Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene

Probing young drinking water biofilms with hard and soft particles

The aim of our study was to investigate, through the use of soft (Escherichia coli) and hard (polystyrene microspheres) particles, the distribution and persistence of allochthonous particles inoculated in drinking water flow chambers. Biofilms were allowed to grow for 7-10 months in tap water from Nancy's drinking water network and were composed of bacterial aggregates and filamentous fungi. Both model particles adhered almost exclusively on the biofilms (i.e. on the bacterial aggregates and on the filamentous structures) and not directly on the uncolonized walls (glass or Plexiglas). Biofilm age (i.e. bacterial density and biofilm properties) and convective-diffusion were found to govern particle accumulation: older biofilms and higher wall shear rates both increased the velocity and the amount of particle deposition on the biofilm. Persistence of the polystyrene particles was measured over a two-month period after inoculation. Accumulation amounts were found to be very different between hard and soft particles as only 0.03 per thousand of the soft particles inoculated accumulated in the biofilm against 0.3-0.8% for hard particles.

Characterization of the Cpx regulon in Escherichia coli strain MC4100

The Cpx two-component signal transduction pathway of Escherichia coli mediates adaptation to envelope protein misfolding. However, there is experimental evidence that at least 50 genes in 34 operons are part of the Cpx regulon and many have functions that are undefined or unrelated to envelope protein maintenance. No comprehensive analysis of the Cpx regulon has been presented to date. In order to identify strongly Cpx-regulated genes that might play an important role(s) in envelope protein folding and/or to further define the role of the Cpx response and to gain insight into what makes a gene subject to strong Cpx regulation, we have carried out a uniform characterization of a Cpx-regulated lux reporter library in a single-strain background. Strongly Cpx-regulated genes encode proteins that are directly linked to envelope protein folding, localized to the envelope but uncharacterized, or involved in limiting the cellular concentration of noxious molecules. Moderately Cpx-regulated gene clusters encode products implicated in biofilm formation. An analysis of CpxR binding sites in strongly regulated genes indicates that while neither a consensus match nor their orientation predicts the strength of Cpx regulation, most genes contain a CpxR binding site within 100 bp of the transcriptional start site. Strikingly, we found that while there appears to be little overlap between the Cpx and Bae envelope stress responses, the sigma(E) and Cpx responses reciprocally regulate a large group of strongly Cpx-regulated genes, most of which are uncharacterized.

The roles of two-component systems in virulence of pathogenic Escherichia coli and Shigella spp

Two-component systems (TCSs) are well conserved among E. coli strains, including pathogenic E. coli and also closely related Shigella spp. Although 25% of the genome of pathogenic E. coli is strain-specific, only small number of strain-specific TCSs is found. Regulation of virulence genes in response to environmental stimuli is partly dependent on TCSs commonly present in nonpathogenic E. coli strains. Some virulence genes are directly regulated by response regulator ofTCS but some are affected at posttranscriptional steps of production or assembly ofmacromolecule by TCS-induced products. In the process ofacquiringvirulence traits, regulatory systems for virulence genes expression seem to be built by integrating E. coli backbone TCSs with the virulence regulatory network via transcription regulatory gene.

Extracellular DNA chelates cations and induces antibiotic resistance in Pseudomonas aeruginosa biofilms

Biofilms are surface-adhered bacterial communities encased in an extracellular matrix composed of DNA, bacterial polysaccharides and proteins, which are up to 1000-fold more antibiotic resistant than planktonic cultures. To date, extracellular DNA has been shown to function as a structural support to maintain Pseudomonas aeruginosa biofilm architecture. Here we show that DNA is a multifaceted component of P. aeruginosa biofilms. At physiologically relevant concentrations, extracellular DNA has antimicrobial activity, causing cell lysis by chelating cations that stabilize lipopolysaccharide (LPS) and the outer membrane (OM). DNA-mediated killing occurred within minutes, as a result of perturbation of both the outer and inner membrane (IM) and the release of cytoplasmic contents, including genomic DNA. Sub-inhibitory concentrations of DNA created a cation-limited environment that resulted in induction of the PhoPQ- and PmrAB-regulated cationic antimicrobial peptide resistance operon PA3552–PA3559 in P. aeruginosa. Furthermore, DNA-induced expression of this operon resulted in up to 2560-fold increased resistance to cationic antimicrobial peptides and 640-fold increased resistance to aminoglycosides, but had no effect on β-lactam and fluoroquinolone resistance. Thus, the presence of extracellular DNA in the biofilm matrix contributes to cation gradients, genomic DNA release and inducible antibiotic resistance. DNA-rich environments, including biofilms and other infection sites like the CF lung, are likely the in vivo environments where extracellular pathogens such as P. aeruginosa encounter cation limitation.

Pseudomonas aeruginosa is an opportunistic pathogen, which causes a variety of serious infections in immunocompromised patients and cystic fibrosis (CF) sufferers. The biofilm-forming ability of P. aeruginosa is thought to contribute to chronic P. aeruginosa infection of the CF lung. Biofilms are dense communities of bacteria, encased in an extracellular matrix, that are practically impossible to eradicate using available antimicrobial therapies. Understanding the mechanisms by which biofilm bacteria develop resistance to antibiotics is paramount to expanding the treatment options available to patients with chronic biofilm infections. In this study we have identified a novel mechanism of biofilm-specific antibiotic resistance. Extracellular DNA, a known component of biofilms, was found to induce antibiotic resistance. This previously unidentified function of DNA was due to its ability to bind and sequester cations, including magnesium, from the surrounding environment. This environmental cue was then detected by P. aeruginosa leading to induction of genes involved in modification of the cell surface component, lipopolysaccharide (LPS), resulting in physical alterations in the bacterial outer membrane (OM). These results demonstrate a novel function for DNA in biofilms and identify cation chelation by DNA as a previously unrecognized mechanism, which can explain the increased resistance of biofilms to antimicrobial agents.

Impact of rpoS deletion on the proteome of Escherichia coli grown planktonically and as biofilm

To investigate the role of rpoS in gene expression of Escherichia coli cells grown as biofilms, we compared the proteomes of a rpoS mutant and the wild-type strain. Experiments were performed on planktonic cells (in exponential or stationary growth phase) and biofilms developed on glass wool. Spot-by-spot comparison of gels obtained from biofilm and planktonic wild-type organisms showed that the intensity of between 22 and 30% of detected spots was affected by the growth mode, depending of the control used. Principal component analysis, used to interpret the variations in protein spot densities, discriminated exponential-phase cells (wild-type and mutant) from the other incubation conditions and secondarily 72-old cultures. The statistical analysis demonstrated that the rpoS mutation did not significantly modify the proteome of exponential-growth phase cells, the differences involving only 3% of the proteome. However, increasing the incubation time from 8 to 72 h noticeably increased the number of changed proteins. A cluster analysis showed that RpoS plays a role in the special nature of the gene expression of biofilm cells but lower than in stationary-phase bacteria. We identified 35 rpoS-regulated proteins that were already or not described as controlled by this sigma factor. For some of them, the mode of regulation by RpoS was obviously dependent on the culture condition (planktonic vs biofilm).

