase A and histidine kinase-like ATPase domains of PA1611 were found to play crucial roles in the PA1611-RetS interaction and had profound effects on phenotypes. Corresponding mutations in RetS demonstrated similar results. We further confirmed that these mutations in PA1611 function through the GacS/GacA-RsmY/Z signaling pathway. Collectively, our findings provide a noncognate sensor kinase direct interaction model for a signaling pathway, key for lifestyle selection in P. aeruginosa, and targeting such interaction may serve as a novel way of controlling infections with P. aeruginosa.
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Affiliation(s)
- Anjali Y. Bhagirath
- Department of Oral
Biology and Manitoba Chemosensory Biology Research Group, College
of Dentistry, Rady Faculty of Health Sciences, 780 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0W2, Canada
- Biology of Breathing
Group, Children’s Hospital Research Institute of Manitoba, 715 McDermot Avenue, Winnipeg, Manitoba R3E 3P4, Canada
| | - Sai P. Pydi
- Department of Oral
Biology and Manitoba Chemosensory Biology Research Group, College
of Dentistry, Rady Faculty of Health Sciences, 780 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0W2, Canada
| | - Yanqi Li
- Department of Oral
Biology and Manitoba Chemosensory Biology Research Group, College
of Dentistry, Rady Faculty of Health Sciences, 780 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0W2, Canada
- Biology of Breathing
Group, Children’s Hospital Research Institute of Manitoba, 715 McDermot Avenue, Winnipeg, Manitoba R3E 3P4, Canada
| | - Chen Lin
- Department of Oral
Biology and Manitoba Chemosensory Biology Research Group, College
of Dentistry, Rady Faculty of Health Sciences, 780 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0W2, Canada
| | - Weina Kong
- Department of Oral
Biology and Manitoba Chemosensory Biology Research Group, College
of Dentistry, Rady Faculty of Health Sciences, 780 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0W2, Canada
| | - Prashen Chelikani
- Department of Oral
Biology and Manitoba Chemosensory Biology Research Group, College
of Dentistry, Rady Faculty of Health Sciences, 780 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0W2, Canada
- Biology of Breathing
Group, Children’s Hospital Research Institute of Manitoba, 715 McDermot Avenue, Winnipeg, Manitoba R3E 3P4, Canada
| | - Kangmin Duan
- Department of Oral
Biology and Manitoba Chemosensory Biology Research Group, College
of Dentistry, Rady Faculty of Health Sciences, 780 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0W2, Canada
- Department of Medical
Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
- Biology of Breathing
Group, Children’s Hospital Research Institute of Manitoba, 715 McDermot Avenue, Winnipeg, Manitoba R3E 3P4, Canada
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7
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Willett JW, Crosson S. Atypical modes of bacterial histidine kinase signaling. Mol Microbiol 2016; 103:197-202. [PMID: 27618209 DOI: 10.1111/mmi.13525] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2016] [Indexed: 11/28/2022]
Abstract
The environment of a cell has a profound influence on its physiology, development and evolution. Accordingly, the capacity to sense and respond to physical and chemical signals in the environment is an important feature of cellular biology. In bacteria, environmental sensory perception is often regulated by two-component signal transduction systems (TCSTs). Canonical TCST entails signal-induced autophosphorylation of a sensor histidine kinase (HK) followed by phosphoryl transfer to a cognate response regulator (RR) protein, which may affect gene expression at multiple levels. Recent studies provide evidence for systems that do not adhere to this archetypal TCST signaling model. We present selected examples of atypical modes of signal transduction including inactivation of HK activity via homo- and hetero oligomerization, and cross-phosphorylation between HKs. These examples highlight mechanisms bacteria use to integrate environmental signals to control complex adaptive processes.
