701
|
Geske GD, O'Neill JC, Miller DM, Mattmann ME, Blackwell HE. Modulation of bacterial quorum sensing with synthetic ligands: systematic evaluation of N-acylated homoserine lactones in multiple species and new insights into their mechanisms of action. J Am Chem Soc 2007; 129:13613-25. [PMID: 17927181 DOI: 10.1021/ja074135h] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria use a language of low molecular weight ligands to assess their population densities in a process called quorum sensing. This chemical signaling process plays a pivotal role both in the pathogenesis of infectious disease and in beneficial symbioses. There is intense interest in the development of synthetic ligands that can intercept quorum-sensing signals and attenuate these divergent outcomes. Both broad-spectrum and species-selective modulators of quorum sensing hold significant value as small-molecule tools for fundamental studies of this complex cell-cell signaling process and for future biomedical and environmental applications. Here, we report the design and synthesis of focused collections of non-native N-acylated homoserine lactones and the systematic evaluation of these approximately 90 ligands across three Gram-negative bacterial species: the pathogens Agrobacterium tumefaciens and Pseudomonas aeruginosa; the model symbiont Vibrio fischeri. This study is the first to report and compare the activities of a set of ligands across multiple species and has revealed some of the most potent synthetic modulators of quorum sensing to date. Moreover, several of these ligands exhibit agonistic or antagonistic activity in all three species, while other ligands are only active in one or two species. Analysis of the screening data revealed that at least a subset of these ligands modulate quorum sensing via a partial agonism mechanism. We also demonstrate that selected ligands can either inhibit or promote the production of elastase B, a key virulence factor in wild-type P. aeruginosa, depending on their concentrations. Overall, this work provides broad insights into the molecular features required for small-molecule inhibition or activation of quorum sensing in Gram-negative bacteria. In addition, this study has supplied an expansive set of chemical tools for the further investigation of quorum-sensing pathways and responses.
Collapse
Affiliation(s)
- Grant D Geske
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
| | | | | | | | | |
Collapse
|
702
|
Hecht I, Ben-Jacob E, Levine H. Correlated phenotypic transitions to competence in bacterial colonies. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:040901. [PMID: 17994927 DOI: 10.1103/physreve.76.040901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 06/06/2007] [Indexed: 05/25/2023]
Abstract
Genetic competence is a phenotypic state of a bacterial cell in which it is capable of importing DNA, presumably to improve survival under stress. Motivated by several colony-level known responses, we present a model for the influence of quorum sensing on the transition to competence of B. Subtilis. Coupling to the external signal creates an effective inhibitory mechanism, which results in anticorrelation between the cycles of adjacent cells. We show that this is consistent with recent experimental measurements and propose measurement methods to verify the role of quorum-sensing signals.
Collapse
Affiliation(s)
- Inbal Hecht
- Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093, USA
| | | | | |
Collapse
|
703
|
Antunes LCM, Schaefer AL, Ferreira RBR, Qin N, Stevens AM, Ruby EG, Greenberg EP. Transcriptome analysis of the Vibrio fischeri LuxR-LuxI regulon. J Bacteriol 2007; 189:8387-91. [PMID: 17827287 PMCID: PMC2168698 DOI: 10.1128/jb.00736-07] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Vibrio fischeri quorum-sensing signal N-3-oxohexanoyl-l-homoserine lactone (3OC6-HSL) activates expression of the seven-gene luminescence operon. We used microarrays to unveil 18 additional 3OC6-HSL-controlled genes, 3 of which had been identified by other means previously. We show most of these genes are regulated by the 3OC6-HSL-responsive transcriptional regulator LuxR directly. This demonstrates that V. fischeri quorum sensing regulates a substantial number of genes other than those involved in light production.
Collapse
|
704
|
Marguet P, Balagadde F, Tan C, You L. Biology by design: reduction and synthesis of cellular components and behaviour. J R Soc Interface 2007; 4:607-23. [PMID: 17251159 PMCID: PMC2373384 DOI: 10.1098/rsif.2006.0206] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Biological research is experiencing an increasing focus on the application of knowledge rather than on its generation. Thanks to the increased understanding of cellular systems and technological advances, biologists are more frequently asking not only 'how can I understand the structure and behaviour of this biological system?', but also 'how can I apply that knowledge to generate novel functions in different biological systems or in other contexts?' Active pursuit of the latter has nurtured the emergence of synthetic biology. Here, we discuss the motivation behind, and foundational technologies enabling, the development of this nascent field. We examine some early successes and applications while highlighting the challenges involved. Finally, we consider future directions and mention non-scientific considerations that can influence the field's growth.