Cellulose modulates biofilm formation by counteracting curli-mediated colonization of solid surfaces in Escherichia coli

In enterobacteria, the CsgD protein activates production of two extracellular structures: thin aggregative fimbriae (curli) and cellulose. While curli fibres promote biofilm formation and cell aggregation, the evidence for a direct role of cellulose as an additional determinant for biofilm formation is not as straightforward. The MG1655 laboratory strain of Escherichia coli only produces limited amounts of curli and cellulose; however, ectopic csgD expression results in strong stimulation of curli and cellulose production. We show that, in a csgD-overexpressing derivative of MG1655, cellulose production negatively affects curli-mediated surface adhesion and cell aggregation, thus acting as a negative determinant for biofilm formation. Consistent with this observation, deletion of the bcsA gene, necessary for cellulose production, resulted in a significant increase in curli-dependent adhesion. We found that cellulose production increased tolerance to desiccation, suggesting that the function of cellulose might be related to resistance to environmental stresses rather than to biofilm formation. Production of the curli/cellulose network in enterobacteria typically takes place at low growth temperature (<32 degrees C), but not at 37 degrees C. We show that CsgD overexpression can overcome temperature-dependent control of the curli-encoding csgBA operon, but not of the cellulose-related adrA gene, suggesting very tight temperature control of cellulose production in E. coli MG1655.

A short-time scale colloidal system reveals early bacterial adhesion dynamics

The development of bacteria on abiotic surfaces has important public health and sanitary consequences. However, despite several decades of study of bacterial adhesion to inert surfaces, the biophysical mechanisms governing this process remain poorly understood, due, in particular, to the lack of methodologies covering the appropriate time scale. Using micrometric colloidal surface particles and flow cytometry analysis, we developed a rapid multiparametric approach to studying early events in adhesion of the bacterium Escherichia coli. This approach simultaneously describes the kinetics and amplitude of early steps in adhesion, changes in physicochemical surface properties within the first few seconds of adhesion, and the self-association state of attached and free-floating cells. Examination of the role of three well-characterized E. coli surface adhesion factors upon attachment to colloidal surfaces—curli fimbriae, F-conjugative pilus, and Ag43 adhesin—showed clear-cut differences in the very initial phases of surface colonization for cell-bearing surface structures, all known to promote biofilm development. Our multiparametric analysis revealed a correlation in the adhesion phase with cell-to-cell aggregation properties and demonstrated that this phenomenon amplified surface colonization once initial cell-surface attachment was achieved. Monitoring of real-time physico-chemical particle surface properties showed that surface-active molecules of bacterial origin quickly modified surface properties, providing new insight into the intricate relations connecting abiotic surface physicochemical properties and bacterial adhesion. Hence, the biophysical analytical method described here provides a new and relevant approach to quantitatively and kinetically investigating bacterial adhesion and biofilm development.

When bacteria grow on solid surfaces, they can form three-dimensional communities called biofilms. Within these complex structures, bacteria can develop specific tolerance to different microbiocides, causing serious health and economic problems. Investigations of the key molecular events involved in biofilm formation have shown that surface-exposed adhesin proteins promote this process, but many questions remain regarding the mechanisms and biophysics of surface adhesion. We introduced an original approach to investigating the very early steps in bacterial adhesion that uses dispersed colloidal surfaces as microbial adhesion substrates. Using flow cytometry, we performed a quantitative real-time analysis of adhesion kinetics of several strains of the bacterium Escherichia coli, which were genetically engineered to produce well-characterized cell-surface adhesins that are known to promote biofilm development. We provide evidence for previously unknown adhesin-dependent behaviors, such as clear-cut differences in the very initial phases of surface colonization. We also demonstrate that initial adhesion correlates with almost instant surface property changes, and that cell-to-cell association might serve as an amplification mechanism for surface colonization. We therefore provide a new understanding of the intricate relationships between the physico-chemistry of abiotic surfaces and bacterial adhesion.

Combining micrometric colloidal beads as adhesion substrates with flow cytometric analysis allows for a high-resolution analysis that reveals adhesin-dependent behavior in the very first steps of surface colonization by bacteria.

Adherence of Aggregatibacter actinomycetemcomitans via serotype-specific polysaccharide antigens in lipopolysaccharides

INTRODUCTION

Gram-negative Aggregatibacter actinomycetemcomitans is recognized as an important periodontal pathogen. A striking property of this bacterium is its ability to form a tenacious biofilm adhering to abiotic surfaces. Both fimbrial and non-fimbrial adhesins are believed to be responsible for this ability. In our study, specific markerless mutants in the biosynthesis genes of cell surface polysaccharides were constructed with the Cre-loxP recombination system to identify non-fimbrial adhesin(s).

METHODS

Non-fimbriated A. actinomycetemcomitans strain ATCC29523 (serotype a) was used to construct a deletion mutant of serotype-a specific polysaccharide antigen (SPA-a) in lipopolysaccharide (LPS). The LPS was purified through a polymyxin B column following phenol extraction, and verified by silver staining following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by immunoblot analysis using rabbit antisera raised against SPA-a. Strains were grown in broth for 2 days and examined for the adherence of bacterial cells on the glass surface.

RESULTS

Strain ATCC29523 formed a thin film of bacterial growth on the glass surface. The deletion of SPA-a affected its ability to form this thin film. When this mutant was rescued with the wild-type SPA-a gene cluster, its adherence-positive phenotype was restored.

CONCLUSION

SPA-a in the LPS molecule appears to promote the adherence of A. actinomycetemcomitans cells to abiotic surfaces.