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Affiliation(s)
- Jonathan W Willett
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,Howard Taylor Ricketts Laboratory, University of Chicago, Argonne National Laboratory, Argonne, IL, USA
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,Howard Taylor Ricketts Laboratory, University of Chicago, Argonne National Laboratory, Argonne, IL, USA.,Department of Microbiology, University of Chicago, Chicago, IL, USA
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8
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Raran-Kurussi S, Waugh DS. A dual protease approach for expression and affinity purification of recombinant proteins. Anal Biochem 2016; 504:30-7. [PMID: 27105777 PMCID: PMC4877217 DOI: 10.1016/j.ab.2016.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/01/2016] [Accepted: 04/07/2016] [Indexed: 11/29/2022]
Abstract
We describe a new method for affinity purification of recombinant proteins using a dual protease protocol. Escherichia coli maltose binding protein (MBP) is employed as an N-terminal tag to increase the yield and solubility of its fusion partners. The MBP moiety is then removed by rhinovirus 3C protease, prior to purification, to yield an N-terminally His6-tagged protein. Proteins that are only temporarily rendered soluble by fusing them to MBP are readily identified at this stage because they will precipitate after the MBP tag is removed by 3C protease. The remaining soluble His6-tagged protein, if any, is subsequently purified by immobilized metal affinity chromatography (IMAC). Finally, the N-terminal His6 tag is removed by His6-tagged tobacco etch virus (TEV) protease to yield the native recombinant protein, and the His6-tagged contaminants are removed by adsorption during a second round of IMAC, leaving only the untagged recombinant protein in the column effluent. The generic strategy described here saves time and effort by removing insoluble aggregates at an early stage in the process while also reducing the tendency of MBP to "stick" to its fusion partners during affinity purification.
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Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David S Waugh
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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9
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LeRoux M, Kirkpatrick RL, Montauti EI, Tran BQ, Peterson SB, Harding BN, Whitney JC, Russell AB, Traxler B, Goo YA, Goodlett DR, Wiggins PA, Mougous JD. Kin cell lysis is a danger signal that activates antibacterial pathways of Pseudomonas aeruginosa. eLife 2015; 4. [PMID: 25643398 PMCID: PMC4348357 DOI: 10.7554/elife.05701] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/30/2015] [Indexed: 12/21/2022] Open
Abstract
The perception and response to cellular death is an important aspect of multicellular eukaryotic life. For example, damage-associated molecular patterns activate an inflammatory cascade that leads to removal of cellular debris and promotion of healing. We demonstrate that lysis of Pseudomonas aeruginosa cells triggers a program in the remaining population that confers fitness in interspecies co-culture. We find that this program, termed P. aeruginosa response to antagonism (PARA), involves rapid deployment of antibacterial factors and is mediated by the Gac/Rsm global regulatory pathway. Type VI secretion, and, unexpectedly, conjugative type IV secretion within competing bacteria, induce P. aeruginosa lysis and activate PARA, thus providing a mechanism for the enhanced capacity of P. aeruginosa to target bacteria that elaborate these factors. Our finding that bacteria sense damaged kin and respond via a widely distributed pathway to mount a complex response raises the possibility that danger sensing is an evolutionarily conserved process. DOI:http://dx.doi.org/10.7554/eLife.05701.001 Bacteria live in diverse and changing environments where resources such as nutrients and space are often limited. They have thus evolved many survival strategies, including competitive and cooperative behaviors. In the first case, bacteria antagonize or prevent the growth of other microorganisms competing with them for resources, such as by generating antibiotics that specifically target rivals. During cooperation, bacteria may coordinate the production of compounds that have a shared benefit for members of their community. In multicellular organisms, some cell types sense harmful microorganisms by the injury they cause in neighboring cells. This triggers a process that can lead to the production of molecules that kill the invaders and factors that promote the repair of cellular damage. An equivalent process has so far not been described for single-celled organisms such as bacteria. However, bacteria often live in structured groups containing many different species. In this type of growth environment, the ability of bacteria to sense when others of their species are attacked and to respond by taking measures to defend themselves could improve their chances of survival. Now, LeRoux et al. reveal that the bacterium Pseudomonas aeruginosa is able to detect ‘danger signals’ released when neighboring P. aeruginosa cells are killed by other bacteria. These signals trigger a response in surviving cells by turning on a pathway that controls a number of antibacterial factors. These include the production of the so-called ‘type VI secretion system’, a molecular machine that delivers a potent cocktail of antibacterial toxins directly into nearby bacteria. This process, which LeRoux et al. have named ‘P. aeruginosa response to antagonism’, or PARA for short, enables P. aeruginosa to thrive when grown with competing bacterial species. P. aeruginosa is notorious for infecting the lungs of people with the genetic disease cystic fibrosis, as well as chronic wounds often found in people with diabetes. In both cases, when P. aeruginosa is present, the numbers of other, often less harmful organisms, tend to decrease. PARA may be one reason for the success of P. aeruginosa in these multi-species infections. DOI:http://dx.doi.org/10.7554/eLife.05701.002