Collapse
Affiliation(s)
- Philippe Marguet
- Department of Biochemistry, Duke University Medical CenterDurham, NC 27710, USA
| | - Frederick Balagadde
- Department of Bioengineering, Stanford UniversityStanford, CA 94305-9505, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, Duke UniversityDurham, NC 27708-0320, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke UniversityDurham, NC 27708-0320, USA
- Institute for Genome Sciences and Policy, Duke University Medical CenterDurham, NC 27710, USA
- Author and address for correspondence: CIEMAS 2345, 101 Science Drive, Durham, NC 27708, USA ()
| |
Collapse
|
705
|
Dalton KA, Thibessard A, Hunter JIB, Kelemen GH. A novel compartment, the 'subapical stem' of the aerial hyphae, is the location of a sigN-dependent, developmentally distinct transcription in Streptomyces coelicolor. Mol Microbiol 2007; 64:719-37. [PMID: 17462019 DOI: 10.1111/j.1365-2958.2007.05684.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Streptomyces coelicolor has nine SigB-like RNA polymerase sigma factors, several of them implicated in morphological differentiation and/or responses to different stresses. One of the nine, SigN, is the focus of this article. A constructed sigN null mutant was delayed in development and exhibited a bald phenotype when grown on minimal medium containing glucose as carbon source. One of two distinct sigN promoters, sigNP1, was active only during growth on solid medium, when its activation coincided with aerial hyphae formation. Transcription from sigNP1 was readily detected in several whi mutants (interrupted in morphogenesis of aerial mycelium into spores), but was absent from all bld mutants tested, suggesting that sigNP1 activity was restricted to the aerial hyphae. It also depended on sigN, thus sigN was autoregulated. Mutational and transcription studies revealed no functional significance to the location of sigN next to sigF, encoding another SigB-like sigma factor. We identified another potential SigN target, nepA, encoding a putative small secreted protein. Transcription of nepA originated from a single, aerial hyphae-specific and sigN-dependent promoter. While in vitro run-off transcription using purified SigN on the Bacillus subtilis ctc promoter confirmed that SigN is an RNA polymerase sigma factor, SigN failed to initiate transcription from sigNP1 and from the nepA promoter in vitro. Additional in vivo data indicated that further nepA upstream sequences, which are likely to bind a potential activator, are required for successful transcription. Using a nepA-egfp transcriptional fusion we located nepA transcription to a novel compartment, the 'subapical stem' of the aerial hyphae. We suggest that this newly recognized compartment defines an interface between the aerial and vegetative parts of the Streptomyces colony and might also be involved in communication between these two compartments.
Collapse
Affiliation(s)
- Kate A Dalton
- University of East Anglia, School of Biological Sciences, Norwich NR47TJ, UK
| | | | | | | |
Collapse
|
706
|
Affiliation(s)
- Clarissa J Nobile
- Department of Microbiology, Columbia University, New York, New York 10032, USA
| | | |
Collapse
|
707
|
Anderson JC, Voigt CA, Arkin AP. Environmental signal integration by a modular AND gate. Mol Syst Biol 2007; 3:133. [PMID: 17700541 PMCID: PMC1964800 DOI: 10.1038/msb4100173] [Citation(s) in RCA: 284] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 07/06/2007] [Indexed: 11/25/2022] Open
Abstract
Microorganisms use genetic circuits to integrate environmental information. We have constructed a synthetic AND gate in the bacterium Escherichia coli that integrates information from two promoters as inputs and activates a promoter output only when both input promoters are transcriptionally active. The integration occurs via an interaction between an mRNA and tRNA. The first promoter controls the transcription of a T7 RNA polymerase gene with two internal amber stop codons blocking translation. The second promoter controls the amber suppressor tRNA supD. When both components are transcribed, T7 RNA polymerase is synthesized and this in turn activates a T7 promoter. Because inputs and outputs are promoters, the design is modular; that is, it can be reconnected to integrate different input signals and the output can be used to drive different cellular responses. We demonstrate this modularity by wiring the gate to integrate natural promoters (responding to Mg2+ and AI-1) and using it to implement a phenotypic output (invasion of mammalian cells). A mathematical model of the transfer function is derived and parameterized using experimental data.
