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Pollock AJ, Zaver SA, Woodward JJ. A STING-based biosensor affords broad cyclic dinucleotide detection within single living eukaryotic cells. Nat Commun 2020; 11:3533. [PMID: 32669552 PMCID: PMC7363834 DOI: 10.1038/s41467-020-17228-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Cyclic dinucleotides (CDNs) are second messengers conserved across all three domains of life. Within eukaryotes they mediate protective roles in innate immunity against malignant, viral, and bacterial disease, and exert pathological effects in autoimmune disorders. Despite their ubiquitous role in diverse biological contexts, CDN detection methods are limited. Here, using structure guided design of the murine STING CDN binding domain, we engineer a Förster resonance energy transfer (FRET) based biosensor deemed BioSTING. Recombinant BioSTING affords real-time detection of CDN synthase activity and inhibition. Expression of BioSTING in live human cells allows quantification of localized bacterial and eukaryotic CDN levels in single cells with low nanomolar sensitivity. These findings establish BioSTING as a powerful kinetic in vitro platform amenable to high throughput screens and as a broadly applicable cellular tool to interrogate the temporal and spatial dynamics of CDN signaling in a variety of infectious, malignant, and autoimmune contexts.
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Affiliation(s)
- Alex J Pollock
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Shivam A Zaver
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
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52
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Duvall SW, Childers WS. Design of a Histidine Kinase FRET Sensor to Detect Complex Signal Integration within Living Bacteria. ACS Sens 2020; 5:1589-1596. [PMID: 32495620 DOI: 10.1021/acssensors.0c00008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Histidine kinases (HK) switch between conformational states that promote kinase and phosphatase activities to regulate diverse cellular processes. Past studies have shown that these functional states can display heterogeneity between cells in microbial communities and can vary at the subcellular level. Methods to track and correlate the kinase conformational state with the phenotypic response of living bacteria cells will offer new opportunities to interrogate bacterial signaling mechanisms. As a proof of principle, we incorporated both mClover3 (donor) and mRuby3 (acceptor) fluorescent proteins into the Caulobacter crescentus cell-cycle HK CckA as an in vivo fluorescence resonance energy transfer (FRET) sensor to detect these structural changes. Our engineered FRET sensor was responsive to CckA-specific input signals and detected subcellular changes in CckA signal integration that occurs as cells develop. We demonstrated the potential of using the CckA FRET sensor as an in vivo screening tool for HK inhibitors. In summary, we have developed a new HK FRET sensor design strategy that can be adopted to monitor in vivo changes for interrogation of a broad range of signaling mechanisms in living bacteria.
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Affiliation(s)
- Samuel W. Duvall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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53
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Petchiappan A, Naik SY, Chatterji D. Tracking the homeostasis of second messenger cyclic-di-GMP in bacteria. Biophys Rev 2020; 12:719-730. [PMID: 32060735 PMCID: PMC7311556 DOI: 10.1007/s12551-020-00636-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is an important second messenger in bacteria which regulates the bacterial transition from motile to sessile phase and also plays a major role in processes such as cell division, exopolysaccharide synthesis, and biofilm formation. Due to its crucial role in dictating the bacterial phenotype, the synthesis and hydrolysis of c-di-GMP is tightly regulated via multiple mechanisms. Perturbing the c-di-GMP homeostasis affects bacterial growth and survival, so it is necessary to understand the underlying mechanisms related to c-di-GMP metabolism. Most techniques used for estimating the c-di-GMP concentration lack single-cell resolution and do not provide information about any heterogeneous distribution of c-di-GMP inside cells. In this review, we briefly discuss how the activity of c-di-GMP metabolising enzymes, particularly bifunctional proteins, is modulated to maintain c-di-GMP homeostasis. We further highlight how fluorescence-based methods aid in understanding the spatiotemporal regulation of c-di-GMP signalling. Finally, we discuss the blind spots in our understanding of second messenger signalling and outline how they can be addressed in the future.
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Affiliation(s)
| | - Sujay Y Naik
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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54
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Liu C, Sun D, Zhu J, Liu J, Liu W. The Regulation of Bacterial Biofilm Formation by cAMP-CRP: A Mini-Review. Front Microbiol 2020; 11:802. [PMID: 32528421 PMCID: PMC7247823 DOI: 10.3389/fmicb.2020.00802] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/03/2020] [Indexed: 12/30/2022] Open
Abstract
Biofilms are communities of microorganisms that live in a self-produced extracellular matrix in order to survive in hostile environments. Second messengers, such as c-di-GMP and cAMP, participate in the regulation of biofilm formation. c-di-GMP is a major molecule that is involved in modulating the bacterial transition between a planktonic lifestyle and biofilm formation. Aside from regulating carbon catabolism repression in most bacteria, cAMP has also been found to mediate biofilm formation in many bacteria. Although the underlying mechanisms of biofilm formation mediated by cAMP-CRP have been well-investigated in several bacteria, the regulatory pathways of cAMP-CRP are still poorly understood compared to those of c-di-GMP. Moreover, some bacteria appear to form biofilm in response to changes in carbon source type or concentration. However, the relationship between the carbon metabolisms and biofilm formation remains unclear. This mini-review provides an overview of the cAMP-CRP-regulated pathways involved in biofilm formation in some bacteria. This information will benefit future investigations of the underlying mechanisms that connect between biofilm formation with nutrient metabolism, as well as the cross-regulation between multiple second messengers.
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Affiliation(s)
- Cong Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Di Sun
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jiawen Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Weijie Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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55
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Del Medico L, Cerletti D, Schächle P, Christen M, Christen B. The type IV pilin PilA couples surface attachment and cell-cycle initiation in Caulobacter crescentus. Proc Natl Acad Sci U S A 2020; 117:9546-9553. [PMID: 32295877 PMCID: PMC7196804 DOI: 10.1073/pnas.1920143117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding how bacteria colonize surfaces and regulate cell-cycle progression in response to cellular adhesion is of fundamental importance. Here, we use transposon sequencing in conjunction with fluorescence resonance energy transfer (FRET) microscopy to uncover the molecular mechanism for how surface sensing drives cell-cycle initiation in Caulobacter crescentus We identify the type IV pilin protein PilA as the primary signaling input that couples surface contact to cell-cycle initiation via the second messenger cyclic di-GMP (c-di-GMP). Upon retraction of pili filaments, the monomeric pilin reservoir in the inner membrane is sensed by the 17-amino acid transmembrane helix of PilA to activate the PleC-PleD two-component signaling system, increase cellular c-di-GMP levels, and signal the onset of the cell cycle. We termed the PilA signaling sequence CIP for "cell-cycle initiating pilin" peptide. Addition of the chemically synthesized CIP peptide initiates cell-cycle progression and simultaneously inhibits surface attachment. The broad conservation of the type IV pili and their importance in pathogens for host colonization suggests that CIP peptide mimetics offer strategies to inhibit surface sensing, prevent biofilm formation and control persistent infections.
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Affiliation(s)
- Luca Del Medico
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Dario Cerletti
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Philipp Schächle
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Beat Christen
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
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56
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Cho KH, Tryon RG, Kim JH. Screening for Diguanylate Cyclase (DGC) Inhibitors Mitigating Bacterial Biofilm Formation. Front Chem 2020. [DOI: 10.3389/fchem.2020.00264 [doi link]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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57
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Cho KH, Tryon RG, Kim JH. Screening for Diguanylate Cyclase (DGC) Inhibitors Mitigating Bacterial Biofilm Formation. Front Chem 2020; 8:264. [PMID: 32373581 PMCID: PMC7186502 DOI: 10.3389/fchem.2020.00264] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/18/2020] [Indexed: 01/08/2023] Open
Abstract
The majority of bacteria in the natural environment organize themselves into communal biofilms. Biofilm formation benefits bacteria conferring resistance to harmful molecules (e.g., antibiotics, disinfectants, and host immune factors) and coordinating their gene expression through quorum sensing (QS). A primary signaling molecule promoting bacterial biofilm formation is the universal second messenger cyclic di-GMP. This dinucleotide predominantly controls the gene expression of motility, adhesins, and capsule production to coordinate biofilm formation. Cyclic di-GMP is synthesized by diguanylate cyclases (DGCs) that have a GGDEF domain and is degraded by phosphodiesterases (PDEs) containing either an EAL or an HD-GYP domain. Since high cellular c-di-GMP concentrations are correlated with promoting the ability of bacteria to form biofilms, numerous research endeavors to identify chemicals capable of inhibiting the c-di-GMP synthesis activity of DGCs have been performed in order to inhibit bacterial biofilm formation. This review describes currently identified chemical inhibitors that disturb the activity of DGCs and the methods of screening and assay for their discovery.
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Affiliation(s)
- Kyu Hong Cho
- Department of Biology, Indiana State University, Terre Haute, IN, United States
| | - R Grant Tryon
- Department of Biology, Indiana State University, Terre Haute, IN, United States
| | - Jeong-Ho Kim
- Department of Biology and Chemistry, Liberty University, Lynchburg, VA, United States
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58
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Dippel AB, Anderson WA, Park JH, Yildiz FH, Hammond MC. Development of Ratiometric Bioluminescent Sensors for in Vivo Detection of Bacterial Signaling. ACS Chem Biol 2020; 15:904-914. [PMID: 32186367 DOI: 10.1021/acschembio.9b00800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Second messenger signaling networks allow cells to sense and adapt to changing environmental conditions. In bacteria, the nearly ubiquitous second messenger molecule cyclic di-GMP coordinates diverse processes such as motility, biofilm formation, and virulence. In bacterial pathogens, these signaling networks allow the bacteria to survive changing environmental conditions that are experienced during infection of a mammalian host. While studies have examined the effects of cyclic di-GMP levels on virulence in these pathogens, it has not been possible to visualize cyclic di-GMP levels in real time during the stages of host infection. Toward this goal, we generate the first ratiometric, chemiluminescent biosensor scaffold that selectively responds to c-di-GMP. By engineering the biosensor scaffold, a suite of Venus-YcgR-NLuc (VYN) biosensors is generated that provide extremely high sensitivity (KD < 300 pM) and large changes in the bioluminescence resonance energy transfer (BRET) signal (up to 109%). As a proof-of-concept that VYN biosensors can image cyclic di-GMP in tissues, we show that the VYN biosensors function in the context of a tissue phantom model, with only ∼103-104 biosensor-expressing E. coli cells required for the measurement. Furthermore, we utilize the biosensor in vitro to assess changes in cyclic di-GMP in V. cholerae grown with different inputs found in the host environment. The VYN sensors developed here can serve as robust in vitro diagnostic tools for high throughput screening, as well as genetically encodable tools for monitoring the dynamics of c-di-GMP in live cells, and lay the groundwork for live cell imaging of c-di-GMP dynamics in bacteria within tissues and other complex environments.