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Affiliation(s)
- Michele LeRoux
- Department of Microbiology, University of Washington, Seattle, United States
| | - Robin L Kirkpatrick
- Department of Microbiology, University of Washington, Seattle, United States
| | - Elena I Montauti
- Department of Microbiology, University of Washington, Seattle, United States
| | - Bao Q Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, United States
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, United States
| | - Brittany N Harding
- Department of Microbiology, University of Washington, Seattle, United States
| | - John C Whitney
- Department of Microbiology, University of Washington, Seattle, United States
| | - Alistair B Russell
- Department of Microbiology, University of Washington, Seattle, United States
| | - Beth Traxler
- Department of Microbiology, University of Washington, Seattle, United States
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, United States
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, United States
| | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, United States
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, United States
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10
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The diguanylate cyclase SadC is a central player in Gac/Rsm-mediated biofilm formation in Pseudomonas aeruginosa. J Bacteriol 2014; 196:4081-8. [PMID: 25225264 PMCID: PMC4248864 DOI: 10.1128/jb.01850-14] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen and a threat for immunocompromised and cystic fibrosis patients. It is responsible for acute and chronic infections and can switch between these lifestyles upon taking an informed decision involving complex regulatory networks. The RetS/LadS/Gac/Rsm network and the cyclic-di-GMP (c-di-GMP) signaling pathways are both central to this phenomenon redirecting the P. aeruginosa population toward a biofilm mode of growth, which is associated with chronic infections. While these two pathways were traditionally studied independently from each other, we recently showed that cellular levels of c-di-GMP are increased in the hyperbiofilm retS mutant. Here, we have formally established the link between the two networks by showing that the SadC diguanylate cyclase is central to the Gac/Rsm-associated phenotypes, notably, biofilm formation. Importantly, SadC is involved in the signaling that converges onto the RsmA translational repressor either via RetS/LadS or via HptB/HsbR. Although the level of expression of the sadC gene does not seem to be impacted by the regulatory cascade, the production of the SadC protein is tightly repressed by RsmA. This adds to the growing complexity of the signaling network associated with c-di-GMP in P. aeruginosa. While this organism possesses more than 40 c-di-GMP-related enzymes, it remains unclear how signaling specificity is maintained within the c-di-GMP network. The finding that SadC but no other diguanylate cyclase is related to the formation of biofilm governed by the Gac/Rsm pathway further contributes to understanding of this insulation mechanism.
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11
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Zhang Z, Liu Q, Hendrickson WA. Crystal structures of apparent saccharide sensors from histidine kinase receptors prevalent in a human gut symbiont. FEBS J 2014; 281:4263-79. [PMID: 24995510 DOI: 10.1111/febs.12904] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/19/2014] [Accepted: 06/24/2014] [Indexed: 12/14/2022]
Abstract
UNLABELLED The adult human gut is a complicated ecosystem in which host-bacterium symbiosis plays an important role. Bacteroides thetaiotaomicron is a predominant member of the gut microflora, providing the human digestive tract with a large number of glycolytic enzymes. Expression of many of these enzymes appears to be controlled by histidine kinase receptors that are fused into unusual hybrid two-component systems that share homologous periplasmic sensor domains. These sensor domains belong to the third most populated (HK3) family based on a previous unpublished bioinformatics analysis of predicted histidine kinase sensors. Here, we present the crystal structures of two sensor domains representative of the HK3 family. Each sensor is folded into three domains: two-seven-bladed β-propeller domains and one β-sandwich domain. Both sensors form dimers in crystals, and one sensor appears to be physiologically relevant. The folding characteristics in the individual domains, the domain organization, and the oligomeric architecture are all unique to HK3 sensors. Sequence analysis of the HK3 sensors indicates that these sensor domains are shared among other signaling molecules, implying combinatorial molecular evolution. DATABASE The structural data for the crystallographic results for HK3 BT4673S and HK3 BT3049S have been deposited in the Protein Data Bank under accession numbers 3OTT and 3V9F, respectively. STRUCTURED DIGITAL ABSTRACT HK3BT3049S and HK3BT3049S bind by x-ray crystallography (View interaction) HK3BT3049S and HK3BT3049S bind by molecular sieving (View interaction) HK3BT3049S and HK3BT3049S bind by cosedimentation through density gradient (View interaction) HK3BT4673s and HK3BT4673s bind by cosedimentation through density gradient (View interaction) HK3BT4673s and HK3BT4673s bind by molecular sieving (View interaction).