Collapse
MESH Headings
- Arabinose/pharmacology
- Bacteriophage T7/enzymology
- Bacteriophage T7/genetics
- Codon, Nonsense
- DNA-Directed RNA Polymerases/biosynthesis
- DNA-Directed RNA Polymerases/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial/drug effects
- Gene Expression Regulation, Viral/drug effects
- Genes, Reporter
- Genes, Suppressor
- Genes, Viral/drug effects
- Genetic Engineering/methods
- Green Fluorescent Proteins/biosynthesis
- Green Fluorescent Proteins/genetics
- Magnesium/pharmacology
- Models, Genetic
- Promoter Regions, Genetic/drug effects
- Protein Biosynthesis
- RNA, Bacterial/genetics
- RNA, Messenger/genetics
- RNA, Transfer/genetics
- RNA, Transfer, Ser/genetics
- RNA, Viral/genetics
- Salicylates/pharmacology
- Systems Biology
- Viral Proteins/biosynthesis
- Viral Proteins/genetics
Collapse
Affiliation(s)
- J Christopher Anderson
- Department of Pharmaceutical Chemistry, QB3: California Institute for Quantitative Biological Research, The University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering, University of California, Howard Hughes Medical Institute, QB3: California Institute for Quantitative Biological Research, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher A Voigt
- Department of Pharmaceutical Chemistry, QB3: California Institute for Quantitative Biological Research, The University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, The University of California—San Francisco, Box 2540, Room 408C, 1700 4th Street, San Francisco, CA 94158-2330, USA. Tel.: +1 41 55027050; Fax: +1 41 55024690;
| | - Adam P Arkin
- Department of Bioengineering, University of California, Howard Hughes Medical Institute, QB3: California Institute for Quantitative Biological Research, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| |
Collapse
|
708
|
Sher D, Fishman Y, Melamed-Book N, Zhang M, Zlotkin E. Osmotically driven prey disintegration in the gastrovascular cavity of the green hydra by a pore‐forming protein. FASEB J 2007; 22:207-14. [PMID: 17679608 DOI: 10.1096/fj.07-9133com] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Pore-forming proteins (PFPs) are water-soluble proteins able to integrate into target membranes to form transmembrane pores. They are common determinants of bacterial pathogenicity and are often found in animal venoms. We recently isolated and characterized Hydralysins (Hlns), paralytic PFPs from the venomous green hydra Chlorohydra viridissima that are not found within the nematocytes, suggesting they are not involved in prey capture. The present study aimed to decipher the biological role of Hlns. Using in situ hybridization and immunohistochemistry, we show that Hlns are expressed by digestive cells surrounding the gastrovascular cavity (GVC) of Chlorohydra and secreted onto the prey during feeding. At biologically relevant concentrations, Hlns bind prey membranes and form pores, lysing the cells and disintegrating the prey tissue. Hlns are unable to bind Chlorohydra membranes, thus protecting the producing animal from the destructive effect of its own cytolytic protein. We suggest that osmotic disintegration of the prey within the GVC by Hlns, followed by phagocytosis and intracellular digestion, allows the soft-bodied green hydra to feed on hard, cuticle-covered prey while lacking the physical means to mechanically disintegrate it. Our results extend the biological significance of PFPs beyond the commonly expected offensive or defensive roles.
Collapse
Affiliation(s)
- Daniel Sher
- Department of Cell and Animal Biology, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
| | | | | | | | | |
Collapse
|
709
|
Abstract
In this issue of Chemistry & Biology, Angell et al. demonstrate synergism between two bacterial species, isolated from the same sediment sample, to produce a secondary metabolite not found in their respective pure cultures.