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Affiliation(s)
- Andrew B. Dippel
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Wyatt A. Anderson
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jin Hwan Park
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Ming C. Hammond
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
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59
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Edwards-Gayle CC, Barrett G, Roy S, Castelletto V, Seitsonen J, Ruokolainen J, Hamley IW. Selective Antibacterial Activity and Lipid Membrane Interactions of Arginine-Rich Amphiphilic Peptides. ACS APPLIED BIO MATERIALS 2020; 3:1165-1175. [PMID: 32296775 PMCID: PMC7147261 DOI: 10.1021/acsabm.9b00894] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/21/2020] [Indexed: 12/22/2022]
Abstract
The self-assembly behavior and antimicrobial activity of two designed amphiphilic peptides, R3F3 and R4F4, containing short hydrophobic phenylalanine (F) and cationic arginine (R) sequences, are investigated. The conformation of the peptides was examined using circular dichroism and FTIR spectroscopy, which show that they have a disordered secondary structure. Concentration-dependent fluorescence assays show the presence of a critical aggregation concentration (cac) for each peptide. Above the cac, small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) reveal a population of twisted tapes for R3F3 and nanosheets for R4F4. The interaction of the peptides with model bacterial membranes comprising mixtures of the lipids DPPG [1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol] and DPPE [1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine], was studied using SAXS and cryogenic-TEM. Analysis of the SAXS structure factor indicates that R3F3 interacts with lipid bilayers by inducing correlation between bilayers, whereas R4F4 interacts with the bilayers causing an increase in polydispersity of the vesicle wall thickness. Both peptides break vesicles with a 1:3 DPPG:DPPE composition, which is close to the ratio of PG and PE lipids observed in the lipid membrane of Pseudomonas aeruginosa, a pathogen responsible for serious infections and which has developed antimicrobial resistant strains. Both peptides show activity against this bacterium in planktonic form. Peptide R4F4 shows particularly strong bioactivity against this microbe, with a minimum inhibitory concentration (MIC) value in the range of concentrations where the peptide is cytocompatible. It was further shown to have activity against other Pseudomonas species including the common plant pathogen Pseudomonas syringae. Finally, we show that R4F4 inhibits the development of P. aeruginosa biofilms. This was examined in detail and a proposed mechanism involving binding of the signaling molecule c-di-GMP is suggested, based on circular dichroism spectroscopy studies and Congo red assays of extracellular polysaccharides produced by the stressed bacteria. Thus, R4F4 is a promising candidate antimicrobial peptide with activity against Pseudomonas species.
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Affiliation(s)
| | - Glyn Barrett
- School
of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Shyamali Roy
- School
of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Valeria Castelletto
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Jani Seitsonen
- Nanomicroscopy
Center, Aalto University, Puumiehenkuja 2, FIN-02150 Espoo, Finland
| | - Janne Ruokolainen
- Nanomicroscopy
Center, Aalto University, Puumiehenkuja 2, FIN-02150 Espoo, Finland
| | - Ian W. Hamley
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
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60
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Precise timing of transcription by c-di-GMP coordinates cell cycle and morphogenesis in Caulobacter. Nat Commun 2020; 11:816. [PMID: 32041947 PMCID: PMC7010744 DOI: 10.1038/s41467-020-14585-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/13/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria adapt their growth rate to their metabolic status and environmental conditions by modulating the length of their G1 period. Here we demonstrate that a gradual increase in the concentration of the second messenger c-di-GMP determines precise gene expression during G1/S transition in Caulobacter crescentus. We show that c-di-GMP stimulates the kinase ShkA by binding to its central pseudo-receiver domain, activates the TacA transcription factor, and initiates a G1/S-specific transcription program leading to cell morphogenesis and S-phase entry. Activation of the ShkA-dependent genetic program causes c-di-GMP to reach peak levels, which triggers S-phase entry and promotes proteolysis of ShkA and TacA. Thus, a gradual increase of c-di-GMP results in precise control of ShkA-TacA activity, enabling G1/S-specific gene expression that coordinates cell cycle and morphogenesis. Bacteria adapt their growth rate to their metabolic status and environmental conditions by modulating the length of their G1 period. Here the authors show that an increase in c-di-GMP concentration modulates the activity of kinase ShkA and transcription factor TacA, thus enabling G1/S transition in Caulobacter.
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61
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Hartl J, Kiefer P, Kaczmarczyk A, Mittelviefhaus M, Meyer F, Vonderach T, Hattendorf B, Jenal U, Vorholt JA. Untargeted metabolomics links glutathione to bacterial cell cycle progression. Nat Metab 2020; 2:153-166. [PMID: 32090198 PMCID: PMC7035108 DOI: 10.1038/s42255-019-0166-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
Abstract
Cell cycle progression requires the coordination of cell growth, chromosome replication, and division. Consequently, a functional cell cycle must be coupled with metabolism. However, direct measurements of metabolome dynamics remained scarce, in particular in bacteria. Here, we describe an untargeted metabolomics approach with synchronized Caulobacter crescentus cells to monitor the relative abundance changes of ~400 putative metabolites as a function of the cell cycle. While the majority of metabolite pools remains homeostatic, ~14% respond to cell cycle progression. In particular, sulfur metabolism is redirected during the G1-S transition, and glutathione levels periodically change over the cell cycle with a peak in late S phase. A lack of glutathione perturbs cell size by uncoupling cell growth and division through dysregulation of KefB, a K+/H+ antiporter. Overall, we here describe the impact of the C. crescentus cell cycle progression on metabolism, and in turn relate glutathione and potassium homeostasis to timely cell division.
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Affiliation(s)
- Johannes Hartl
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland.
| | - Patrick Kiefer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | | | | | - Fabian Meyer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | - Thomas Vonderach
- ETH Zurich, Laboratory of Inorganic Chemistry, Zurich, Switzerland
| | - Bodo Hattendorf
- ETH Zurich, Laboratory of Inorganic Chemistry, Zurich, Switzerland
| | - Urs Jenal
- Biozentrum of the University of Basel, Basel, Switzerland
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62
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Structural Conservation and Diversity of PilZ-Related Domains. J Bacteriol 2020; 202:JB.00664-19. [PMID: 31740493 DOI: 10.1128/jb.00664-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/12/2019] [Indexed: 01/13/2023] Open
Abstract
The widespread bacterial second messenger cyclic diguanylate (c-di-GMP) regulates a variety of processes, including protein secretion, motility, cell development, and biofilm formation. c-di-GMP-dependent responses are often mediated by its binding to the cytoplasmic receptors that contain the PilZ domain. Here, we present comparative structural and sequence analysis of various PilZ-related domains and describe three principal types of them: (i) the canonical PilZ domain, whose structure includes a six-stranded beta-barrel and a C-terminal alpha helix, (ii) an atypical PilZ domain that contains two extra alpha helices and forms stable tetramers, and (iii) divergent PilZ-related domains, which include the eponymous PilZ protein and PilZN (YcgR_N) and PilZNR (YcgR_2) domains. We refine the second c-di-GMP binding motif of PilZ as [D/N]hSXXG and show that the hydrophobic residue h of this motif interacts with a cluster of conserved hydrophobic residues, helping maintain the PilZ domain fold. We describe several novel PilZN-type domains that are fused to the canonical PilZ domains in specific taxa, such as spirochetes, actinobacteria, aquificae, cellulose-degrading clostridia, and deltaproteobacteria. We propose that the evolution of the three major groups of PilZ domains included (i) fusion of pilZ with other genes, which produced Alg44, cellulose synthase, and other multidomain proteins; (ii) insertion of an ∼200-bp fragment, which resulted in the formation of tetramer-forming PilZ proteins; and (iii) tandem duplication of pilZ genes, which led to the formation of PilZ dimers and YcgR-like proteins.IMPORTANCE c-di-GMP is a ubiquitous bacterial second messenger that regulates motility, biofilm formation, and virulence of many bacterial pathogens. The PilZ domain is a widespread c-di-GMP receptor that binds c-di-GMP through its RXXXR and [D/N]hSXXG motifs; some PilZ domains lack these motifs and are unable to bind c-di-GMP. We used structural and sequence analysis to assess the diversity of PilZ-related domains and define their common features. We show that the hydrophobic residue h in the second position of the second motif is highly conserved; it may serve as a readout for c-di-GMP binding. We describe three principal classes of PilZ-related domains, canonical, tetramer-forming, and divergent PilZ domains, and propose the evolutionary pathways that led to the emergence of these PilZ types.
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63
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Abstract
Small-molecule metabolites regulate many cellular processes but are often present at low concentrations, confounding studies of their signaling networks. In this issue of Cell Chemical Biology, You et al. (2019) describe RNA "integrators" that measure the concentrations of metabolites in live cells to enable in-depth studies of signaling pathways.