Functional organisation of Escherichia coli transcriptional regulatory network

Taking advantage of available functional data associated with 115 transcription and 7 sigma factors, we have performed a structural analysis of the regulatory network of Escherichia coli. While the mode of regulatory interaction between transcription factors (TFs) is predominantly positive, TFs are frequently negatively autoregulated. Furthermore, feedback loops, regulatory motifs and regulatory pathways are unevenly distributed in this network. Short pathways, multiple feed-forward loops and negative autoregulatory interactions are particularly predominant in the subnetwork controlling metabolic functions such as the use of alternative carbon sources. In contrast, long hierarchical cascades and positive autoregulatory loops are overrepresented in the subnetworks controlling developmental processes for biofilm and chemotaxis. We propose that these long transcriptional cascades coupled with regulatory switches (positive loops) for external sensing enable the coexistence of multiple bacterial phenotypes. In contrast, short regulatory pathways and negative autoregulatory loops enable an efficient homeostatic control of crucial metabolites despite external variations. TFs at the core of the network coordinate the most basic endogenous processes by passing information onto multi-element circuits. Transcriptional expression data support broader and higher transcription of global TFs compared to specific ones. Global regulators are also more broadly conserved than specific regulators in bacteria, pointing to varying functional constraints.

Evolvability and hierarchy in rewired bacterial gene networks

Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily moulded the contents of a given genome. Though the effect of knocking out or overexpressing a particular gene has been studied in many organisms, no study has systematically explored the effect of adding new links in a biological network. To explore network evolvability, we constructed 598 recombinations of promoters (including regulatory regions) with different transcription or sigma-factor genes in Escherichia coli, added over a wild-type genetic background. Here we show that approximately 95% of new networks are tolerated by the bacteria, that very few alter growth, and that expression level correlates with factor position in the wild-type network hierarchy. Most importantly, we find that certain networks consistently survive over the wild type under various selection pressures. Therefore new links in the network are rarely a barrier for evolution and can even confer a fitness advantage.

Environmental influences on biofilm development

Bacterial biofilms are found under diverse environmental conditions, from sheltered and specialized environments found within mammalian hosts to the extremes of biological survival. The process of forming a biofilm and the eventual return of cells to the planktonic state involve the coordination of vast amounts of genetic information. Nevertheless, the prevailing evidence suggests that the overall progression of this cycle within a given species or strain of bacteria responds to environmental conditions via a finite number of key regulatory factors and pathways, which affect enzymatic and structural elements that are needed for biofilm formation and dispersal. Among the conditions that affect biofilm development are temperature, pH, O2 levels, hydrodynamics, osmolarity, the presence of specific ions, nutrients, and factors derived from the biotic environment. The integration of these influences ultimately determines the pattern of behavior of a given bacterium with respect to biofilm development. This chapter will present examples of how environmental conditions affect biofilm development, most of which come from studies of species that have mammalian hosts.

Escherichia coli biofilms

Escherichia coli is a predominant species among facultative anaerobic bacteria of the gastrointestinal tract. Both its frequent community lifestyle and the availability of a wide array of genetic tools contributed to establish E. coli as a relevant model organism for the study of surface colonization. Several key factors, including different extracellular appendages, are implicated in E. coli surface colonization and their expression and activity are finely regulated, both in space and time, to ensure productive events leading to mature biofilm formation. This chapter will present known molecular mechanisms underlying biofilm development in both commensal and pathogenic E. coli.

Biofilm-grown Mycoplasma mycoides subsp. mycoides SC exhibit both phenotypic and genotypic variation compared with planktonic cells

Biofilm formation where bacterial cells adhere to a surface and surround themselves in a polysaccharide matrix is thought to be an important factor in disease initiation and persistence for many bacterial species. We have examined biofilm formation by Mycoplasma mycoides subsp. mycoides small colony using a simple model without an air/liquid interface and have found that adherent Mmm SC was more resistant to many stresses, including heat, osmotic shock and oxidative stress. Biofilms of Mmm SC also exhibited remarkable persistence and were able to survive for up to 20 weeks in stationary phase. Significant variation was seen between Mmm SC strains in their ability to form a biofilm and the morphology of the biofilm produced with some strains unable to produce microcolonies. Proteomic analysis found that a number of proteins linked to adherence were over-expressed in biofilms compared with planktonic cells.

The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production

The RcsCDB phosphorelay was originally identified as the main regulator of colanic acid biosynthesis in Escherichia coli K-12. However, recent transcriptomic analyses have identified more than 150 genes belonging to the Rcs regulon, including yjbE, yjbF, yjbG and yjbH. These genes are clustered on the genome and oriented in the same direction but their function remains unknown. In this work it is shown that yjbE, yjbF, yjbG and yjbH are transcribed as a single operon and it is confirmed that the expression of this operon is controlled by the Rcs phosphorelay, in a manner that is dependent on the auxiliary regulatory protein RcsA. Interestingly, Northern blot analysis revealed that the amount of yjbE transcripts in the cell is higher than the amount of yjbEFGH transcripts and it is proposed that this differential expression is mediated by the presence of a strong stem-loop structure in the yjbE-yjbF intergenic region. Finally, evidence is provided that the overexpression of yjbEFGH affects colony morphology and leads to the production of an extracellular polysaccharide that binds Congo red and toluidine blue-O.

AgfC and AgfE facilitate extracellular thin aggregative fimbriae synthesis in Salmonella enteritidis

Salmonella thin aggregative fimbriae (Tafi; curli) are important in pathogenesis and biofilm formation; however, less is known of their structure and morphogenesis. In the Salmonella agfBAC Tafi operon, the transcription and role of agfC have been elusive. In this study, agfBAC transcripts were detected using a sensitive reverse transcriptase technique. Native AgfC was not detected using polyclonal antibodies generated against purified hexahistidine-tagged AgfC; however, in trans expression revealed that AgfC was localized to the periplasm as a mature form. An isogenic DeltaagfC mutant displayed an abundance of 20 nm fibres, in addition to native Tafi (5-7 nm), and had an increase in cell surface hydrophobicity. Purified 20 nm fibres were depolymerized under exceptionally stringent conditions to release what proved to be AgfA subunits. This revealed that the 20 nm fibres represented a different form of Tafi. The role of AgfC in Tafi assembly was investigated further using an antibody-capture assay of isogenic Deltaagf mutants. A soluble antibody-accessible form of AgfA was captured in wild-type (wt), DeltaagfB and DeltaagfF strains, in support of the extracellular nucleation-precipitation pathway of Tafi assembly, but not in DeltaagfC or DeltaagfE mutants. This indicates that AgfC and AgfE are important for AgfA extracellular assembly, facilitating the synthesis of Tafi.