Collapse
Affiliation(s)
- Helge B Bode
- Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, P.O. Box 151150, 66041 Saarbrücken, Germany
| |
Collapse
|
710
|
Affiliation(s)
- Elizabeth A George
- Rockefeller University, Tri-Institutional Training Program in Chemical Biology, NY 10021, USA
| | | |
Collapse
|
711
|
Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res 2007; 35:4809-19. [PMID: 17621584 PMCID: PMC1950547 DOI: 10.1093/nar/gkm487] [Citation(s) in RCA: 231] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in ε-proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered.
Collapse
Affiliation(s)
- Zasha Weinberg
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
- *To whom correspondence should be addressed.(203) 432-6554(203) 432-6161
| | - Jeffrey E. Barrick
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Zizhen Yao
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Adam Roth
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Jane N. Kim
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Jeremy Gore
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Joy Xin Wang
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Elaine R. Lee
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Kirsten F. Block
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Narasimhan Sudarsan
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Shane Neph
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Martin Tompa
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Walter L. Ruzzo
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington, Box 352350, Seattle, WA 98195-2350, USA
| |
Collapse
|
712
|
Gao M, Chen H, Eberhard A, Gronquist MR, Robinson JB, Connolly M, Teplitski M, Rolfe BG, Bauer WD. Effects of AiiA-mediated quorum quenching in Sinorhizobium meliloti on quorum-sensing signals, proteome patterns, and symbiotic interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:843-56. [PMID: 17601171 DOI: 10.1094/mpmi-20-7-0843] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Many behaviors in bacteria, including behaviors important to pathogenic and symbiotic interactions with eukaryotic hosts, are regulated by a mechanism called quorum sensing (QS). A "quorum-quenching" approach was used here to identify QS-regulated behaviors in the N-fixing bacterial symbiont Sinorhizobium meliloti. The AiiA lactonase from Bacillus produced in S. meliloti was shown to enzymatically inactivate S. meliloti's N-acyl homoserine lactone (AHL) QS signals, thereby disrupting normal QS regulation. Sixty proteins were differentially accumulated in the AiiA-producing strain versus the control in early log or early stationary phase cultures. Fifty-two of these QS-regulated proteins, with putative functions that include cell division, protein processing and translation, metabolite transport, oxidative stress, and amino acid metabolism, were identified by peptide mass fingerprinting. Transcription of representative genes was reduced significantly in the AiiA-producing strain, although the effects of AiiA on protein accumulation did not always correspond to effects on transcription. The QS signal-deficient strain was reduced significantly in nodule initiation during the first 12 h after inoculation onto Medicago truncatula host plants. The AiiA lactonase also was found to substantially inactivate two of the AHL mimic compounds secreted by M. truncatula. This suggests some structural similarity between bacterial AHLs and these mimic compounds. It also indicates that quorum quenching could be useful in identifying Sinorhizobium genes that are affected by such host QS mimics in planta.
Collapse
Affiliation(s)
- Mengsheng Gao
- Department of Soil and Water Sciences, 2159 McCarty Hall A, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville 32611-0290, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
713
|
Zhang L, Jia Y, Wang L, Fang R. A proline iminopeptidase gene upregulatedin plantaby a LuxR homologue is essential for pathogenicity ofXanthomonas campestrispv.campestris. Mol Microbiol 2007; 65:121-36. [PMID: 17581124 DOI: 10.1111/j.1365-2958.2007.05775.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Expression of bacterial genes is often regulated by complex mechanisms, some of which involve host cues. Analysis of the Xanthomonas campestris pv. campestris (Xcc) genome sequence revealed the presence of an xccR/pip locus. The upstream gene xccR is a luxR homologue, while pip codes for a proline iminopeptidase. A lux box-like element, named luxXc box, locates in the pip promoter region. In this work, we show that disruption of either xccR or pip resulted in significantly attenuated virulence of Xcc. Under medium culture conditions, the pip expression was significantly enhanced by overexpression of XccR and the luxXc box is necessary for this enhancement. We further show that expression of a pip promoter-gusA fusion either inserted in the bacterial chromosome or resided in a plasmid was markedly induced when the bacteria grew in planta. Disruption of either xccR or the luxXc box abolished the in planta induction, while disruption of pip enhanced the induction. Taken together, these data demonstrate that pip is indispensable for Xcc virulence and suggest a model for Xcc-host interaction in which the pathogen senses some host factor(s) to activate XccR that subsequently interacts with the luxXc box to induce the expression of pip for facilitating Xcc infection.