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64
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Wang ZQ, Xuan TF, Liu J, Chen WM, Lin J. A fluorescence-based high-throughput screening method for determining the activity of diguanylate cyclases and c-di-GMP phosphodiesterases. RSC Adv 2020; 10:19482-19489. [PMID: 35515470 PMCID: PMC9054106 DOI: 10.1039/d0ra02540b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/08/2020] [Indexed: 12/31/2022] Open
Abstract
The dinucleotide 3′,5′-cyclic diguanylic acid (c-di-GMP) is a critical second messenger found in bacteria. High cellular levels of c-di-GMP are associated with a sessile, biofilm lifestyle in many bacteria, which is associated with more than 70% of clinically resistant infections. Cellular c-di-GMP concentrations are regulated by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), which are responsible for the production and degradation, respectively, of c-di-GMP. Therefore, DGCs and PDEs might be attractive drug targets for controlling biofilm formation. In this study, a simple and universal high-throughput method based on a c-di-GMP-specific fluorescent probe for the determination of DGC and PDE activity was described. By using the proposed method, the c-di-GMP content in samples was rapidly quantified by measuring the fluorescence intensity in a 96-well plate by using a microplate reader. In addition, the probe molecule A18 directly interacted with the substrate c-di-GMP, and the method was not limited by the structure of enzymes. The dinucleotide 3′,5′-cyclic diguanylic acid (c-di-GMP) is a critical second messenger found in bacteria.![]()
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Affiliation(s)
- Zi-Qiang Wang
- College of Pharmacy
- Jinan University
- Guangzhou 510632
- P. R. China
| | - Teng-Fei Xuan
- College of Pharmacy
- Jinan University
- Guangzhou 510632
- P. R. China
| | - Jun Liu
- College of Pharmacy
- Jinan University
- Guangzhou 510632
- P. R. China
| | - Wei-Min Chen
- College of Pharmacy
- Jinan University
- Guangzhou 510632
- P. R. China
| | - Jing Lin
- College of Pharmacy
- Jinan University
- Guangzhou 510632
- P. R. China
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65
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Castelletto V, Edwards-Gayle CJC, Hamley IW, Barrett G, Seitsonen J, Ruokolainen J, de Mello LR, da Silva ER. Model self-assembling arginine-based tripeptides show selective activity against Pseudomonas bacteria. Chem Commun (Camb) 2020; 56:615-618. [DOI: 10.1039/c9cc07257h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Three model arginine-rich tripeptides RXR (X = W, F or non-natural residue 2-napthylalanine) were investigated as antimicrobial agents, with a specific focus to target Pseudomonas aeruginosa through membrane lysis.
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Affiliation(s)
| | | | - Ian W. Hamley
- Department of Chemistry
- University of Reading
- Reading RG6 6AD
- UK
| | - Glyn Barrett
- School of Biological Sciences
- University of Reading
- Reading RG6 6UR
- UK
| | - Jani Seitsonen
- Nanomicroscopy Center
- Aalto University
- FIN-02150 Espoo
- Finland
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66
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Jin Y, Zheng H, Ibanez ACS, Patil PD, Lv S, Luo M, Duncan TM, Luk YY. Cell-Wall-Targeting Antibiotics Cause Lag-Phase Bacteria to Form Surface-Mediated Filaments Promoting the Formation of Biofilms and Aggregates. Chembiochem 2019; 21:825-835. [PMID: 31553819 DOI: 10.1002/cbic.201900508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Indexed: 01/01/2023]
Abstract
Antibiotics are known to promote bacterial formation of enhanced biofilms, the mechanism of which is not well understood. Here, using biolayer interferometry, we have shown that bacterial cultures containing antibiotics that target cell walls cause biomass deposition on surfaces over time with a linear profile rather than the Langmuir-like profiles exhibited by bacterial adherence in the absence of antibiotics. We observed about three times the initial rate and 12 times the final biomass deposition on surfaces for cultures containing carbenicillin than without. Unexpectedly, in the presence of antibiotics, the rate of biomass deposition inversely correlated with bacterial densities from different stages of a culture. Detailed studies revealed that carbenicillin caused faster growth of filaments that were seeded on surfaces from young bacteria (from lag phase) than those from high-density fast-growing bacteria, with rates of filament elongation of about 0.58 and 0.13 μm min-1 , respectively. With surfaces that do not support bacterial adherence, few filaments were observed even in solution. These filaments aggregated in solution and formed increased amounts of biofilms on surfaces. These results reveal the lifestyle of antibiotic-induced filamentous bacteria, as well as one way in which the antibiotics promote biofilm formation.
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Affiliation(s)
- Yuchen Jin
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Hewen Zheng
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Arizza Chiara S Ibanez
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Pankaj D Patil
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Suqi Lv
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Minrui Luo
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
| | - Thomas M Duncan
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY, 13210, USA
| | - Yan-Yeung Luk
- Department of Chemistry, Syracuse University, 1-014 Center of Science and Technology, Syracuse, NY, 13244-4100, USA
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67
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Petersen E, Miller SI. The cellular microbiology of Salmonellae interactions with macrophages. Cell Microbiol 2019; 21:e13116. [PMID: 31509644 DOI: 10.1111/cmi.13116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/27/2022]
Abstract
Salmonellae are important enteric pathogens that cause gastroenteritis and systemic illnesses. Macrophages are important components of both the innate and acquired immune system, acting as phagocytes with significant antimicrobial killing activities that present antigen to the adaptive immune system. Macrophages can also be cultured from a variety of sites as primary cells, and the study of the survival and interactions of Salmonellae with these cells is a very early model of infection and cellular microbiology. This review traces the history of discoveries made using Salmonellae infection of macrophages and addresses the possibility of future research in this area, in particular with regards to understanding the complexity of individual bacteria and macrophage cell variability and how such heterogeneity may alter the outcome of infection.
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Affiliation(s)
- Erik Petersen
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Samuel I Miller
- Department of Microbiology, University of Washington, Seattle, WA, USA.,Department of Immunology, University of Washington, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
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68
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Ozaki S. Regulation of replication initiation: lessons from Caulobacter crescentus. Genes Genet Syst 2019; 94:183-196. [PMID: 31495806 DOI: 10.1266/ggs.19-00011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chromosome replication is a fundamental process in all domains of life. To accurately transmit genetic material to offspring, the initiation of chromosome replication is tightly regulated to ensure that it occurs only once in each cell division cycle. In the model bacterium Caulobacter crescentus, the CtrA response regulator inhibits the origin of replication at the pre-replication stage. Inactivation of CtrA permits the universal DnaA initiator to form an initiation complex at the origin, leading to replication initiation. Subsequently, the initiation complex is inactivated to prevent extra initiation. Whereas DNA replication occurs periodically in exponentially growing cells, replication initiation is blocked under various stress conditions to halt cell cycle progression until the normal condition is restored or the cells adapt to the stress. Thus, regulating the initiation complex plays an important role in not only driving cell cycle progression, but also maintaining cell integrity under stress. Multiple regulatory signaling pathways controlling CtrA and DnaA have been identified and recent studies have advanced our knowledge of the underlying mechanistic and molecular processes. This review focuses on how bacterial cells control replication initiation, highlighting the latest findings that have emerged from studies in C. crescentus.
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Affiliation(s)
- Shogo Ozaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University
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69
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Sankaran J, Karampatzakis A, Rice SA, Wohland T. Quantitative imaging and spectroscopic technologies for microbiology. FEMS Microbiol Lett 2019; 365:4953418. [PMID: 29718275 DOI: 10.1093/femsle/fny075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/23/2018] [Indexed: 12/17/2022] Open
Abstract
Light microscopy has enabled the observation of the structure and organisation of biofilms. Typically, the contrast in an image obtained from light microscopy is given by the time-averaged intensity that is effective in visualising the overall structure. Technological advancements in light microscopy have led to the creation of techniques that not only provide a static intensity image of the biofilm, but also enable one to quantify various dynamic physicochemical properties of biomolecules in microbial biofilms. Such light microscopy-based techniques can be grouped into two main classes, those that are based on luminescence and those that are based on scattering. Here, we review the fundamentals and applications of luminescence and scattering-based techniques, specifically, fluorescence lifetime imaging, Förster resonance energy transfer, fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single-particle tracking, transient state imaging, and Brillouin and Raman microscopy. These techniques provide information about the abundance, interactions and mobility of various molecules in the biofilms and also properties of the local microenvironment at optical resolution. Further, one could use any of these techniques to probe the real-time changes in these physical parameters upon the addition of external agents or at different stages during the growth of biofilms.
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Affiliation(s)
- Jagadish Sankaran
- Departments of Biological Sciences and Chemistry, National University of Singapore, Singapore 117558, Singapore.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Andreas Karampatzakis
- Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering and School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.,ithree Institute, University of Technology, Sydney 2007, Australia
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry, National University of Singapore, Singapore 117558, Singapore.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
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70
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Mushnikov NV, Fomicheva A, Gomelsky M, Bowman GR. Inducible asymmetric cell division and cell differentiation in a bacterium. Nat Chem Biol 2019; 15:925-931. [PMID: 31406376 PMCID: PMC7439754 DOI: 10.1038/s41589-019-0340-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 07/08/2019] [Indexed: 12/14/2022]
Abstract
Multicellular organisms achieve greater complexity through cell divisions that generate different cell types. We engineered a simple genetic circuit that induces asymmetric cell division and subsequent cell differentiation in Escherichia coli. The circuit involves a scaffolding protein, PopZ, that is stably maintained at a single cell pole over multiple asymmetric cell divisions. PopZ was functionalized to degrade the signaling molecule, c-di-GMP. By regulating synthesis of functionalized PopZ via small molecules or light, we can chemically or optogenetically control the relative abundance of two distinct cell types, characterized by either low or high c-di-GMP levels. Differences in c-di-GMP levels can be transformed into genetically programmable differences in protein complex assembly or gene expression, which in turn produce differential behavior or biosynthetic activities. This study shows emergence of complex biological phenomena from a simple genetic circuit and adds programmable bacterial cell differentiation to the genetic toolbox of synthetic biology and biotechnology.
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Affiliation(s)
| | | | - Mark Gomelsky
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Grant R Bowman
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA.
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71
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Weiss CA, Hoberg JA, Liu K, Tu BP, Winkler WC. Single-Cell Microscopy Reveals That Levels of Cyclic di-GMP Vary among Bacillus subtilis Subpopulations. J Bacteriol 2019; 201:e00247-19. [PMID: 31138629 PMCID: PMC6657594 DOI: 10.1128/jb.00247-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/21/2019] [Indexed: 11/20/2022] Open
Abstract
The synthesis of signaling molecules is one strategy bacteria employ to sense alterations in their environment and rapidly adjust to those changes. In Gram-negative bacteria, bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulates the transition from a unicellular motile state to a multicellular sessile state. However, c-di-GMP signaling has been less intensively studied in Gram-positive organisms. To that end, we constructed a fluorescent yfp reporter based on a c-di-GMP-responsive riboswitch to visualize the relative abundance of c-di-GMP for single cells of the Gram-positive model organism Bacillus subtilis Coupled with cell-type-specific fluorescent reporters, this riboswitch reporter revealed that c-di-GMP levels are markedly different among B. subtilis cellular subpopulations. For example, cells that have made the decision to become matrix producers maintain higher intracellular c-di-GMP concentrations than motile cells. Similarly, we find that c-di-GMP levels differ between sporulating and competent cell types. These results suggest that biochemical measurements of c-di-GMP abundance are likely to be inaccurate for a bulk ensemble of B. subtilis cells, as such measurements will average c-di-GMP levels across the population. Moreover, the significant variation in c-di-GMP levels between cell types hints that c-di-GMP might play an important role during B. subtilis biofilm formation. This study therefore emphasizes the importance of using single-cell approaches for analyzing metabolic trends within ensemble bacterial populations.IMPORTANCE Many bacteria have been shown to differentiate into genetically identical yet morphologically distinct cell types. Such population heterogeneity is especially prevalent among biofilms, where multicellular communities are primed for unexpected environmental conditions and can efficiently distribute metabolic responsibilities. Bacillus subtilis is a model system for studying population heterogeneity; however, a role for c-di-GMP in these processes has not been thoroughly investigated. Herein, we introduce a fluorescent reporter, based on a c-di-GMP-responsive riboswitch, to visualize the relative abundance of c-di-GMP for single B. subtilis cells. Our analysis shows that c-di-GMP levels are conspicuously different among B. subtilis cellular subtypes, suggesting a role for c-di-GMP during biofilm formation. These data highlight the utility of riboswitches as tools for imaging metabolic changes within individual bacterial cells. Analyses such as these offer new insight into c-di-GMP-regulated phenotypes, especially given that other biofilms also consist of multicellular communities.