Crystal structure of a novel prokaryotic Ser/Thr kinase and its implication in the Cpx stress response pathway

The Cpx signalling system of Escherichia coli and Salmonella enterica senses extracytoplasmic stress and controls expression of factors that allow the bacterium to adapt to these stressors and thereby enhance survival. Many of the Cpx-responsive genes products are of unknown function. We determined the crystal structure of one of these gene products, called YihE in E. coli, which exhibits a eukaryotic kinase fold. Functional assays established that both YihE and the S. enterica YihE homologue, RdoA, undergo autophosphorylation and phosphorylate protein substrates at Ser/Thr residues in vitro, demonstrating that YihE/RdoA is a novel Ser/Thr protein kinase in prokaryotic cells. Phenotypic analysis of yihE/rdoA null strains indicates that this kinase is most abundant in stationary phase, and is important for long-term cell survival and for expression of surface appendages in both a Cpx-independent and -dependent manner. YihE/RdoA is therefore a previously unknown kinase component of a new type of bacterial phosphorelay mechanism, adding kinase activity as another response to the Cpx sensing system that functions to maintain cellular homeostasis.

Biofilm formation-gene expression relay system in Escherichia coli: modulation of sigmaS-dependent gene expression by the CsgD regulatory protein via sigmaS protein stabilization

Bacteria can switch from a single-cell (planktonic) mode to a multicellular community (biofilm) mode via production of cell-cell aggregation and surface adhesion factors. In this report, we present evidence that the CsgD protein, a transcription regulator involved in biofilm formation in Escherichia coli, modulates the expression of the rpoS (sigma(S)) regulon. Protein pattern analysis of E. coli cells in stationary phase shows that CsgD affects the expression of several proteins encoded by sigma(S)-dependent genes. CsgD regulation of sigma(S)-dependent genes takes place at gene transcription level, does not bypass the need for rpoS, and is abolished in an rpoS-null mutant. Consistent with these results, we find that CsgD expression leads to an increase in sigma(S) intracellular concentration. Increase in sigma(S) cellular amount is mediated by CsgD-dependent transcription activation of iraP, encoding a factor involved in sigma(S) protein stabilization. Our results strongly suggest that the CsgD regulatory protein plays a major role as a relay between adhesion factors production and sigma(S)-dependent gene expression via sigma(S) protein stabilization. Direct coordination between biofilm formation and expression of the rpoS regulon could positively impact important biological processes, such as host colonization or response to environmental stresses.

Regulation of Fimbrial Expression

Fimbria-mediated interaction with the host elicits both innate and adaptive immune responses, and thus their expression may not always be beneficial in vivo. Furthermore, the metabolic drain of producing fimbriae is significant. It is not surprising, therefore, to find that fimbrial production in Escherichia coli and Salmonella enterica is under extensive environmental regulation. In many instances, fimbrial expression is regulated by phase variation, in which individual cells are capable of switching between fimbriate and afimbriate states to produce a mixed population. Mechanisms of phase variation vary considerably between different fimbriae and involve both genetic and epigenetic processes. Notwithstanding this, fimbrial expression is also sometimes controlled at the posttranscriptional level. In this chapter, we review key features of the regulation of fimbrial gene expression in E. coli and Salmonella. The occurrence and distribution of fimbrial operons vary significantly among E. coli pathovars and even among the many Salmonella serovars. Therefore, general principles are presented on the basis of detailed discussion of paradigms that have been extensively studied, including Pap, type 1 fimbriae, and curli. The roles of operon specific regulators like FimB or CsgD and of global regulatory proteins like Lrp, CpxR, and the histone-like proteins H-NS and IHF are reviewed as are the roles of sRNAs and of signalling nucleotide cyclic-di-GMP. Individual examples are discussed in detail to illustrate how the regulatory factors cooperate to allow tight control of expression of single operons. Molecular networks that allow coordinated expression between multiple fimbrial operons and with flagella in a single isolate are also presented. This chapter illustrates how adhesin expression is controlled, and the model systems also illustrate general regulatory principles germane to our overall understanding of bacterial gene regulation.

Arsukibacterium ikkense gen. nov., sp. nov, a novel alkaliphilic, enzyme-producing γ-Proteobacterium isolated from a cold and alkaline environment in Greenland

A novel aerobic, Gram-negative, non-pigmented bacterium, GCM72(T), was isolated from the alkaline, low-saline ikaite columns in the Ikka Fjord, SW Greenland. Strain GCM72(T) is a motile, non-pigmented, amylase- and protease-producing, oxidase-positive, and catalase-negative bacterium, showing optimal growth at pH 9.2-10.0, at 15 degrees C, and at 3% (w/v) NaCl. Major fatty acids were C(12:0) 3-OH (12.2+/-0.1%), C(16:00) (18.0+/-0.1%), C(18:1)omega7c (10.7+/-0.5%), and summed feature 3 comprising C(16:1)omega7c and/or iso-C(15:0) 2-OH (36.3+/-0.7%). Phylogenetic analysis based on 16S rRNA gene sequences showed that isolate GCM72(T) was most closely related to Rheinheimera baltica and Alishewanella fetalis of the gamma-Proteobacteria with a 93% sequence similarity to both. The G+C content of DNA isolated from GCM72(T) was 49.9mol% and DNA-DNA hybridization between GCM72T and R. baltica was 9.5%. Fatty acid analysis and G+C content supports a relationship primarily to R. baltica, but several different features, such as a negative catalase-response and optimal growth at low temperature and high pH, together with the large phylogenetic distance and low DNA similarity to its closest relatives, lead us to propose a new genus, Arsukibacterium, gen. nov., with the new species Arsukibacterium ikkense sp. nov. (type strain is GCM72(T)).

Mutual Regulation of Crl and Fur in Escherichia coli W3110

The small regulatory protein Crl controls the expression of curli. Recently we have shown that Crl interacts directly with one of the most global regulators of Escherichia coli, the stress-related sigma factor RpoS, suggesting a more global role for Crl. We show here by a proteomics analysis that the expression of at least nine cellular proteins was considerably modified when Crl was overexpressed. We assessed the part of transcriptional and post-transcriptional regulation for five of these genes. The results showed that Crl regulates the expression of another global regulator, the central regulator of iron homeostasis, Fur. A molecular analysis revealed that Crl and Fur affect their own and each other's expression. We provide physical evidence for the binding of Fur to the crl and fur promoter regions. Crl modulated the affinity of Fur at the fur promoter but not at the crl promoter. The triad RpoS-Crl-Fur may thus represent the centerpiece of a global regulatory system of response to different stresses.