Collapse
Affiliation(s)
- Lili Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | |
Collapse
|
714
|
Rader BA, Campagna SR, Semmelhack MF, Bassler BL, Guillemin K. The quorum-sensing molecule autoinducer 2 regulates motility and flagellar morphogenesis in Helicobacter pylori. J Bacteriol 2007; 189:6109-17. [PMID: 17586631 PMCID: PMC1951907 DOI: 10.1128/jb.00246-07] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The genome of the gastric pathogen Helicobacter pylori contains a homologue of the gene luxS, which has been shown to be responsible for production of the quorum-sensing signal autoinducer 2 (AI-2). We report here that deletion of the luxS gene in strain G27 resulted in decreased motility on soft agar plates, a defect that was complemented by a wild-type copy of the luxS gene and by the addition of cell-free supernatant containing AI-2. The flagella of the luxS mutant appeared normal; however, in genetic backgrounds lacking any of three flagellar regulators--the two-component sensor kinase flgS, the sigma factor sigma28 (also called fliA), and the anti-sigma factor flgM--loss of luxS altered flagellar morphology. In all cases, the double mutant phenotypes were restored to the luxS+ phenotype by the addition of synthetic 4,5-dihydroxy-2,3-pentanedione (DPD), which cyclizes to form AI-2. Furthermore, in all mutant backgrounds loss of luxS caused a decrease in transcript levels of the flagellar regulator flhA. Addition of DPD to luxS cells induced flhA transcription in a dose-dependent manner. Deletion of flhA in a wild-type or luxS mutant background resulted in identical loss of motility, flagella, and flagellar gene expression. These data demonstrate that AI-2 functions as a secreted signaling molecule upstream of FlhA and plays a critical role in global regulation of flagellar gene transcription in H. pylori.
Collapse
Affiliation(s)
- Bethany A Rader
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | | | | | | | | |
Collapse
|
715
|
Verhamme DT, Kiley TB, Stanley-Wall NR. DegU co-ordinates multicellular behaviour exhibited by Bacillus subtilis. Mol Microbiol 2007; 65:554-68. [PMID: 17590234 DOI: 10.1111/j.1365-2958.2007.05810.x] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Unicellular organisms use a variety of mechanisms to co-ordinate activity within a community and accomplish complex multicellular processes. Because some of the processes that are exhibited by one species can be physiologically incompatible, it raises the question of how entry into these different pathways is regulated. In the Gram-positive bacterium Bacillus subtilis, genetic competence, swarming motility, biofilm formation, complex colony architecture and protease production are all regulated by the response regulator DegU. DegU appears to integrate environmental signals and co-ordinate multicellular behaviours that are subsequently manifested at different levels of DegU phosphorylation. Data are presented which indicate that: (i) swarming motility is activated by very low levels of DegU approximately P that can be generated independently from its cognate sensor kinase DegS; (ii) complex colony architecture is activated by low levels of DegU approximately P that are produced in a DegS-dependent manner to activate transcription of yvcA, a novel gene required for complex colony architecture; and (iii) high levels of DegU approximately P inhibit complex colony architecture and swarming motility but are required prior to the activation of exoprotease production. A model is proposed to explain why such a system may have evolved within B. subtilis to control these multicellular processes through a single regulator.
Collapse
Affiliation(s)
- Daniël T Verhamme
- Division of Environmental and Applied Biology, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, Dundee DD1 4EH, UK
| | | | | |
Collapse
|
716
|
Abstract
Pathogenic bacteria have developed numerous mechanisms to survive inside a hostile host environment. The human pathogen Mycobacterium tuberculosis (M. tb) is thought to control the human immune response with diverse biomolecules, including a variety of exotic lipids. One prevalent M. tb-specific sulfated metabolite, termed sulfolipid-1 (SL-1), has been correlated with virulence though its specific biological function is not known. Recent advances in our understanding of SL-1 biosynthesis will help elucidate the role of this curious metabolite in M. tb infection. Furthermore, the study of SL-1 has led to questions regarding the significance of sulfation in mycobacteria. Examples of sulfated metabolites as mediators of interactions between bacteria and plants suggest that sulfation is a key modulator of extracellular signaling between prokaryotes and eukaryotes. The discovery of novel sulfated metabolites in M. tb and related mycobacteria strengthens this hypothesis. Finally, mechanistic and structural data from sulfate-assimilation enzymes have revealed how M. tb controls the flux of sulfate in the cell. Mutants with defects in sulfate assimilation indicate that the fate of sulfur in M. tb is a critical survival determinant for the bacteria during infection and suggest novel targets for tuberculosis drug therapy.