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Affiliation(s)
- Cordelia A Weiss
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Jakob A Hoberg
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Kuanqing Liu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Benjamin P Tu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
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72
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McCarthy RR, Yu M, Eilers K, Wang Y, Lai E, Filloux A. Cyclic di-GMP inactivates T6SS and T4SS activity in Agrobacterium tumefaciens. Mol Microbiol 2019; 112:632-648. [PMID: 31102484 PMCID: PMC6771610 DOI: 10.1111/mmi.14279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 01/17/2023]
Abstract
The Type VI secretion system (T6SS) is a bacterial nanomachine that delivers effector proteins into prokaryotic and eukaryotic preys. This secretion system has emerged as a key player in regulating the microbial diversity in a population. In the plant pathogen Agrobacterium tumefaciens, the signalling cascades regulating the activity of this secretion system are poorly understood. Here, we outline how the universal eubacterial second messenger cyclic di-GMP impacts the production of T6SS toxins and T6SS structural components. We demonstrate that this has a significant impact on the ability of the phytopathogen to compete with other bacterial species in vitro and in planta. Our results suggest that, as opposed to other bacteria, c-di-GMP turns down the T6SS in A. tumefaciens thus impacting its ability to compete with other bacterial species within the rhizosphere. We also demonstrate that elevated levels of c-di-GMP within the cell decrease the activity of the Type IV secretion system (T4SS) and subsequently the capacity of A. tumefaciens to transform plant cells. We propose that such peculiar control reflects on c-di-GMP being a key second messenger that silences energy-costing systems during early colonization phase and biofilm formation, while low c-di-GMP levels unleash T6SS and T4SS to advance plant colonization.
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Affiliation(s)
- Ronan R. McCarthy
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
- Division of Biosciences, Department of Life SciencesCollege of Health and Life Sciences, Brunel University LondonUxbridgeUB8 3PHUK
| | - Manda Yu
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| | - Yi‐Chieh Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Erh‐Min Lai
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei11529Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonSW7 2AZUK
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73
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Rossy T, Nadell CD, Persat A. Cellular advective-diffusion drives the emergence of bacterial surface colonization patterns and heterogeneity. Nat Commun 2019; 10:2471. [PMID: 31171786 PMCID: PMC6554397 DOI: 10.1038/s41467-019-10469-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/13/2019] [Indexed: 01/10/2023] Open
Abstract
Microorganisms navigate and divide on surfaces to form multicellular structures called biofilms, the most widespread survival strategy found in the bacterial world. One common assumption is that cellular components guide the spatial architecture and arrangement of multiple species in a biofilm. However, bacteria must contend with mechanical forces generated through contact with surfaces and under fluid flow, whose contributions to colonization patterns are poorly understood. Here, we show how the balance between motility and flow promotes the emergence of morphological patterns in Caulobacter crescentus biofilms. By modeling transport of single cells by flow and Brownian-like swimming, we show that the emergence of these patterns is guided by an effective Péclet number. By analogy with transport phenomena we show that, counter-intuitively, fluid flow represses mixing of distinct clonal lineages, thereby affecting the interaction landscapes between biofilm-dwelling bacteria. This demonstrates that hydrodynamics influence species interaction and evolution within surface-associated communities. In the wild, bacteria grow into structures called biofilms. Here the authors demonstrate that their spatial organization and heterogeneity depends on the interplay between fluid flow and single cell motility; this highlights the role of hydrodynamics in biofilm formation.
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Affiliation(s)
- Tamara Rossy
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth, Hanover, NH, 03755, USA.
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
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74
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Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. Proc Natl Acad Sci U S A 2019; 116:8070-8079. [PMID: 30936302 PMCID: PMC6475421 DOI: 10.1073/pnas.1818259116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The fundamental biological functions of a living cell are stored within the DNA sequence of its genome. Classical genetic approaches dissect the functioning of biological systems by analyzing individual genes, yet uncovering the essential gene set of an organism has remained very challenging. It is argued that the rewriting of entire genomes through the process of chemical synthesis provides a powerful and complementary research concept to understand how essential functions are programed into genomes. Understanding how to program biological functions into artificial DNA sequences remains a key challenge in synthetic genomics. Here, we report the chemical synthesis and testing of Caulobacter ethensis-2.0 (C. eth-2.0), a rewritten bacterial genome composed of the most fundamental functions of a bacterial cell. We rebuilt the essential genome of Caulobacter crescentus through the process of chemical synthesis rewriting and studied the genetic information content at the level of its essential genes. Within the 785,701-bp genome, we used sequence rewriting to reduce the number of encoded genetic features from 6,290 to 799. Overall, we introduced 133,313 base substitutions, resulting in the rewriting of 123,562 codons. We tested the biological functionality of the genome design in C. crescentus by transposon mutagenesis. Our analysis revealed that 432 essential genes of C. eth-2.0, corresponding to 81.5% of the design, are equal in functionality to natural genes. These findings suggest that neither changing mRNA structure nor changing the codon context have significant influence on biological functionality of synthetic genomes. Discovery of 98 genes that lost their function identified essential genes with incorrect annotation, including a limited set of 27 genes where we uncovered noncoding control features embedded within protein-coding sequences. In sum, our results highlight the promise of chemical synthesis rewriting to decode fundamental genome functions and its utility toward the design of improved organisms for industrial purposes and health benefits.
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75
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Petersen E, Mills E, Miller SI. Cyclic-di-GMP regulation promotes survival of a slow-replicating subpopulation of intracellular Salmonella Typhimurium. Proc Natl Acad Sci U S A 2019; 116:6335-6340. [PMID: 30862737 PMCID: PMC6442585 DOI: 10.1073/pnas.1901051116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Salmonella Typhimurium can invade and survive within macrophages where the bacterium encounters a range of host environmental conditions. Like many bacteria, S. Typhimurium rapidly responds to changing environments by the use of second messengers such as cyclic di-GMP (c-di-GMP). Here, we generate a fluorescent biosensor to measure c-di-GMP concentrations in thousands of individual bacteria during macrophage infection and to define the sensor enzymes important to c-di-GMP regulation. Three sensor phosphodiesterases were identified as critical to maintaining low c-di-GMP concentrations generated after initial phagocytosis by macrophages. Maintenance of low c-di-GMP concentrations by these phosphodiesterases was required to promote survival within macrophages and virulence for mice. Attenuation of S Typhimurium virulence was due to overproduction of c-di-GMP-regulated cellulose, as deletion of the cellulose synthase machinery restored virulence to a strain lacking enzymatic activity of the three phosphodiesterases. We further identified that the cellulose-mediated reduction in survival was constrained to a slow-replicating persister population of S. Typhimurium induced within the macrophage intracellular environment. As utilization of glucose has been shown to be required for S. Typhimurium macrophage survival, one possible hypothesis is that this persister population requires the glucose redirected to the synthesis of cellulose to maintain a slow-replicating, metabolically active state.
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Affiliation(s)
- Erik Petersen
- Department of Microbiology, University of Washington, Seattle, WA 98195
| | - Erez Mills
- Department of Microbiology, University of Washington, Seattle, WA 98195
| | - Samuel I Miller
- Department of Microbiology, University of Washington, Seattle, WA 98195;
- Department of Immunology, University of Washington, Seattle, WA 98195
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Department of Medicine, University of Washington, Seattle, WA 98195
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76
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Kharadi RR, Sundin GW. Physiological and Microscopic Characterization of Cyclic-di-GMP-Mediated Autoaggregation in Erwinia amylovora. Front Microbiol 2019; 10:468. [PMID: 30930874 PMCID: PMC6423407 DOI: 10.3389/fmicb.2019.00468] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/21/2019] [Indexed: 11/13/2022] Open
Abstract
The second messenger cyclic-di-GMP (c-di-GMP) is a critical regulator of biofilm formation in the plant pathogen Erwinia amylovora. Phosphodiesterase (PDE) enzymes are responsible for the degradation of intracellular c-di-GMP. Previously, we found that the deletion of one or more of the three PDE enzyme encoding genes (pdeA, pdeB, and pdeC) in E. amylovora Ea1189 led to an increase in biofilm formation. However, in mutants Ea1189ΔpdeAC and Ea1189ΔpdeABC, biofilm formation was reduced compared to the other single and double deletion mutants. Here, we attribute this to an autoaggregation phenotype observed in these two mutants. Examination of Ea1189ΔpdeABC cellular aggregates using scanning electron microscopy indicated that a subset of cells were impaired in cell separation post cell division. Concomitant with this phenotype, Ea1189ΔpdeABC also exhibited increased transcription of the cell-division inhibitor gene sulA and reduced transcription of ftsZ. Ea1189ΔpdeABC showed a significant reduction in biofilm formation, and biofilms formed by Ea1189ΔpdeABC exhibited a distinctive morphology of sparsely scattered aggregates rather than an evenly distributed biofilm as observed in WT Ea1189. Our results suggest that highly elevated levels of c-di-GMP lead to increased cell-cell interactions that contribute to autoaggregation and impair cell-surface interaction, negatively affecting biofilm formation.
