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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 23 August 2011, Vol.108(34), pp.14181-5
    Description: Bacteria commonly grow in densely populated surface-bound communities, termed biofilms, where they gain benefits including superior access to nutrients and resistance to environmental insults. The secretion of extracellular polymeric substances (EPS), which bind bacterial collectives together, is ubiquitously associated with biofilm formation. It is generally assumed that EPS secretion is a cooperative phenotype that benefits all neighboring cells, but in fact little is known about the competitive and evolutionary dynamics of EPS production. By studying Vibrio cholerae biofilms in microfluidic devices, we show that EPS-producing cells selectively benefit their clonemates and gain a dramatic advantage in competition against an isogenic EPS-deficient strain. However, this advantage carries an ecological cost beyond the energetic requirement for EPS production: EPS-producing cells are impaired for dispersal to new locations. Our study establishes that a fundamental tradeoff between local competition and dispersal exists among bacteria. Furthermore, this tradeoff can be governed by a single phenotype.
    Keywords: Biofilms ; Biological Evolution ; Vibrio Cholerae -- Physiology
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States, March 12, 2013, Vol.110(11), p.4345(6)
    Description: Biofilms are antibiotic-resistant, sessile bacterial communities that occupy most moist surfaces on Earth and cause chronic and medical device-associated infections. Despite their importance, basic information about biofilm dynamics in common ecological environments is lacking. Here, we demonstrate that flow through soil-like porous materials, industrial filters, and medical stents dramatically modifies the morphology of Pseudomonas aeruginosa biofilms to form 3D streamers, which, over time, bridge the spaces between obstacles and corners in nonuniform environments. We discovered that accumulation of surface-attached biofilm has little effect on flow through such environments, whereas biofilm streamers cause sudden and rapid clogging. We demonstrate that flow-induced shedding of extracellular matrix from surface-attached biofilms generates a sieve-like network that captures cells and other biomass, which add to the existing network, causing exponentially fast clogging independent of growth. These results suggest that biofilm streamers are ubiquitous in nature and strongly affect flow through porous materials in environmental, industrial, and medical systems. bioclogging | biofouling | porous media doi/10.1073/pnas.1300321110
    Keywords: Medical Equipment -- Research
    ISSN: 0027-8424
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  • 3
    In: The Journal of Bacteriology, 2011, Vol. 193(15), p.3871
    Description: The bacterial pathogen Chromobacterium violaceum uses a LuxIR-type quorum-sensing system to detect and respond to changes in cell population density. CviI synthesizes the autoinducer C...-homoserine lactone (C...-HSL), and CviR is a cytoplasmic DNA binding transcription factor that activates gene expression following binding to C...-HSL. A number of behaviors are controlled by quorum sensing in C. violaceum. However, few genes have been shown to be directly controlled by CviR, in part because the DNA motif bound by CviR is not well characterized. Here, we define the DNA sequence required for promoter recognition by CviR. Using in vivo data generated from a library of point mutations in a CviR-regulated promoter, we find that CviR binds to a palindrome with the ideal sequence CTGNCCNNNNGGNCAG. We constructed a position weight matrix using these in vivo data and scanned the C. violaceum genome to predict CviR binding sites. We measured direct activation of the identified promoters by CviR and found that CviR controls the expression of the promoter for a chitinase, a type VI secretion-related gene, a transcriptional regulator gene, a guanine deaminase gene, and cviI. Indeed, regulation of cviI expression by CviR generates a canonical quorum-sensing positive-feedback loop. (ProQuest: ... denotes formulae/symbols omitted.)
    Keywords: Gram-Negative Bacteria ; Deoxyribonucleic Acid–DNA ; Gene Expression ; Binding Sites ; Biosynthesis;
    ISSN: 0021-9193
    ISSN: 00219193
    E-ISSN: 10985530
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  • 4
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 03 November 2015, Vol.112(44), pp.E6038-47
    Description: Five homologous noncoding small RNAs (sRNAs), called the Qrr1-5 sRNAs, function in the Vibrio harveyi quorum-sensing cascade to drive its operation. Qrr1-5 use four different regulatory mechanisms to control the expression of ∼ 20 mRNA targets. Little is known about the roles individual nucleotides play in mRNA target selection, in determining regulatory mechanism, or in defining Qrr potency and dynamics of target regulation. To identify the nucleotides vital for Qrr function, we developed a method we call RSort-Seq that combines saturating mutagenesis, fluorescence-activated cell sorting, high-throughput sequencing, and mutual information theory to explore the role that every nucleotide in Qrr4 plays in regulation of two mRNA targets, luxR and luxO. Companion biochemical assays allowed us to assign specific regulatory functions/underlying molecular mechanisms to each important base. This strategy yielded a regional map of nucleotides in Qrr4 vital for stability, Hfq interaction, stem-loop formation, and base pairing to both luxR and luxO, to luxR only, and to luxO only. In terms of nucleotides critical for sRNA function, the RSort-Seq analysis provided strikingly different results from those predicted by commonly used regulatory RNA-folding algorithms. This approach is applicable to any RNA-RNA interaction, including sRNAs in other bacteria and regulatory RNAs in higher organisms.