Collapse
Affiliation(s)
- Michael W Schelle
- Department of Chemistry, University of California Berkeley, CA 94720, USA
| | | |
Collapse
|
717
|
Pomianek ME, Semmelhack MF. Making bacteria behave: new agonists and antagonists of quorum sensing. ACS Chem Biol 2007; 2:293-5. [PMID: 17518429 DOI: 10.1021/cb700098c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small-molecule agonists and antagonists of bacterial quorum sensing can enhance our understanding of this form of cell-cell communication. A recent effort has discovered effective modulators of the autoinducer-1 circuit for bacterial quorum sensing by the synthesis and evaluation of a small library of aryl-substituted acyl-homoserine lactone analogues. This series highlights the sensitivity to structure of the contrasting responses of agonism and antagonism of the natural signal and identifies an analogue that provokes the same response as the natural signal but at 10-fold lower concentration, a "superagonist".
Collapse
Affiliation(s)
- Megan E Pomianek
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | | |
Collapse
|
718
|
Geske GD, O’Neill JC, Blackwell HE. N-phenylacetanoyl-L-homoserine lactones can strongly antagonize or superagonize quorum sensing in Vibrio fischeri. ACS Chem Biol 2007; 2:315-9. [PMID: 17480049 PMCID: PMC2635011 DOI: 10.1021/cb700036x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria monitor their population densities using low-molecular-weight ligands in a process known as quorum sensing. At sufficient cell densities, bacteria can change their mode of growth and behave as multicellular communities that play critical roles in both beneficial symbioses and the pathogenesis of infectious disease. The development of non-native ligands that can block quorum-sensing signals has emerged as a promising new strategy to attenuate these divergent outcomes. Here, we report that N-phenylacetanoyl-L-homoserine lactones are capable of either inhibiting or, in some cases, strongly inducing quorum sensing in the bacterial symbiont Vibrio fischeri. Moreover, simple structural modifications to these ligands have remarkable effects on activity. These studies have revealed one of the first synthetic superagonists of quorum sensing, N-(3-nitro-phenylacetanoyl)-L-homoserine lactone. Together, these ligands represent a powerful new class of chemical probes with the potential to significantly expand the current understanding of quorum sensing and its role in host/bacteria interactions.
Collapse
|
719
|
Bejerano-Sagie M, Xavier KB. The role of small RNAs in quorum sensing. Curr Opin Microbiol 2007; 10:189-98. [PMID: 17387037 DOI: 10.1016/j.mib.2007.03.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Accepted: 03/14/2007] [Indexed: 11/16/2022]
Abstract
Quorum sensing is a form of cell-cell signaling in bacteria that provides information regarding population density, species composition, and environmental and metabolic signals. It enables community-wide coordination of gene expression, and presumably benefits group behaviors. Multiple regulatory small RNAs (sRNAs) act centrally in quorum sensing, integrating signals with other environmental stimuli, to produce an appropriate output.
Collapse
|
720
|
Abstract
This Review summarizes methods for constructing systems and structures at micron or submicron scales that have applications in microbiology. These tools make it possible to manipulate individual cells and their immediate extracellular environments and have the capability to transform the study of microbial physiology and behaviour. Because of their simplicity, low cost and use in microfabrication, we focus on the application of soft lithographic techniques to the study of microorganisms, and describe several key areas in microbiology in which the development of new microfabricated materials and tools can have a crucial role.