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Affiliation(s)
| | - George W. Sundin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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77
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You M, Litke JL, Wu R, Jaffrey SR. Detection of Low-Abundance Metabolites in Live Cells Using an RNA Integrator. Cell Chem Biol 2019; 26:471-481.e3. [PMID: 30773480 DOI: 10.1016/j.chembiol.2019.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/05/2018] [Accepted: 01/10/2019] [Indexed: 01/05/2023]
Abstract
Genetically encoded biosensors are useful tools for detecting the presence and levels of diverse biomolecules in living cells. However, low-abundance targets are difficult to detect because they are often unable to bind and activate enough biosensors to detect using standard microscopic imaging approaches. Here we describe a type of RNA-based biosensor, an RNA integrator, which enables detection of low-abundance targets in vitro and in living cells. The RNA integrator is an RNA sequence comprising a ribozyme and an unfolded form of the fluorogenic aptamer Broccoli. Upon binding its target, the ribozyme undergoes cleavage and releases Broccoli, which subsequently folds and becomes fluorescent. Importantly, each target molecule can bind and induce cleavage of multiple copies of the integrator sensor, resulting in an amplified signal. We show that this approach can be generalized to numerous different ribozyme types for the detection of various small molecules.
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Affiliation(s)
- Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA; Department of Pharmacology, Weill Medical College, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jacob L Litke
- Department of Pharmacology, Weill Medical College, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Weill Cornell Medicine, New York, NY 10065, USA.
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78
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Almblad H, Rybtke M, Hendiani S, Andersen JB, Givskov M, Tolker-Nielsen T. High levels of cAMP inhibit Pseudomonas aeruginosa biofilm formation through reduction of the c-di-GMP content. MICROBIOLOGY-SGM 2019; 165:324-333. [PMID: 30663958 DOI: 10.1099/mic.0.000772] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The human pathogen Pseudomonas aeruginosa can cause both acute infections and chronic biofilm-based infections. Expression of acute virulence factors is positively regulated by cAMP, whereas biofilm formation is positively regulated by c-di-GMP. We provide evidence that increased levels of cAMP, caused by either a lack of degradation or increased production, inhibit P. aeruginosa biofilm formation. cAMP-mediated inhibition of P. aeruginosa biofilm formation required Vfr, and involved a reduction of the level of c-di-GMP, as well as reduced production of biofilm matrix components. A mutant screen and characterization of defined knockout mutants suggested that a subset of c-di-GMP-degrading phosphodiesterases is involved in cAMP-Vfr-mediated biofilm inhibition in P. aeruginosa.
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Affiliation(s)
- Henrik Almblad
- 1Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,‡Present address: Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Morten Rybtke
- 1Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Saghar Hendiani
- 2Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Jens Bo Andersen
- 1Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Givskov
- 1Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,3Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Tim Tolker-Nielsen
- 1Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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79
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Christen M, Kamischke C, Kulasekara HD, Olivas KC, Kulasekara BR, Christen B, Kline T, Miller SI. Identification of Small-Molecule Modulators of Diguanylate Cyclase by FRET-Based High-Throughput Screening. Chembiochem 2018; 20:394-407. [PMID: 30395379 DOI: 10.1002/cbic.201800593] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Indexed: 12/20/2022]
Abstract
The bacterial second messenger cyclic diguanosine monophosphate (c-di-GMP) is a key regulator of cellular motility, the cell cycle, and biofilm formation with its resultant antibiotic tolerance, which can make chronic infections difficult to treat. Therefore, diguanylate cyclases, which regulate the spatiotemporal production of c-di-GMP, might be attractive drug targets for control of biofilm formation that is part of chronic infections. We present a FRET-based biochemical high-throughput screening approach coupled with detailed structure-activity studies to identify synthetic small-molecule modulators of the diguanylate cyclase DgcA from Caulobacter crescentus. We identified a set of seven small molecules that regulate DgcA enzymatic activity in the low-micromolar range. Subsequent structure-activity studies on selected scaffolds revealed a remarkable diversity of modulatory behavior, including slight chemical substitutions that reverse the effects from allosteric enzyme inhibition to activation. The compounds identified represent new chemotypes and are potentially developable into chemical genetic tools for the dissection of c-di-GMP signaling networks and alteration of c-di-GMP-associated phenotypes. In sum, our studies underline the importance of detailed mechanism-of-action studies for inhibitors of c-di-GMP signaling and demonstrate the complex interplay between synthetic small molecules and the regulatory mechanisms that control the activity of diguanylate cyclases.
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Affiliation(s)
- Matthias Christen
- Eidgenössische Technische Hochschule Zürich, Department of Biology, Auguste-Piccard-Hof 1, 8093, Zürich, Switzerland
| | - Cassandra Kamischke
- University of Washington, Department of Microbiology, 1959 NE Pacific St., Box 357710, Seattle, WA, 98195, USA
| | - Hemantha D Kulasekara
- University of Washington, Department of Microbiology, 1959 NE Pacific St., Box 357710, Seattle, WA, 98195, USA
| | - Kathleen C Olivas
- Seattle Genetics, Inc., 21823 30th Drive SE, Bothell, WA, 98021, USA
| | - Bridget R Kulasekara
- University of Washington, Department of Genome Sciences, 1959 NE Pacific St., Box 357710, Seattle, WA, 98195, USA
| | - Beat Christen
- Eidgenössische Technische Hochschule Zürich, Department of Biology, Otto-Stern-Weg-3, 8093, Zürich, Switzerland
| | - Toni Kline
- Sutro Biopharma, 310 Utah Avenue, Suite 150, San Francisco, CA, 94080, USA
| | - Samuel I Miller
- University of Washington, Department of Microbiology, 1959 NE Pacific St., Box 357710, Seattle, WA, 98195, USA
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80
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Laventie BJ, Sangermani M, Estermann F, Manfredi P, Planes R, Hug I, Jaeger T, Meunier E, Broz P, Jenal U. A Surface-Induced Asymmetric Program Promotes Tissue Colonization by Pseudomonas aeruginosa. Cell Host Microbe 2018; 25:140-152.e6. [PMID: 30581112 DOI: 10.1016/j.chom.2018.11.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/28/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022]
Abstract
The opportunistic human pathogen Pseudomonas aeruginosa effectively colonizes host epithelia using pili as primary adhesins. Here we uncover a surface-specific asymmetric virulence program that enhances P. aeruginosa host colonization. We show that when P. aeruginosa encounters surfaces, the concentration of the second messenger c-di-GMP increases within a few seconds. This leads to surface adherence and virulence induction by stimulating pili assembly through activation of the c-di-GMP receptor FimW. Surface-attached bacteria divide asymmetrically to generate a piliated, surface-committed progeny (striker) and a flagellated, motile offspring that leaves the surface to colonize distant sites (spreader). Cell differentiation is driven by a phosphodiesterase that asymmetrically positions to the flagellated pole, thereby maintaining c-di-GMP levels low in the motile offspring. Infection experiments demonstrate that cellular asymmetry strongly boosts infection spread and tissue damage. Thus, P. aeruginosa promotes surface colonization and infection transmission through a cooperative virulence program that we termed Touch-Seed-and-Go.
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Affiliation(s)
| | - Matteo Sangermani
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Fabienne Estermann
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Pablo Manfredi
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | | | - Isabelle Hug
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Tina Jaeger
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | | | - Petr Broz
- Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Urs Jenal
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland.
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81
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Fernandez N, Waters CM. Analyzing Diguanylate Cyclase Activity In Vivo using a Heterologous Escherichia coli Host. ACTA ACUST UNITED AC 2018; 52:e74. [PMID: 30489040 DOI: 10.1002/cpmc.74] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bacterial biofilms are notorious for their deleterious effects on human health and industrial biofouling. Key processes in biofilm formation are regulated by the second messenger signal cyclic dimeric guanosine monophosphate (c-di-GMP); accumulation of c-di-GMP promotes biofilm formation, while lowering c-di-GMP promotes motility. Complex networks of modular enzymes are involved in regulating c-di-GMP homeostasis. Understanding how these enzymes function in bacterial cells can help enlighten how bacteria use environmental cues to modulate c-di-GMP and cell physiology. In this article, we describe a workflow that utilizes Escherichia coli as a heterologous host to allow the researcher to identify genes encoding potential c-di-GMP-metabolizing proteins, to express the gene of interest from an inducible plasmid, and to directly detect changes in intracellular c-di-GMP using ultra-performance liquid chromatography-tandem mass spectrometry. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nicolas Fernandez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
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82
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Ghequire MGK, Öztürk B. A Colicin M-Type Bacteriocin from Pseudomonas aeruginosa Targeting the HxuC Heme Receptor Requires a Novel Immunity Partner. Appl Environ Microbiol 2018; 84:e00716-18. [PMID: 29980560 PMCID: PMC6121995 DOI: 10.1128/aem.00716-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/28/2018] [Indexed: 12/16/2022] Open
Abstract
Pyocins are bacteriocins secreted by Pseudomonas aeruginosa, and they assist in the colonization of different niches. A major subset of these antibacterial proteins adopt a modular organization characteristic of polymorphic toxins. They include a receptor-binding domain, a segment enabling membrane passage, and a toxin module at the carboxy terminus, which eventually kills the target cells. To protect themselves from their own products, bacteriocin-producing strains express an immunity gene concomitantly with the bacteriocin. We show here that a pyocin equipped with a phylogenetically distinct ColM toxin domain, PaeM4, mediates antagonism against a large set of P. aeruginosa isolates. Immunity to PaeM4 is provided by the inner membrane protein PmiC, which is equipped with a transmembrane topology not previously described for the ColM family. Given that strains lacking a pmiC gene are killed by PaeM4, the presence of such an immunity partner likely is a key criterion for escaping cellular death mediated by PaeM4. The presence of a TonB box in PaeM4 and enhanced bacteriocin activity under iron-poor conditions strongly suggested the targeting of a TonB-dependent receptor. Evaluation of PaeM4 activities against TonB-dependent receptor knockout mutants in P. aeruginosa PAO1 revealed that the heme receptor HxuC (PA1302) serves as a PaeM4 target at the cellular surface. Because other ColM-type pyocins may target the ferrichrome receptor FiuA, our results illustrate the versatility in target recognition conferred by the polymorphic nature of ColM-type bacteriocins.IMPORTANCE The antimicrobial armamentarium of a bacterium is a major asset for colonizing competitive environments. Bacteriocins comprise a subset of these compounds. Pyocins are an example of such antibacterial proteins produced by Pseudomonas aeruginosa, killing other P. aeruginosa strains. A large group of these molecules show a modular protein architecture that includes a receptor-binding domain for initial target cell attachment and a killer domain. In this study, we have shown that a novel modular pyocin (PaeM4) that kills target bacteria via interference with peptidoglycan assembly takes advantage of the HxuC heme receptor. Cells can protect themselves from killing by the presence of a dedicated immunity partner, an integral inner membrane protein that adopts a transmembrane topology distinct from that of proteins currently known to provide immunity against such toxin activity. Understanding the receptors with which pyocins interact and how immunity to pyocins is achieved is a pivotal step toward the rational design of bacteriocin cocktails for the treatment of P. aeruginosa infections.