Temporal gene-expression in Escherichia coli K-12 biofilms

Analysis of the temporal development of Escherichia coli K-12 biofilms in complex medium indicates the greatest differential gene expression between biofilm and suspension cells occurred in young biofilms at 4 and 7 h (versus 15 and 24 h). The main classes of genes differentially expressed (biofilm versus biofilm and biofilm versus suspension cells) include 42 related to stress response (e.g. cspABFGI), 66 related to quorum sensing (e.g. ydgG, gadABC, hdeABD), 20 related to motility (e.g. flgBCEFH, fliLMQR, motB), 13 related to fimbriae (e.g. sfmCHM, fimZ, csgC), 24 related to sulfur and tryptophan metabolism (e.g. trpLBA, tnaLA, cysDNCJH), 80 related to transport (e.g. gatABC, agaBC, ycjJ, ydfJ, phoU, phnCJKM), and six related to extracellular matrix (e.g. wcaBDEC). Of the 93 mutants identified and studied, 76 showed altered biofilm formation. Biofilm architecture changed from thin and dense to globular and dispersed to dense and smooth. The quorum-sensing signal AI-2 controls gene expression most clearly in mature biofilms (24 h) when intracellular AI-2 levels are highest. Sulfate transport and metabolism genes (cysAUWDN) and genes with unknown functions (ymgABCZ) were repressed in young (4, 7 h) biofilms, induced in developed biofilms (15 h), and repressed in mature (24 h) biofilms. Genes related to both motility and fimbriae were induced in biofilms at all sampling time points and colanic acid genes were induced in mature biofilms (24 h). Genes related to dihydroxyacetone phosphate synthesis from galactitol and galactosamine (e.g. gatZABCDR, agaBCY) were highly regulated in biofilms. Genes involved in the biosynthesis of indole and sulfide (tnaLA) are repressed in biofilms after 7 h (corroborated by decreasing intracellular indole concentrations in biofilms). Cold-shock protein transcriptional regulators (cspABFGI) appear to be positive biofilm regulators, and deletions in respiratory genes (e.g. hyaACD, hyfCG, appC, narG) increased biofilm formation sevenfold.

Curli biogenesis and function

Curli are the major proteinaceous component of a complex extracellular matrix produced by many Enterobacteriaceae. Curli were first discovered in the late 1980s on Escherichia coli strains that caused bovine mastitis, and have since been implicated in many physiological and pathogenic processes of E. coli and Salmonella spp. Curli fibers are involved in adhesion to surfaces, cell aggregation, and biofilm formation. Curli also mediate host cell adhesion and invasion, and they are potent inducers of the host inflammatory response. The structure and biogenesis of curli are unique among bacterial fibers that have been described to date. Structurally and biochemically, curli belong to a growing class of fibers known as amyloids. Amyloid fiber formation is responsible for several human diseases including Alzheimer's, Huntington's, and prion diseases, although the process of in vivo amyloid formation is not well understood. Curli provide a unique system to study macromolecular assembly in bacteria and in vivo amyloid fiber formation. Here, we review curli biogenesis, regulation, role in biofilm formation, and role in pathogenesis.

Rhodonellum psychrophilum gen. nov., sp. nov., a novel psychrophilic and alkaliphilic bacterium of the phylum Bacteroidetes isolated from Greenland

A novel alkaliphilic and psychrophilic bacterium was isolated from the cold and alkaline ikaite tufa columns of the Ikka Fjord in south-west Greenland. According to 16S rRNA gene sequence analysis, strain GCM71T belonged to the family ‘Flexibacteraceae’ in the phylum Bacteroidetes. Strain GCM71T, together with five related isolates from ikaite columns, formed a separate cluster with 86–93 % gene sequence similarity to their closest relative, Belliella baltica. The G+C content of the DNA from strain GCM71T was 43.1 mol%, whereas that of B. baltica was reported to be 35 mol%. DNA–DNA hybridization between strain GCM71T and B. baltica was 9.5 %. The strain was red pigmented, Gram-negative, strictly aerobic with non-motile, rod-shaped cells. The optimal growth conditions for strain GCM71T were pH 9.2–10.0, 5 °C and 0.6 % NaCl. The fatty acid profile of the novel strain was dominated by branched and unsaturated fatty acids (90–97 %), with a high abundance of iso-C17 : 1 ω9c (17.5 %), iso-C17 : 0 3-OH (17.5 %) and summed feature 3, comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c (12.6 %). Phylogenetic, chemotaxonomic and physiological characteristics showed that the novel strain could not be affiliated to any known genus. A new genus, Rhodonellum gen. nov., is proposed to accommodate the novel strain. Strain GCM71T (=DSM 17998T=LMG 23454T) is proposed as the type strain of the type species, Rhodonellum psychrophilum sp. nov.

Effects of nutritional and environmental conditions on Sinorhizobium meliloti biofilm formation

Rhizobia are non-spore-forming soil bacteria that fix atmospheric nitrogen into ammonia in a symbiosis with legume roots. However, in the absence of a legume host, rhizobia manage to survive and hence must have evolved strategies to adapt to diverse environmental conditions. The capacity to respond to variations in nutrient availability enables the persistence of rhizobial species in soil, and consequently improves their ability to colonize and to survive in the host plant. Rhizobia, like many other soil bacteria, persist in nature most likely in sessile communities known as biofilms, which are most often composed of multiple microbial species. We have been employing in vitro assays to study environmental parameters that might influence biofilm formation in the Medicago symbiont Sinorhizobium meliloti. These parameters include carbon source, amount of nitrate, phosphate, calcium and magnesium as well as the effects of osmolarity and pH. The microtiter plate assay facilitates the detection of subtle differences in rhizobial biofilms in response to these parameters, thereby providing insight into how environmental stress or nutritional status influences rhizobial survival. Nutrients such as sucrose, phosphate and calcium enhance biofilm formation as their concentrations increase, whereas extreme temperatures and pH negatively affect biofilm formation.

Escherichia coli biofilms formed under low-shear modeled microgravity in a ground-based system

Bacterial biofilms cause chronic diseases that are difficult to control. Since biofilm formation in space is well documented and planktonic cells become more resistant and virulent under modeled microgravity, it is important to determine the effect of this gravity condition on biofilms. Inclusion of glass microcarrier beads of appropriate dimensions and density with medium and inoculum, in vessels specially designed to permit ground-based investigations into aspects of low-shear modeled microgravity (LSMMG), facilitated these studies. Mathematical modeling of microcarrier behavior based on experimental conditions demonstrated that they satisfied the criteria for LSMMG conditions. Experimental observations confirmed that the microcarrier trajectory in the LSMMG vessel concurred with the predicted model. At 24 h, the LSMMG Escherichia coli biofilms were thicker than their normal-gravity counterparts and exhibited increased resistance to the general stressors salt and ethanol and to two antibiotics (penicillin and chloramphenicol). Biofilms of a mutant of E. coli, deficient in sigma(s), were impaired in developing LSMMG-conferred resistance to the general stressors but not to the antibiotics, indicating two separate pathways of LSMMG-conferred resistance.

Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli

Bis-(3'-5')-cyclic-di-guanosine monophosphate (c-di-GMP) is a bacterial signalling molecule produced by diguanylate cyclases (DGC, carrying GGDEF domains) and degraded by specific phosphodiesterases (PDE, carrying EAL domains). Neither its full physiological impact nor its effector mechanisms are currently understood. Also, the existence of multiple GGDEF/EAL genes in the genomes of most species raises questions about output specificity and robustness of c-di-GMP signalling. Using microarray and gene fusion analyses, we demonstrate that at least five of the 29 GGDEF/EAL genes in Escherichia coli are not only stationary phase-induced under the control of the general stress response master regulator sigma(S) (RpoS), but also exhibit differential control by additional environmental and temporal signals. Two of the corresponding proteins, YdaM (GGDEF only) and YciR (GGDEF + EAL), which in vitro show DGC and PDE activity, respectively, play an antagonistic role in the expression of the biofilm-associated curli fimbriae. This control occurs at the level of transcription of the curli and cellulose regulator CsgD. Moreover, we show that H-NS positively affects curli expression by inversely controlling the expression of ydaM and yciR. Furthermore, we demonstrate a temporally fine-tuned GGDEF cascade in which YdaM controls the expression of another GGDEF protein, YaiC. By genome-wide microarray analysis, evidence is provided that YdaM and YciR strongly and nearly exclusively control CsgD-regulated genes. We conclude that specific GGDEF/EAL proteins have very distinct expression patterns, and when present in physiological amounts, can act in a highly precise, non-global and perhaps microcompartmented manner on a few or even a single specific target(s).

Comparative genetics of the rdar morphotype in Salmonella

The Salmonella rdar morphotype is a distinct, rough and dry colony morphology formed by the extracellular interaction of thin aggregative fimbriae (Tafi or curli), cellulose, and other polysaccharides. Cells in rdar colonies are more resistant to desiccation and exogenous stresses, which is hypothesized to aid in the passage of pathogenic Salmonella spp. between hosts. Here we analyzed the genetic and phenotypic conservation of the rdar morphotype throughout the entire Salmonella genus. The rdar morphotype was conserved in 90% of 80 isolates representing all 7 Salmonella groups; however, the frequency was only 31% in a reference set of 16 strains (Salmonella reference collection C [SARC]). Comparative gene expression analysis was used to separate cis- and trans-acting effects on promoter activity for the 16 SARC strains, focusing on the 780-bp intergenic region containing divergent promoters for the master regulator of the rdar morphotype (agfD) and the Tafi structural genes (agfB). Surprisingly, promoter functionality was conserved in most isolates, and loss of the phenotype was due primarily to defects in trans-acting regulatory factors. We hypothesize that trans differences have been caused by domestication, whereas cis differences, detected for Salmonella enterica subsp. arizonae isolates, may reflect an evolutionary change in lifestyle. Our results demonstrate that the rdar morphotype is conserved throughout the salmonellae, but they also emphasize that regulation is an important source of variability among isolates.

The cation-responsive protein NhaR of Escherichia coli activates pgaABCD transcription, required for production of the biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine

The pgaABCD operon of Escherichia coli is required for production of the biofilm adhesin poly-beta-1,6-N-acetyl-d-glucosamine (PGA). We establish here that NhaR, a DNA-binding protein of the LysR family of transcriptional regulators, activates transcription of this operon. Disruption of the nhaR gene decreased biofilm formation without affecting planktonic growth. PGA production was undetectable in an nhaR mutant strain. Expression of a pgaA'-'lacZ translational fusion was induced by NaCl and alkaline pH, but not by CaCl(2) or sucrose, in an nhaR-dependent fashion. Primer extension and quantitative real-time reverse transcription-PCR analyses further revealed that NhaR affects the steady-state level of pga mRNA. A purified recombinant NhaR protein bound specifically and with high affinity within the pgaABCD promoter region; one apparent binding site overlaps the -35 element, and a second site lies immediately upstream of the first. This protein was necessary and sufficient for activation of in vitro transcription from the pgaA promoter. These results define a novel mechanism for regulation of biofilm formation in response to environmental conditions and suggest an expanded role for NhaR in promoting bacterial survival.

Biofilms: a role in recurrent mastitis infections?

Mastitis remains one the most important diseases in dairy cattle despite the progress made in improving general udder health in recent years. Epidemiological studies have revealed that following treatment with antimicrobials, bacteriological cure rates vary between 0% and 80% but with no evidence of a significant loss of activity of the major classes of antibiotics licensed for the treatment of bovine mastitis. Recurrent infections are often attributable to biofilm growth of bacteria and this review provides an overview of those mechanisms related to bacterial biofilm growth in mastitis. Biofilm formation is accompanied by significant genetic and subsequent physiological changes in the microorganisms resulting, inter alia, in a loss of sensitivity to virtually all classes of antibiotics.

In vitro biofilm formation of commensal and pathogenic Escherichia coli strains: impact of environmental and genetic factors

Our understanding of Escherichia coli biofilm formation in vitro is based on studies of laboratory K-12 strains grown in standard media. However, pathogenic E. coli isolates differ substantially in their genetic repertoire from E. coli K-12 and are subject to heterogeneous environmental conditions. In this study, in vitro biofilm formation of 331 nondomesticated E. coli strains isolated from healthy (n = 105) and diarrhea-afflicted children (n = 68), bacteremia patients (n = 90), and male patients with urinary tract infections (n = 68) was monitored using a variety of growth conditions and compared to in vitro biofilm formation of prototypic pathogenic and laboratory strains. Our results revealed remarkable variation among the capacities of diverse E. coli isolates to form biofilms in vitro. Notably, we could not identify an association of increased biofilm formation in vitro with a specific strain collection that represented pathogenic E. coli strains. Instead, analysis of biofilm data revealed a significant dependence on growth medium composition (P < 0.05). Poor correlation between biofilm formation in the various media suggests that diverse E. coli isolates respond very differently to changing environmental conditions. The data demonstrate that prevalence and expression of three factors known to strongly promote biofilm formation in E. coli K-12 (F-like conjugative pili, aggregative adherence fimbriae, and curli) cannot adequately account for the increased biofilm formation of nondomesticated E. coli isolates in vitro. This study highlights the complexity of genetic and environmental effectors of the biofilm phenotype within the species E. coli.