    Keywords: Qrr ; Rsort-Seq ; Quorum Sensing ; Regulation ; Regulatory Srna ; Quorum Sensing ; Escherichia Coli -- Physiology ; Nucleotides -- Physiology ; RNA, Untranslated -- Physiology ; Vibrio -- Physiology
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 17 February 2015, Vol.112(7), pp.E766-75
    Description: Quorum sensing (QS) is a process of cell-to-cell communication that enables bacteria to transition between individual and collective lifestyles. QS controls virulence and biofilm formation in Vibrio cholerae, the causative agent of cholera disease. Differential RNA sequencing (RNA-seq) of wild-type V. cholerae and a locked low-cell-density QS-mutant strain identified 7,240 transcriptional start sites with ∼ 47% initiated in the antisense direction. A total of 107 of the transcripts do not appear to encode proteins, suggesting they specify regulatory RNAs. We focused on one such transcript that we name VqmR. vqmR is located upstream of the vqmA gene encoding a DNA-binding transcription factor. Mutagenesis and microarray analyses demonstrate that VqmA activates vqmR transcription, that vqmR encodes a regulatory RNA, and VqmR directly controls at least eight mRNA targets including the rtx (repeats in toxin) toxin genes and the vpsT transcriptional regulator of biofilm production. We show that VqmR inhibits biofilm formation through repression of vpsT. Together, these data provide to our knowledege the first global annotation of the transcriptional start sites in V. cholerae and highlight the importance of posttranscriptional regulation for collective behaviors in this human pathogen.
    Keywords: RNA-Seq ; Vibrio Cholerae ; Biofilm ; Quorum Sensing ; Srna ; Biofilms ; Sequence Analysis, RNA ; RNA, Viral -- Genetics ; Vibrio Cholerae -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 29 October 2013, Vol.110(44), pp.17981-6
    Description: Quorum sensing is a chemical communication process that bacteria use to regulate collective behaviors. Disabling quorum-sensing circuits with small molecules has been proposed as a potential strategy to prevent bacterial pathogenicity. The human pathogen Pseudomonas aeruginosa uses quorum sensing to control virulence and biofilm formation. Here, we analyze synthetic molecules for inhibition of the two P. aeruginosa quorum-sensing receptors, LasR and RhlR. Our most effective compound, meta-bromo-thiolactone (mBTL), inhibits both the production of the virulence factor pyocyanin and biofilm formation. mBTL also protects Caenorhabditis elegans and human lung epithelial cells from killing by P. aeruginosa. Both LasR and RhlR are partially inhibited by mBTL in vivo and in vitro; however, RhlR, not LasR, is the relevant in vivo target. More potent antagonists do not exhibit superior function in impeding virulence. Because LasR and RhlR reciprocally control crucial virulence factors, appropriately tuning rather than completely inhibiting their activities appears to hold the key to blocking pathogenesis in vivo.
    Keywords: Bacterial Proteins -- Antagonists & Inhibitors ; Biofilms -- Growth & Development ; Pseudomonas Aeruginosa -- Pathogenicity ; Quorum Sensing -- Physiology ; Trans-Activators -- Antagonists & Inhibitors
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 7
    In: Molecular Microbiology, June 2014, Vol.92(5), pp.921-930
    Description: Type secretion is critical for to successfully combat phagocytic eukaryotes and to survive in the presence of competing bacterial species. type secretion system genes are encoded in one large and two small clusters. In , type secretion is controlled by quorum sensing, the cell–cell communication process that enables bacteria to orchestrate group behaviours. The quorum‐sensing response regulator represses type secretion genes at low cell density and the quorum‐sensing regulator activates type secretion genes at high cell density. We demonstrate that the quorum regulatory small () that function between and in the quorum‐sensing cascade are required for these regulatory effects. The control type secretion via two mechanisms: they repress expression of the large type secretion system cluster through base pairing and they repress , the activator of the two small type secretion clusters. This regulatory arrangement ensures that the large cluster encoding many components of the secretory machine is expressed prior to the two small clusters that encode the secreted effectors. ‐dependent regulation of the type secretion system is conserved in pandemic and non‐pandemic strains.