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Affiliation(s)
| | - Başak Öztürk
- Leibniz Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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83
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Swain J, El Khoury M, Kempf J, Briée F, Van Der Smissen P, Décout JL, Mingeot-Leclercq MP. Effect of cardiolipin on the antimicrobial activity of a new amphiphilic aminoglycoside derivative on Pseudomonas aeruginosa. PLoS One 2018; 13:e0201752. [PMID: 30125281 PMCID: PMC6101366 DOI: 10.1371/journal.pone.0201752] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/20/2018] [Indexed: 11/22/2022] Open
Abstract
Amphiphilic aminoglycoside derivatives are promising new antibacterials active against Gram-negative bacteria such as Pseudomonas aeruginosa, including colistin resistant strains. In this study, we demonstrated that addition of cardiolipin to the culture medium delayed growth of P. aeruginosa, favored asymmetrical growth and enhanced the efficiency of a new amphiphilic aminoglycoside derivative, the 3’,6-dinonylneamine. By using membrane models mimicking P. aeruginosa plasma membrane composition (POPE:POPG:CL), we demonstrated the ability of 3’6-dinonylneamine to induce changes in the biophysical properties of membrane model lipid systems in a cardiolipin dependent manner. These changes include an increased membrane permeability associated with a reduced hydration and a decreased ability of membrane to mix and fuse as shown by monitoring calcein release, Generalized Polarization of Laurdan and fluorescence dequenching of octadecyl rhodamine B, respectively. Altogether, results shed light on how cardiolipin may be critical for improving antibacterial action of new amphiphilic aminoglycoside derivatives.
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Affiliation(s)
- Jitendriya Swain
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Micheline El Khoury
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Julie Kempf
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Florian Briée
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, CNRS, Grenoble, France
| | | | - Jean-Luc Décout
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Marie-Paule Mingeot-Leclercq
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
- * E-mail:
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84
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Dippel AB, Anderson WA, Evans RS, Deutsch S, Hammond MC. Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP. ACS Chem Biol 2018; 13:1872-1879. [PMID: 29466657 DOI: 10.1021/acschembio.7b01019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria colonize highly diverse and complex environments, from gastrointestinal tracts to soil and plant surfaces. This colonization process is controlled in part by the intracellular signal cyclic di-GMP, which regulates bacterial motility and biofilm formation. To interrogate cyclic di-GMP signaling networks, a variety of fluorescent biosensors for live cell imaging of cyclic di-GMP have been developed. However, the need for external illumination precludes the use of these tools for imaging bacteria in their natural environments, including in deep tissues of whole organisms and in samples that are highly autofluorescent or photosensitive. The need for genetic encoding also complicates the analysis of clinical isolates and environmental samples. Toward expanding the study of bacterial signaling to these systems, we have developed the first chemiluminescent biosensors for cyclic di-GMP. The biosensor design combines the complementation of split luciferase (CSL) and bioluminescence resonance energy transfer (BRET) approaches. Furthermore, we developed a lysate-based assay for biosensor activity that enabled reliable high-throughput screening of a phylogenetic library of 92 biosensor variants. The screen identified biosensors with very large signal changes (∼40- and 90-fold) as well as biosensors with high affinities for cyclic di-GMP ( KD < 50 nM). These chemiluminescent biosensors then were applied to measure cyclic di-GMP levels in E. coli. The cellular experiments revealed an unexpected challenge for chemiluminescent imaging in Gram negative bacteria but showed promising application in lysates. Taken together, this work establishes the first chemiluminescent biosensors for studying cyclic di-GMP signaling and provides a foundation for using these biosensors in more complex systems.
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Affiliation(s)
- Andrew B. Dippel
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wyatt A. Anderson
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert S. Evans
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Samuel Deutsch
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Ming C. Hammond
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
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85
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Abstract
Spatial control of intracellular signaling relies on signaling proteins sensing their subcellular environment. In many cases, a large number of upstream signals are funneled to a master regulator of cellular behavior, but it remains unclear how individual proteins can rapidly integrate a complex array of signals within the appropriate spatial niche within the cell. As a model for how subcellular spatial information can control signaling activity, we have reconstituted the cell pole-specific control of the master regulator kinase/phosphatase CckA from the asymmetrically dividing bacterium Caulobacter crescentus CckA is active as a kinase only when it accumulates within a microdomain at the new cell pole, where it colocalizes with the pseudokinase DivL. Both proteins contain multiple PAS domains, a multifunctional class of sensory domains present across the kingdoms of life. Here, we show that CckA uses its PAS domains to integrate information from DivL and its own oligomerization state to control the balance of its kinase and phosphatase activities. We reconstituted the DivL-CckA complex on liposomes in vitro and found that DivL directly controls the CckA kinase/phosphatase switch, and that stimulation of either CckA catalytic activity depends on the second of its two PAS domains. We further show that CckA oligomerizes through a multidomain interaction that is critical for stimulation of kinase activity by DivL, while DivL stimulation of CckA phosphatase activity is independent of CckA homooligomerization. Our results broadly demonstrate how signaling factors can leverage information from their subcellular niche to drive spatiotemporal control of cell signaling.
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86
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Differential Production of Psl in Planktonic Cells Leads to Two Distinctive Attachment Phenotypes in Pseudomonas aeruginosa. Appl Environ Microbiol 2018; 84:AEM.00700-18. [PMID: 29752273 PMCID: PMC6029103 DOI: 10.1128/aem.00700-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/05/2018] [Indexed: 01/21/2023] Open
Abstract
The attachment of planktonic cells to surfaces is the first and most crucial step in biofilm formation. In this paper, we show that planktonic cells of Pseudomonas aeruginosa differently attach to surfaces. Typically, in the later exponential phase, approximately 80% of the cells can quickly attach to surfaces within 15 min, whereas approximately 20% of the cells slowly attach to surfaces, which greatly affects the initial stage of biofilm formation in the presence of flows. This is because fast-attaching cells are more likely to attach on surfaces to form microcolonies, whereas slow-attaching cells are more likely to remain in the mobile phase. This scenario is different from the previous understanding of biofilm formation in the initial stage, in which planktonic cells were thought to uniformly attach to surfaces. Most notably, the results of this study show that the different attachment manner of planktonic cells to surfaces affects the subsequent stages of biofilm formation. This research highlights that the phenotypic variations in planktonic cells plays significant roles in various stages of biofilm formation. Exponentially growing bacteria in a well-mixed planktonic culture are generally assumed to be physiologically and phenotypically uniform and distinct from their genetically identical counterparts living in biofilms. Using a combination of high spatiotemporal microscopy and a bacterial tracking algorithm, in this study, we showed that planktonic cells of Pseudomonas aeruginosa differently attached to surfaces even when they remained in the exponential phase. We consistently observed that fast- and slow-attaching phenotypes coexist in planktonic cells, regardless of their growth phase. Furthermore, we found that (i) the distinct attaching phenotypes of planktonic cells resulted from the differential production of Psl and (ii) the RsmYZ/RsmA signaling pathway mainly regulated the differential production of Psl. Our results indicate that the differential production of Psl in P. aeruginosa plays a significant role in biofilm development and formation. IMPORTANCE The attachment of planktonic cells to surfaces is the first and most crucial step in biofilm formation. In this paper, we show that planktonic cells of Pseudomonas aeruginosa differently attach to surfaces. Typically, in the later exponential phase, approximately 80% of the cells can quickly attach to surfaces within 15 min, whereas approximately 20% of the cells slowly attach to surfaces, which greatly affects the initial stage of biofilm formation in the presence of flows. This is because fast-attaching cells are more likely to attach on surfaces to form microcolonies, whereas slow-attaching cells are more likely to remain in the mobile phase. This scenario is different from the previous understanding of biofilm formation in the initial stage, in which planktonic cells were thought to uniformly attach to surfaces. Most notably, the results of this study show that the different attachment manner of planktonic cells to surfaces affects the subsequent stages of biofilm formation. This research highlights that the phenotypic variations in planktonic cells plays significant roles in various stages of biofilm formation.
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87
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Tlr1612 is the major repressor of cell aggregation in the light-color-dependent c-di-GMP signaling network of Thermosynechococcus vulcanus. Sci Rep 2018; 8:5338. [PMID: 29593349 PMCID: PMC5871770 DOI: 10.1038/s41598-018-23628-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/16/2018] [Indexed: 11/08/2022] Open
Abstract
Cyclic diguanylate (c-di-GMP) is a bacterial second messenger involved in sessile/motile lifestyle transitions. We previously reported that c-di-GMP is a crucial inducer of cell aggregation of the cyanobacterium Thermosynechococcus vulcanus. The three cooperating cyanobacteriochrome photoreceptors (SesA/B/C) regulate cell aggregation in a light color-dependent manner by synthesizing/degrading c-di-GMP. Although a variety of c-di-GMP signaling proteins are encoded in cyanobacterial genomes, how c-di-GMP signaling networks are organized remains elusive. Here we experimentally demonstrate that the cellulose synthase Tll0007, which is essential for cell aggregation, binds c-di-GMP although the affinity is low (Kd = 63.9 ± 5.1 µM). We also show that SesA-the main trigger of cell aggregation-is subject to strict product feedback inhibition (IC50 = 1.07 ± 0.13 µM). These results suggest that SesA-produced c-di-GMP may not directly bind to Tll0007. We therefore systematically analyzed all 10 of the genes encoding proteins containing a c-di-GMP synthesis/degradation domain. We identified Tlr1612, harboring both domains, as the major repressor of cell aggregation under the repressing teal-green light irradiation. tlr1612 acts downstream of sesA and is not regulated transcriptionally by light color, suggesting that Tlr1612 may be involved in c-di-GMP amplification in the signaling cascade. Post-transcriptional control is likely crucial for the light-regulated c-di-GMP signaling.