Role of sigmaD in regulating genes and signals during Myxococcus xanthus development

Starvation-induced development of Myxococcus xanthus is an excellent model for biofilm formation because it involves cell-cell signaling to coordinate formation of multicellular mounds, gene expression, and cellular differentiation into spores. The role of sigma(D), an alternative sigma factor important for viability in stationary phase and for stress responses, was investigated during development by measuring signal production, gene expression, and sporulation of a sigD null mutant alone and upon codevelopment with wild-type cells or signaling mutants. The sigD mutant responded to starvation by inducing (p)ppGpp synthesis normally but was impaired for production of A-signal, an early cell density signal, and for production of the morphogenetic C-signal. Induction of early developmental genes was greatly reduced, and expression of those that depend on A-signal was not restored by codevelopment with wild-type cells, indicating that sigma(D) is needed for cellular responses to A-signal. Despite these early developmental defects, the sigD mutant responded to C-signal supplied by codeveloping wild-type cells by inducing a subset of late developmental genes. sigma(D) RNA polymerase is dispensable for transcription of this subset, but a distinct regulatory class, which includes genes essential for sporulation, requires sigma(D) RNA polymerase or a gene under its control, cell autonomously. The level of sigD transcript in a relA mutant during growth is much lower than in wild-type cells, suggesting that (p)ppGpp positively regulates sigD transcription in growing cells. The sigD transcript level drops in wild-type cells after 20 min of starvation and remains low after 40 min but rises in a relA mutant after 40 min, suggesting that (p)ppGpp negatively regulates sigD transcription early in development. We conclude that sigma(D) synthesized during growth occupies a position near the top of a regulatory hierarchy governing M. xanthus development, analogous to sigma factors that control biofilm formation of other bacteria.

Deletion of the rpoZ gene, encoding the ω subunit of RNA polymerase, results in pleiotropic surface-related phenotypes in Mycobacterium smegmatis

Theωsubunit, the smallest subunit of bacterial RNA polymerase, is known to be involved in maintaining the conformation of theβ′ subunit and aiding its recruitment to the rest of the core enzyme assembly inEscherichia coli. It has recently been shown inMycobacterium smegmatis, by creating a deletion mutation of therpoZgene encodingω, that the physiological role of theωsubunit also includes providing physical protection toβ′. Interestingly, the mutant had altered colony morphology. This paper demonstrates that the mutant mycobacterium has pleiotropic phenotypes including reduced sliding motility and defective biofilm formation. Analysis of the spatial arrangement of biofilms by electron microscopy suggests that the altered phenotype of the mutant arises from a deficiency in generation of extracellular matrix. Complementation of the mutant strain with a copy of the wild-typerpoZgene integrated in the bacterial chromosome restored both sliding motility and biofilm formation to the wild-type state, unequivocally proving the role ofωin the characteristics observed for the mutant bacterium. Analysis of the cell wall composition demonstrated that the mutant bacterium had an identical glycopeptidolipid profile to the wild-type, but failed to synthesize the short-chain mycolic acids characteristic of biofilm growth inM. smegmatis.

Biofilm formation by Escherichia coli is stimulated by synergistic interactions and co-adhesion mechanisms with adherence-proficient bacteria

Laboratory strains of Escherichia coli do not show significant ability to attach to solid surfaces and to form biofilms. We compared the adhesion properties of the E. coli PHL565 laboratory strain to eight environmental E. coli isolates: only four isolates displayed adhesion properties to glass significantly higher than PHL565. The ability of the adhesion-proficient isolates to attach to glass tubes strongly correlated with their ability to express curli (thin aggregative fimbriae), thus suggesting that curli are a common adhesion determinant in environmental strains. Despite its inability to attach to solid surfaces, growth of E. coli PHL565 in mixed cultures with Pseudomonas putida MT2 resulted in co-adhesion and in formation of a mixed E. coli/P. putida biofilm, which was able to colonize glass surfaces with dramatic efficiency compared to P. putida alone. E. coli/P. putida interactions stimulate initial adhesion to glass, and the presence of both bacterial species in the mature biofilm was confirmed by quantitative PCR. In contrast, no synergistic biofilm formation was observed in mixed cultures of E. coli with the Gram-positive bacterium Staphylococcus epidermidis. Interestingly, E. coli PHL565 also stimulated biofilm formation by bacterial communities isolated from drinking water distribution systems. Our results strongly suggest that co-adhesion and synergistic interaction with biofilm-forming species might represent an important mechanism, and a possible alternative strategy to production of adhesion determinants, for persistence and propagation of E. coli in the environment.

A CsgD-independent pathway for cellulose production and biofilm formation in Escherichia coli

Bacterial growth on a surface often involves the production of a polysaccharide-rich extracellular matrix that provides structural support for the formation of biofilm communities. In Salmonella, cellulose is one of the major constituents of the biofilm matrix. Its production is regulated by CsgD and the diguanylate cyclase AdrA that activates cellulose synthesis at a posttranscriptional level. Here, we studied a collection of Escherichia coli isolates, and we found that the ability to produce cellulose is a common trait shared by more than 50% of the tested strains. We investigated the genetic determinants of cellulose production and its role in biofilm formation in the commensal strain E. coli 1094. By contrast with the Salmonella cellulose regulatory cascade, neither CsgD nor AdrA is required in E. coli 1094 to regulate cellulose production. In this strain, an alternative cellulose regulatory pathway is used, which involves the GGDEF domain protein, YedQ. Although AdrA(1094) is functional, it is weakly expressed in E. coli 1094 compared to YedQ, which constitutively activates cellulose production under all tested environmental conditions. The study of cellulose regulation in several other E. coli isolates showed that, besides the CsgD/AdrA regulatory pathway, both CsgD-independent/YedQ-dependent and CsgD-independent/YedQ-independent pathways are found, indicating that alternative cellulose pathways are common in E. coli and possibly in other cellulose-producing Enterobacteriaceae.