Collapse
Affiliation(s)
- Douglas B Weibel
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.
| | | | | |
Collapse
|
721
|
Kato JY, Funa N, Watanabe H, Ohnishi Y, Horinouchi S. Biosynthesis of gamma-butyrolactone autoregulators that switch on secondary metabolism and morphological development in Streptomyces. Proc Natl Acad Sci U S A 2007; 104:2378-83. [PMID: 17277085 PMCID: PMC1892969 DOI: 10.1073/pnas.0607472104] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) is a representative of the gamma-butyrolactone autoregulators that trigger secondary metabolism and morphogenesis in the Gram-positive, filamentous bacterial genus Streptomyces. Here, we report the A factor biosynthesis pathway in Streptomyces griseus. The monomeric AfsA, containing a tandem repeat domain of approximately 80 aa, catalyzed beta-ketoacyl transfer from 8-methyl-3-oxononanoyl-acyl carrier protein to the hydroxyl group of dihydroxyacetone phosphate (DHAP), thus producing an 8-methyl-3-oxononanoyl-DHAP ester. The fatty acid ester was nonenzymatically converted to a butenolide phosphate by intramolecular aldol condensation. The butenolide phosphate was then reduced by BprA that was encoded just downstream of afsA. The phosphate group on the resultant butanolide was finally removed by a phosphatase, resulting in formation of A factor. The 8-methyl-3-oxononanoyl-DHAP ester produced by the action of AfsA was also converted to A factor in an alternative way; the phosphate group on the ester was first removed by a phosphatase and the dephosphorylated ester was converted nonenzymatically to a butenolide, which was then reduced by a reductase different from BprA, resulting in A factor. Because introduction of afsA alone into Escherichia coli caused the host to produce a substance having A factor activity, the reductase(s) and phosphatase(s) were not specific to the A factor biosynthesis but commonly present in bacteria. AfsA is thus the key enzyme for the biosynthesis of gamma-butyrolactones.
Collapse
Affiliation(s)
| | | | - Hidenori Watanabe
- Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | - Sueharu Horinouchi
- Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
722
|
Shepherd RW, Wagner GJ. Phylloplane proteins: emerging defenses at the aerial frontline? TRENDS IN PLANT SCIENCE 2007; 12:51-6. [PMID: 17208510 DOI: 10.1016/j.tplants.2006.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 10/27/2006] [Accepted: 12/20/2006] [Indexed: 05/13/2023]
Abstract
The phylloplane, or leaf surface, is an interkingdom crossroads between plants and microorganisms, and secretion of antimicrobial biochemicals to aerial surfaces is thought to be one defensive strategy by which plants deter potential pathogens. Secondary metabolites on leaf surfaces are well documented but antimicrobial phylloplane proteins have only recently been identified. In this review, we describe the physical structures and biochemicals of the phylloplane and briefly discuss protein-based surface defenses of animals. We also review the emerging evidence pertaining to antimicrobial phylloplane proteins and mechanisms by which proteins can be released to the phylloplane, including biosynthesis (e.g. phylloplanins) by specific trichomes and delivery in guttation fluid from hydathodes. Future research should lead to exciting advances in our understanding of the phylloplane and to useful biotechnological interventions.
Collapse
Affiliation(s)
- Ryan W Shepherd
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
| | | |
Collapse
|
723
|
Brown SP, Cornell SJ, Sheppard M, Grant AJ, Maskell DJ, Grenfell BT, Mastroeni P. Intracellular demography and the dynamics of Salmonella enterica infections. PLoS Biol 2007; 4:e349. [PMID: 17048989 PMCID: PMC1609125 DOI: 10.1371/journal.pbio.0040349] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 08/21/2006] [Indexed: 11/19/2022] Open
Abstract
An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance. Modeling of infection shows that heterogeneities in bacterial burden per host cell need not be explained by differences in host cell permissiveness; this has important implications for understanding the ecology of infection.
Collapse
Affiliation(s)
- Sam P Brown
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
724
|
Arai T, Matsuoka S, Cho HY, Yukawa H, Inui M, Wong SL, Doi RH. Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation. Proc Natl Acad Sci U S A 2007; 104:1456-60. [PMID: 17244702 PMCID: PMC1785254 DOI: 10.1073/pnas.0610740104] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of two strains of bacteria to cooperate in the synthesis of an enzyme complex (a minicellulosome) was examined. Three strains of Bacillus subtilis were constructed to express Clostridium cellulovorans genes engB, xynB, and minicbpA. MiniCbpA, EngB, and XynB were synthesized and secreted into the medium by B. subtilis. When the strains with the minicbpA and engB genes or with xynB were cocultured, minicellulosomes were synthesized, consisting in one case of miniCbpA and EngB and in the second case of miniCbpA and XynB. Both minicellulosomes showed their respective enzymatic activities. We call this phenomenon "intercellular complementation." Interesting implications concerning bacterial cooperation are suggested from these results.