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88
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A Multimodal Strategy Used by a Large c-di-GMP Network. J Bacteriol 2018; 200:JB.00703-17. [PMID: 29311282 DOI: 10.1128/jb.00703-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/31/2017] [Indexed: 01/05/2023] Open
Abstract
The Pseudomonas fluorescens genome encodes more than 50 proteins predicted to be involved in c-di-GMP signaling. Here, we demonstrated that, tested across 188 nutrients, these enzymes and effectors appeared capable of impacting biofilm formation. Transcriptional analysis of network members across ∼50 nutrient conditions indicates that altered gene expression can explain a subset of but not all biofilm formation responses to the nutrients. Additional organization of the network is likely achieved through physical interaction, as determined via probing ∼2,000 interactions by bacterial two-hybrid assays. Our analysis revealed a multimodal regulatory strategy using combinations of ligand-mediated signals, protein-protein interaction, and/or transcriptional regulation to fine-tune c-di-GMP-mediated responses. These results create a profile of a large c-di-GMP network that is used to make important cellular decisions, opening the door to future model building and the ability to engineer this complex circuitry in other bacteria.IMPORTANCE Cyclic diguanylate (c-di-GMP) is a key signaling molecule regulating bacterial biofilm formation, and many microbes have up to dozens of proteins that make, break, or bind this dinucleotide. A major open issue in the field is how signaling specificity is conferred in the unpartitioned space of a bacterial cell. Here, we took a systems approach, using mutational analysis, transcriptional studies, and bacterial two-hybrid analysis to interrogate this network. We found that a majority of enzymes are capable of impacting biofilm formation in a context-dependent manner, and we revealed examples of two or more modes of regulation (i.e., transcriptional control with protein-protein interaction) being utilized to generate an observable impact on biofilm formation.
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89
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Liu Y, Kim H, Römling U. In vivo Analysis of Cyclic di-GMP Cyclase and Phosphodiesterase Activity in Escherichia coli Using a Vc2 Riboswitch-based Assay. Bio Protoc 2018; 8:e2753. [PMID: 34179279 DOI: 10.21769/bioprotoc.2753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 11/02/2022] Open
Abstract
Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous second messenger that regulates distinct aspects of bacterial physiology. It is synthesized by diguanylate cyclases (DGCs) and hydrolyzed by phosphodiesterases (PDEs). To date, the activities of DGC and PDE are commonly assessed by phenotypic assays, mass spectrometry analysis of intracellular c-di-GMP concentration, or riboswitch-based fluorescent biosensors. However, some of these methods require cutting-edge equipment, which might not be available in every laboratory. Here, we report a new simple, convenient and cost-effective system to assess the function of DGCs and PDEs in E. coli. This system utilizes the high specificity of a riboswitch to c-di-GMP and its ability to regulate the expression of a downstream β-galactosidase reporter gene in response to c-di-GMP concentrations. In this protocol, we delineate the construction of this system and its use to assess the activity of DGC and PDE enzymes.
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Affiliation(s)
- Ying Liu
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hyunhee Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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90
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Zhang Z, Milias-Argeitis A, Heinemann M. Dynamic single-cell NAD(P)H measurement reveals oscillatory metabolism throughout the E. coli cell division cycle. Sci Rep 2018; 8:2162. [PMID: 29391569 PMCID: PMC5795003 DOI: 10.1038/s41598-018-20550-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/22/2018] [Indexed: 11/09/2022] Open
Abstract
Recent work has shown that metabolism between individual bacterial cells in an otherwise isogenetic population can be different. To investigate such heterogeneity, experimental methods to zoom into the metabolism of individual cells are required. To this end, the autofluoresence of the redox cofactors NADH and NADPH offers great potential for single-cell dynamic NAD(P)H measurements. However, NAD(P)H excitation requires UV light, which can cause cell damage. In this work, we developed a method for time-lapse NAD(P)H imaging in single E. coli cells. Our method combines a setup with reduced background emission, UV-enhanced microscopy equipment and optimized exposure settings, overall generating acceptable NAD(P)H signals from single cells, with minimal negative effect on cell growth. Through different experiments, in which we perturb E. coli's redox metabolism, we demonstrated that the acquired fluorescence signal indeed corresponds to NAD(P)H. Using this new method, for the first time, we report that intracellular NAD(P)H levels oscillate along the bacterial cell division cycle. The developed method for dynamic measurement of NAD(P)H in single bacterial cells will be an important tool to zoom into metabolism of individual cells.
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Affiliation(s)
- Zheng Zhang
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
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91
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High Levels of Cyclic Di-GMP in Klebsiella pneumoniae Attenuate Virulence in the Lung. Infect Immun 2018; 86:IAI.00647-17. [PMID: 29158434 DOI: 10.1128/iai.00647-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/15/2017] [Indexed: 01/22/2023] Open
Abstract
The bacterial second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) has been shown to influence the expression of virulence factors in certain pathogenic bacteria, but little is known about its activity in the increasingly antibiotic-resistant pathogen Klebsiella pneumoniae Here, the expression in K. pneumoniae of a heterologous diguanylate cyclase increased the bacterial c-di-GMP concentration and attenuated pathogenesis in murine pneumonia. This attenuation remained evident in mice lacking the c-di-GMP sensor STING, indicating that the high c-di-GMP concentration exerted its influence not on host responses but on bacterial physiology. While serum resistance and capsule expression were unaffected by the increased c-di-GMP concentration, both type 3 and type 1 pili were strongly upregulated. Importantly, attenuation of K. pneumoniae virulence by high c-di-GMP levels was abrogated when type 1 pilus expression was silenced. We conclude that increased type 1 piliation may hamper K. pneumoniae virulence in the respiratory tract and that c-di-GMP signaling represents a potential therapeutic target for antibiotic-resistant K. pneumoniae in this niche.
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92
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Gründling A, Lee VT. Old concepts, new molecules and current approaches applied to the bacterial nucleotide signalling field. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0503. [PMID: 27672152 PMCID: PMC5052745 DOI: 10.1098/rstb.2015.0503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 12/25/2022] Open
Abstract
Signalling nucleotides are key molecules that help bacteria to rapidly coordinate cellular pathways and adapt to changes in their environment. During the past 10 years, the nucleotide signalling field has seen much excitement, as several new signalling nucleotides have been discovered in both eukaryotic and bacterial cells. The fields have since advanced quickly, aided by the development of important tools such as the synthesis of modified nucleotides, which, combined with sensitive mass spectrometry methods, allowed for the rapid identification of specific receptor proteins along with other novel genome-wide screening methods. In this review, we describe the principle concepts of nucleotide signalling networks and summarize the recent work that led to the discovery of the novel signalling nucleotides. We also highlight current approaches applied to the research in the field as well as resources and methodological advances aiding in a rapid identification of nucleotide-specific receptor proteins. This article is part of the themed issue ‘The new bacteriology’.
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Affiliation(s)
- Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Vincent T Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD 20742, USA
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93
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Kreft JU, Plugge CM, Prats C, Leveau JHJ, Zhang W, Hellweger FL. From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality. Front Microbiol 2017; 8:2299. [PMID: 29230200 PMCID: PMC5711835 DOI: 10.3389/fmicb.2017.02299] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/07/2017] [Indexed: 01/04/2023] Open
Abstract
Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy.
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Affiliation(s)
- Jan-Ulrich Kreft
- Centre for Computational Biology, Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Clara Prats
- Department of Physics, School of Agricultural Engineering of Barcelona, Universitat Politècnica de Catalunya-BarcelonaTech, Castelldefels, Spain
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ferdi L Hellweger
- Civil and Environmental Engineering Department, Marine and Environmental Sciences Department, Bioengineering Department, Northeastern University, Boston, MA, United States
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94
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Yeo J, Dippel AB, Wang XC, Hammond MC. In Vivo Biochemistry: Single-Cell Dynamics of Cyclic Di-GMP in Escherichia coli in Response to Zinc Overload. Biochemistry 2017; 57:108-116. [PMID: 29052983 DOI: 10.1021/acs.biochem.7b00696] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intracellular signaling enzymes drive critical changes in cellular physiology and gene expression, but their endogenous activities in vivo remain highly challenging to study in real time and for individual cells. Here we show that flow cytometry can be performed in complex media to monitor single-cell population distributions and dynamics of cyclic di-GMP signaling, which controls the bacterial colonization program. These in vivo biochemistry experiments are enabled by our second-generation RNA-based fluorescent (RBF) biosensors, which exhibit high fluorescence turn-on in response to cyclic di-GMP. Specifically, we demonstrate that intracellular levels of cyclic di-GMP in Escherichia coli are repressed with excess zinc, but not with other divalent metals. Furthermore, in both flow cytometry and fluorescence microscopy setups, we monitor the dynamic increase in cellular cyclic di-GMP levels upon zinc depletion and show that this response is due to de-repression of the endogenous diguanylate cyclase DgcZ. In the presence of zinc, cells exhibit enhanced cell motility and increased sensitivity to antibiotics due to inhibited biofilm formation. Taken together, these results showcase the application of RBF biosensors in visualizing single-cell dynamic changes in cyclic di-GMP signaling in direct response to environmental cues such as zinc and highlight our ability to assess whether observed phenotypes are related to specific signaling enzymes and pathways.
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Affiliation(s)
- Jongchan Yeo
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Andrew B Dippel
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Xin C Wang
- Department of Molecular & Cell Biology, University of California , Berkeley, California 94720, United States
| | - Ming C Hammond
- Department of Chemistry, University of California , Berkeley, California 94720, United States.,Department of Molecular & Cell Biology, University of California , Berkeley, California 94720, United States
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95
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Nesper J, Hug I, Kato S, Hee CS, Habazettl JM, Manfredi P, Grzesiek S, Schirmer T, Emonet T, Jenal U. Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators. eLife 2017; 6:28842. [PMID: 29091032 PMCID: PMC5677366 DOI: 10.7554/elife.28842] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/28/2017] [Indexed: 12/22/2022] Open
Abstract
The flagellar motor is a sophisticated rotary machine facilitating locomotion and signal transduction. Owing to its important role in bacterial behavior, its assembly and activity are tightly regulated. For example, chemotaxis relies on a sensory pathway coupling chemical information to rotational bias of the motor through phosphorylation of the motor switch protein CheY. Using a chemical proteomics approach, we identified a novel family of CheY-like (Cle) proteins in Caulobacter crescentus, which tune flagellar activity in response to binding of the second messenger c-di-GMP to a C-terminal extension. In their c-di-GMP bound conformation Cle proteins interact with the flagellar switch to control motor activity. We show that individual Cle proteins have adopted discrete cellular functions by interfering with chemotaxis and by promoting rapid surface attachment of motile cells. This study broadens the regulatory versatility of bacterial motors and unfolds mechanisms that tie motor activity to mechanical cues and bacterial surface adaptation.