    Keywords: Cholera Toxin;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 8
    Language: English
    In: Molecular Microbiology, Feb, 2012, Vol.83(3), p.599(13)
    Description: To authenticate to the full-text of this article, please visit this link: http://dx.doi.org/10.1111/j.1365-2958.2011.07959.x Byline: Yi Shao (1), Bonnie L. Bassler (1,2) Abstract: Summary Quorum sensing is a mechanism of cell-cell communication that bacteria use to control collective behaviours including bioluminescence, biofilm formation and virulence factor production. In the Vibrio harveyi and Vibrio cholerae quorum-sensing circuits, multiple non-coding small regulatory RNAs called the quorum-regulated small RNAs (Qrr sRNAs) function to establish the global quorum-sensing gene expression pattern by modulating translation of multiple mRNAs encoding quorum-sensing regulatory factors. Here we show that the Qrr sRNAs post-transcriptionally activate production of the low cell density master regulator AphA through base pairing to aphA mRNA, and this is crucial for the accumulation of appropriate levels of AphA protein at low cell density. We find that the Qrr sRNAs use unique pairing regions to discriminate between their different targets. Qrr1 is not as effective as Qrr2-5 in activating aphA because Qrr1 lacks one of two required pairing regions. However, Qrr1 is equally effective as the other Qrr sRNAs at controlling targets like luxR and luxO because it harbours all of the required pairing regions for these targets. Sequence comparisons reveal that Vibrionaceae species possessing only qrr1 do not have the aphA gene under Qrr sRNA control. Our findings suggest co-evolving relationships between particular Qrr sRNAs and particular mRNA targets. Author Affiliation: (1)Department of Molecular Biology, Princeton University, Princeton, NJ, USA (2)Howard Hughes Medical Institute, Chevy Chase, MD, USA Article History: Accepted 13 December, 2011. Article note: (*) E-mail bbassler@princeton.edu; Tel. (+1) 609 258 2857; Fax (+1) 609 258 2957.
    Keywords: Messenger Rna -- Analysis ; Gene Expression -- Analysis ; Cholera Toxin -- Analysis ; Genes -- Analysis
    ISSN: 0950-382X
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  • 9
    Language: English
    In: Cell, 23 August 2018, Vol.174(5), pp.1328-1328.e1
    Description: Quorum sensing (QS) is a chemical communication process that bacteria use to orchestrate group behaviors. QS involves the production, release, and population-wide detection of signaling molecules called autoinducers. QS-controlled behaviors are unproductive when undertaken by a single bacterium but become effective when performed by the group. This SnapShot highlights model QS circuits, the molecules used for communication, QS-controlled behaviors, and exciting future challenges. To view this SnapShot, open or download the PDF. Quorum sensing (QS) is a chemical communication process that bacteria use to orchestrate group behaviors. QS involves the production, release, and population-wide detection of signaling molecules called autoinducers. QS-controlled behaviors are unproductive when undertaken by a single bacterium but become effective when performed by the group. This SnapShot highlights model QS circuits, the molecules used for communication, QS-controlled behaviors, and exciting future challenges. To view this SnapShot, open or download the PDF.
    Keywords: Biology
    ISSN: 0092-8674
    E-ISSN: 1097-4172
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  • 10
    Language: English
    In: Biophysical Journal, 2011, Vol.100(12), pp.3045-3053
    Description: Gene expression is stochastic, and noise that arises from the stochastic nature of biochemical reactions propagates through active regulatory links. Thus, correlations in gene-expression noise can provide information about regulatory links. We present what to our knowledge is a new approach to measure and interpret such correlated fluctuations at the level of single microcolonies, which derive from single cells. We demonstrated this approach mathematically using stochastic modeling, and applied it to experimental time-lapse fluorescence microscopy data. Specifically, we investigated the relationships among LuxO, LuxR, and the small regulatory RNA 4 in the model quorum-sensing bacterium . Our results show that LuxR positively regulates the 4 promoter. Under our conditions, we find that regulation weakly depends on total LuxO levels and that LuxO autorepression is saturated. We also find evidence that the fluctuations in LuxO levels are dominated by intrinsic noise. We furthermore propose LuxO and LuxR interact at all autoinducer levels via an unknown mechanism. Of importance, our new method of evaluating correlations at the microcolony level is unaffected by partition noise at cell division. Moreover, the method is first-order accurate and requires less effort for data analysis than single-cell-based approaches. This new correlation approach can be applied to other systems to aid analysis of gene regulatory circuits.
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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