Collapse
Affiliation(s)
- Takamitsu Arai
- *Section of Molecular and Cellular Biology, University of California, Davis, CA 95616-8535
- Research Institute of Innovative Technology for the Earth, Kyoto 619-0292, Japan; and
| | - Satoshi Matsuoka
- *Section of Molecular and Cellular Biology, University of California, Davis, CA 95616-8535
| | - Hee-Yeon Cho
- *Section of Molecular and Cellular Biology, University of California, Davis, CA 95616-8535
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth, Kyoto 619-0292, Japan; and
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kyoto 619-0292, Japan; and
| | - Sui-Lam Wong
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Roy H. Doi
- *Section of Molecular and Cellular Biology, University of California, Davis, CA 95616-8535
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
725
|
Abstract
For the past five decades, the need for new antibiotics has been met largely by semisynthetic tailoring of natural product scaffolds discovered in the middle of the 20(th) century. More recently, however, advances in technology have sparked a resurgence in the discovery of natural product antibiotics from bacterial sources. In particular, efforts have refocused on finding new antibiotics from old sources (for example, streptomycetes) and new sources (for example, other actinomycetes, cyanobacteria and uncultured bacteria). This has resulted in several newly discovered antibiotics with unique scaffolds and/or novel mechanisms of action, with the potential to form a basis for new antibiotic classes addressing bacterial targets that are currently underexploited.
Collapse
Affiliation(s)
- Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | |
Collapse
|
726
|
|
727
|
Dubuis C, Haas D. Cross-species GacA-controlled induction of antibiosis in pseudomonads. Appl Environ Microbiol 2006; 73:650-4. [PMID: 17098922 PMCID: PMC1796963 DOI: 10.1128/aem.01681-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Signal extracts prepared from culture supernatants of Pseudomonas fluorescens CHA0 and Pseudomonas aeruginosa PAO stimulated GacA-dependent expression of small RNAs and hence of antibiotic compounds in both hosts. Pseudomonas corrugata LMG2172 and P. fluorescens SBW25 also produced signal molecules stimulating GacA-controlled antibiotic synthesis in strain CHA0, illustrating a novel, N-acyl-homoserine lactone-independent type of interspecies communication.
Collapse
Affiliation(s)
- Christophe Dubuis
- Département de Microbiologie Fondamentale, Université de Lausanne, CH-1015 Lausanne, Switzerland
| | | |
Collapse
|
728
|
Graumann PL. Different genetic programmes within identical bacteria under identical conditions: the phenomenon of bistability greatly modifies our view on bacterial populations. Mol Microbiol 2006; 61:560-3. [PMID: 16879638 DOI: 10.1111/j.1365-2958.2006.05264.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two different behavioural or developmental patters can operate within a single bacterial population in which all of the cells are exposed to the same environmental conditions. Investigations of single cells using green fluorescent protein reveal that a bacterial population can be composed of two distinct fractions in different physiological states, and that cells can even switch between states. Such behaviour, termed 'bistability', can occur even in exponentially growing populations, in which cells have always been regarded as behaving almost identically and having the same pattern of gene expression. In this issue of Molecular Microbiology, Dubnau and Losick review four examples of such bistable populations found in two different bacterial species, and explain why this behaviour makes sense. These investigations have established the new concept of genetically identical cells that behave differently, which will profoundly change how we view bacterial populations.
Collapse
Affiliation(s)
- Peter L Graumann
- Institut für Mikrobiologie, Fachbereich Biologie II, Universität Freiburg, Schänzle Strasse 1, 79104 Freiburg, Germany.
| |
Collapse
|
729
|
Abstract
In a process called quorum sensing, bacteria produce and secrete certain signaling compounds (called autoinducers) that bind to receptors on other bacteria and activate transcription of certain genes. A clever genetic selection yields a new quorum-sensing transcriptional regulator that marches to the beat of a different drummer.
Collapse
Affiliation(s)
- Stephen C Winans
- Department of Microbiology, 360A Wing Hall, Cornell University, Ithaca, New York 14853, USA.
| |
Collapse
|