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Affiliation(s)
- Zhen Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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12
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Jones C, Allsopp L, Horlick J, Kulasekara H, Filloux A. Subinhibitory concentration of kanamycin induces the Pseudomonas aeruginosa type VI secretion system. PLoS One 2013; 8:e81132. [PMID: 24260549 PMCID: PMC3832665 DOI: 10.1371/journal.pone.0081132] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/09/2013] [Indexed: 01/01/2023] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium found in natural environments including plants, soils and warm moist surfaces. This organism is also in the top ten of nosocomial pathogens, and prevalent in cystic fibrosis (CF) lung infections. The ability of P. aeruginosa to colonize a wide variety of environments in a lasting manner is associated with the formation of a resistant biofilm and the capacity to efficiently outcompete other microorganisms. Here we demonstrate that sub-inhibitory concentration of kanamycin not only induces biofilm formation but also induces expression of the type VI secretion genes in the H1-T6SS cluster. The H1-T6SS is known for its role in toxin production and bacterial competition. We show that the antibiotic induction of the H1-T6SS only occurs when a functional Gac/Rsm pathway is present. These observations may contribute to understand how P. aeruginosa responds to antibiotic producing competitors. It also suggests that improper antibiotic therapy may enhance P. aeruginosa colonization, including in the airways of CF patients.
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Affiliation(s)
- Cerith Jones
- MRC-Centre for Molecular Bacteriology and Infection (CBMI), Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Luke Allsopp
- MRC-Centre for Molecular Bacteriology and Infection (CBMI), Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jack Horlick
- MRC-Centre for Molecular Bacteriology and Infection (CBMI), Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hemantha Kulasekara
- Departments of Genome Sciences, Medicine, and Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Alain Filloux
- MRC-Centre for Molecular Bacteriology and Infection (CBMI), Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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13
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Structural characterization of the predominant family of histidine kinase sensor domains. J Mol Biol 2010; 400:335-53. [PMID: 20435045 DOI: 10.1016/j.jmb.2010.04.049] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 04/22/2010] [Accepted: 04/24/2010] [Indexed: 02/01/2023]
Abstract
Histidine kinase (HK) receptors are used ubiquitously by bacteria to monitor environmental changes, and they are also prevalent in plants, fungi, and other protists. Typical HK receptors have an extracellular sensor portion that detects a signal, usually a chemical ligand, and an intracellular transmitter portion that includes both the kinase domain itself and the site for histidine phosphorylation. While kinase domains are highly conserved, sensor domains are diverse. HK receptors function as dimers, but the molecular mechanism for signal transduction across cell membranes remains obscure. In this study, eight crystal structures were determined from five sensor domains representative of the most populated family, family HK1, found in a bioinformatic analysis of predicted sensor domains from transmembrane HKs. Each structure contains an inserted repeat of PhoQ/DcuS/CitA (PDC) domains, and similarity between sequence and structure is correlated across these and other double-PDC sensor proteins. Three of the five sensors crystallize as dimers that appear to be physiologically relevant, and comparisons between ligated structures and apo-state structures provide insights into signal transmission. Some HK1 family proteins prove to be sensors for chemotaxis proteins or diguanylate cyclase receptors, implying a combinatorial molecular evolution.
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