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Affiliation(s)
- Jutta Nesper
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
| | - Isabelle Hug
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
| | - Setsu Kato
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Chee-Seng Hee
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Judith Maria Habazettl
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Pablo Manfredi
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
| | - Stephan Grzesiek
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Tilman Schirmer
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Thierry Emonet
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,Department of Physics, Yale University, New Haven, United States
| | - Urs Jenal
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
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96
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Optogenetic Manipulation of Cyclic Di-GMP (c-di-GMP) Levels Reveals the Role of c-di-GMP in Regulating Aerotaxis Receptor Activity in Azospirillum brasilense. J Bacteriol 2017; 199:JB.00020-17. [PMID: 28264994 DOI: 10.1128/jb.00020-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/28/2017] [Indexed: 11/20/2022] Open
Abstract
Bacterial chemotaxis receptors provide the sensory inputs that inform the direction of navigation in changing environments. Recently, we described the bacterial second messenger cyclic di-GMP (c-di-GMP) as a novel regulator of a subclass of chemotaxis receptors. In Azospirillum brasilense, c-di-GMP binds to a chemotaxis receptor, Tlp1, and modulates its signaling function during aerotaxis. Here, we further characterize the role of c-di-GMP in aerotaxis using a novel dichromatic optogenetic system engineered for manipulating intracellular c-di-GMP levels in real time. This system comprises a red/near-infrared-light-regulated diguanylate cyclase and a blue-light-regulated c-di-GMP phosphodiesterase. It allows the generation of transient changes in intracellular c-di-GMP concentrations within seconds of irradiation with appropriate light, which is compatible with the time scale of chemotaxis signaling. We provide experimental evidence that binding of c-di-GMP to the Tlp1 receptor activates its signaling function during aerotaxis, which supports the role of transient changes in c-di-GMP levels as a means of adjusting the response of A. brasilense to oxygen gradients. We also show that intracellular c-di-GMP levels in A. brasilense change with carbon metabolism. Our data support a model whereby c-di-GMP functions to imprint chemotaxis receptors with a record of recent metabolic experience, to adjust their contribution to the signaling output, thus allowing the cells to continually fine-tune chemotaxis sensory perception to their metabolic state.IMPORTANCE Motile bacteria use chemotaxis to change swimming direction in response to changes in environmental conditions. Chemotaxis receptors sense environmental signals and relay sensory information to the chemotaxis machinery, which ultimately controls the swimming pattern of cells. In bacteria studied to date, differential methylation has been known as a mechanism to control the activity of chemotaxis receptors and modulates their contribution to the overall chemotaxis response. Here, we used an optogenetic system to perturb intracellular concentrations of the bacterial second messenger c-di-GMP to show that in some chemotaxis receptors, c-di-GMP functions in a similar feedback loop to connect the metabolic status of the cells to the sensory activity of chemotaxis receptors.
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97
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Optogenetic Module for Dichromatic Control of c-di-GMP Signaling. J Bacteriol 2017; 199:JB.00014-17. [PMID: 28320886 DOI: 10.1128/jb.00014-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/15/2017] [Indexed: 02/08/2023] Open
Abstract
Many aspects of bacterial physiology and behavior, including motility, surface attachment, and the cell cycle, are controlled by cyclic di-GMP (c-di-GMP)-dependent signaling pathways on the scale of seconds to minutes. Interrogation of such processes in real time requires tools for introducing rapid and reversible changes in intracellular c-di-GMP levels. Inducing the expression of genes encoding c-di-GMP-synthetic (diguanylate cyclases) and -degrading (c-di-GMP phosphodiesterase) enzymes by chemicals may not provide adequate temporal control. In contrast, light-controlled diguanylate cyclases and phosphodiesterases can be quickly activated and inactivated. A red/near-infrared-light-regulated diguanylate cyclase, BphS, was engineered previously, yet a complementary light-activated c-di-GMP phosphodiesterase has been lacking. In search of such a phosphodiesterase, we investigated two homologous proteins from Allochromatium vinosum and Magnetococcus marinus, designated BldP, which contain C-terminal EAL-BLUF modules, where EAL is a c-di-GMP phosphodiesterase domain and BLUF is a blue light sensory domain. Characterization of the BldP proteins in Escherichia coli and in vitro showed that they possess light-activated c-di-GMP phosphodiesterase activities. Interestingly, light activation in both enzymes was dependent on oxygen levels. The truncated EAL-BLUF fragment from A. vinosum BldP lacked phosphodiesterase activity, whereas a similar fragment from M. marinus BldP, designated EB1, possessed such activity that was highly (>30-fold) upregulated by light. Following light withdrawal, EB1 reverted to the inactive ground state with a half-life of ∼6 min. Therefore, the blue-light-activated phosphodiesterase EB1 can be used in combination with the red/near-infrared-light-regulated diguanylate cyclase BphS for the bidirectional regulation of c-di-GMP-dependent processes in E. coli as well as other bacterial and nonbacterial cells.IMPORTANCE Regulation of motility, attachment to surfaces, the cell cycle, and other bacterial processes controlled by the c-di-GMP signaling pathways occur at a fast (seconds-to-minutes) pace. Interrogation of these processes at high temporal and spatial resolution using chemicals is difficult or impossible, while optogenetic approaches may prove useful. We identified and characterized a robust, blue-light-activated c-di-GMP phosphodiesterase (hydrolase) that complements a previously engineered red/near-infrared-light-regulated diguanylate cyclase (c-di-GMP synthase). These two enzymes form a dichromatic module for manipulating intracellular c-di-GMP levels in bacterial and nonbacterial cells.
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98
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BsmR degrades c-di-GMP to modulate biofilm formation of nosocomial pathogen Stenotrophomonas maltophilia. Sci Rep 2017; 7:4665. [PMID: 28680041 PMCID: PMC5498567 DOI: 10.1038/s41598-017-04763-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/19/2017] [Indexed: 11/18/2022] Open
Abstract
c-di-GMP is a cellular second messenger that regulates diverse bacterial processes, including swimming, biofilm formation and virulence. However, in Stenotrophomonas maltophilia, a nosocomial pathogen that frequently infects immunodeficient or immunoincompetent patients, the regulatory function of c-di-GMP remains unclear. Here we show that BsmR is a negative regulator of biofilm development that degrades c-di-GMP through its EAL domain. Increasing BsmR expression resulted in significant increase in bacterial swimming and decrease in cell aggregation. BsmR regulates the expression of at least 349 genes. Among them, 34 involved in flagellar assembly and a flagellar-assembly-related transcription factor (fsnR) are positively regulated. Although BsmR is a response regulator of the two-component signaling system, its role in biofilm formation depends on the expression level of its respective gene (bsmR), not on the protein’s phosphorylation level. A transcription factor, BsmT, whose coding gene is located in the same tetra-cistronic operon as bsmR, was shown to directly bind to the promoter region of the operon and, through a positive regulatory loop, modulate bsmR transcription. Thus, our results revealed that the c-di-GMP signaling pathway controls biofilm formation and swimming in S. maltophilia, suggesting c-di-GMP signaling as a target in the development of novel antibacterial agents to resist this pathogen.
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99
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Abstract
Cyclic diguanylate (c-di-GMP) is a near universal signaling molecule produced by diguanylate cyclases that can direct a variety of bacterial behaviors. A major area of research over the last several years has been aimed at understanding how a cell with dozens of diguanylate cyclases can deploy a given subset of them to produce a desired phenotypic outcome without undesired cross talk between c-di-GMP-dependent systems. Several models have been put forward to address this question, including specificity of cyclase activation, tuned binding constants of effector proteins, and physical interaction between cyclases and effectors. Additionally, recent evidence has suggested that there may be a link between the catalytic state of a cyclase and its physical contact with an effector. This review highlights several key studies, examines the proposed global and local models of c-di-GMP signaling specificity in bacteria, and attempts to identify the most fruitful steps that can be taken to better understand how dynamic networks of sibling cyclases and effector proteins result in sensible outputs that govern cellular behavior.
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Affiliation(s)
- Kurt M Dahlstrom
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755;
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755;
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100
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Rodesney CA, Roman B, Dhamani N, Cooley BJ, Katira P, Touhami A, Gordon VD. Mechanosensing of shear by Pseudomonas aeruginosa leads to increased levels of the cyclic-di-GMP signal initiating biofilm development. Proc Natl Acad Sci U S A 2017; 114:5906-5911. [PMID: 28533383 PMCID: PMC5468607 DOI: 10.1073/pnas.1703255114] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Biofilms are communities of sessile microbes that are phenotypically distinct from their genetically identical, free-swimming counterparts. Biofilms initiate when bacteria attach to a solid surface. Attachment triggers intracellular signaling to change gene expression from the planktonic to the biofilm phenotype. For Pseudomonas aeruginosa, it has long been known that intracellular levels of the signal cyclic-di-GMP increase upon surface adhesion and that this is required to begin biofilm development. However, what cue is sensed to notify bacteria that they are attached to the surface has not been known. Here, we show that mechanical shear acts as a cue for surface adhesion and activates cyclic-di-GMP signaling. The magnitude of the shear force, and thereby the corresponding activation of cyclic-di-GMP signaling, can be adjusted both by varying the strength of the adhesion that binds bacteria to the surface and by varying the rate of fluid flow over surface-bound bacteria. We show that the envelope protein PilY1 and functional type IV pili are required mechanosensory elements. An analytic model that accounts for the feedback between mechanosensors, cyclic-di-GMP signaling, and production of adhesive polysaccharides describes our data well.
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Affiliation(s)
- Christopher A Rodesney
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712
| | - Brian Roman
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712
| | - Numa Dhamani
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712
| | - Benjamin J Cooley
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712
| | | | - Ahmed Touhami
- Department of Physics, The University of Texas Rio Grande Valley, Brownsville, TX 78520
| | - Vernita D Gordon
- Department of Physics, Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712;
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
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