Gene expression regulation by the Curli activator CsgD protein: modulation of cellulose biosynthesis and control of negative determinants for microbial adhesion

Curli fibers, encoded by the csgBAC genes, promote biofilm formation in Escherichia coli and other enterobacteria. Curli production is dependent on the CsgD transcription activator, which also promotes cellulose biosynthesis. In this study, we investigated the effects of CsgD expression from a weak constitutive promoter in the biofilm formation-deficient PHL565 strain of E. coli. We found that despite its function as a transcription activator, the CsgD protein is localized in the cytoplasmic membrane. Constitutive CsgD expression promotes biofilm formation by PHL565 and activates transcription from the csgBAC promoter; however, csgBAC expression remains dependent on temperature and the growth medium. Constitutive expression of the CsgD protein results in altered transcription patterns for at least 24 novel genes, in addition to the previously identified CsgD-dependent genes. The cspA and fecR genes, encoding regulatory proteins responding to cold shock and to iron, respectively, and yoaD, encoding a putative negative regulator of cellulose biosynthesis, were found to be some of the novel CsgD-regulated genes. Consistent with the predicted functional role, increased expression of the yoaD gene negatively affects cell aggregation, while yoaD inactivation results in stimulation of cell aggregation and leads to increased cellulose production. Inactivation of fecR results in significant increases in both cell aggregation and biofilm formation, while the effects of cspA are not as strong in the conditions tested. Our results indicate that CsgD can modulate cellulose biosynthesis through activation of the yoaD gene. In addition, the positive effect of CsgD on biofilm formation might be enhanced by repression of the fecR gene.

The transcriptional antiterminator RfaH represses biofilm formation in Escherichia coli

We investigated the influence of regulatory and pathogenicity island-associated factors (Hha, RpoS, LuxS, EvgA, RfaH, and tRNA5Leu) on biofilm formation by uropathogenic Escherichia coli (UPEC) strain 536. Only inactivation of rfaH, which encodes a transcriptional antiterminator, resulted in increased initial adhesion and biofilm formation by E. coli 536. rfaH inactivation in nonpathogenic E. coli K-12 isolate MG1655 resulted in the same phenotype. Transcriptome analysis of wild-type strain 536 and an rfaH mutant of this strain revealed that deletion of rfaH correlated with increased expression of flu orthologs. flu encodes antigen 43 (Ag43), which mediates autoaggregation and biofilm formation. We confirmed that deletion of rfaH leads to increased levels of flu and flu-like transcripts in E. coli K-12 and UPEC. Supporting the hypothesis that RfaH represses biofilm formation through reduction of the Ag43 level, the increased-biofilm phenotype of E. coli MG1655rfaH was reversed upon inactivation of flu. Deletion of the two flu orthologs, however, did not modify the behavior of mutant 536rfaH. Our results demonstrate that the strong initial adhesion and biofilm formation capacities of strain MG1655rfaH are mediated by both increased steady-state production of Ag43 and likely increased Ag43 presentation due to null rfaH-dependent lipopolysaccharide depletion. Although the roles of rfaH in the biofilm phenotype are different in UPEC strain 536 and K-12 strain MG1655, this study shows that RfaH, in addition to affecting the expression of bacterial virulence factors, also negatively controls expression and surface presentation of Ag43 and possibly another Ag43-independent factor(s) that mediates cell-cell interactions and biofilm formation.

Curli fibers are required for development of biofilm architecture in Escherichia coli K-12 and enhance bacterial adherence to human uroepithelial cells

Sessile bacteria show phenotypical, biochemical, and morphological differences from their planktonic counterparts. Curli, extracellular structures important for biofilm formation, are only produced at temperatures below 30 C in Escherichia coli K-12 strains. In this report, we show that E. coli K-12 can produce curli at 37 C when grown as a biofilm community. The curli-expressing strain formed more biofilms on polyurethane sheets than the curli-deficient strain under growth temperatures of both 25 C and 37 C. Curli are required for the formation of a three-dimensional mature biofilm, with characteristic water channels and pillars of bacteria. Observations by electron microscopy revealed the presence at the surfaces of the curli-deficient mutant in biofilm of flagella and type I pili. A wild-type curli-expressing E. coli strain significantly adhered to several lines of human uroepithelial cells, more so than an isogenic curlideficient strain. The finding that curli are expressed at 37 C in biofilm and enhance bacterial adherence to mammalian host cells suggests an important role for curli in pathogenesis.

Hha, YbaJ, and OmpA regulate Escherichia coli K12 biofilm formation and conjugation plasmids abolish motility

Escherichia coli Hha is an environmental-response regulator of the pathogenic hemolysin operon, and Hha and the contiguous YbaJ are both induced 30-fold in E. coli biofilms (Appl. Microbiol. Biotechnol. 64:515, 2004). Here it is shown that Hha and YbaJ regulate biofilm formation since the hha/ybaJ deletion reduces biofilm mass in microtitre plates (81% in minimal medium, 50% in complex medium) and in flow cells (1,000-fold less surface coverage in minimal medium). The addition of the derepressed conjugative plasmid R1drd19, which increases significantly biofilm formation, eliminated motility completely in wild-type E. coli K12, promoted cell aggregation 27.18 +/- 0.05-fold, and produced a flatter biofilm. Deletion of hha/ybaJ or ybaJ restored motility (this motility phenotype may be complemented by providing hha(+)/ybaJ(+) or ybaJ(+) in trans) and reduced cell aggregation to that of the wild-type strain that lacks the conjugation plasmid. This increase in motility due to deleting hha/ybaJ was found to be due to 8-fold induction of fliA transcription. In addition, deletion of ompA reduced biofilm mass by 80% in both LB medium and LB medium with glucose. Also, Hha/YbaJ promotes conjugation since there was five-fold less conjugation in the hha/ybaJ mutant. It appears that conjugation plasmids promote biofilm formation by promoting cell aggregation, and that Hha and YbaJ increase biofilm formation by increasing conjugation and by decreasing motility when a conjugative plasmid (R1drd19) is present (YbaJ plays the most important role in this regulation of motility). When hha/ybaJ are deleted, there is less conjugation, less aggregation, more motility, and less biofilm.

Secretory IgA and mucin-mediated biofilm formation by environmental strains of Escherichia coli: role of type 1 pili

Recent studies suggest the importance of secretory IgA (SIgA) and mucin in the mediation of biofilm formation by commensal bacteria within the mammalian gut. Studies using a variety of strains of Escherichia coli have indicated that the interaction between E. coli and SIgA is dependent on the type 1 pilus. In this study, the importance of the pilus in SIgA-mediated biofilm formation by a laboratory strain (MG1655) and environmental (fecal) strains of E. coli was evaluated. Transient expression of the type 1 pilus by the laboratory strain of E. coli failed to facilitate SIgA-mediated biofilm formation, whereas constitutive expression of the type 1 pilus by the laboratory strain was sufficient. In contrast, transient expression of the type 1 pilus was sufficient to facilitate SIgA-mediated biofilm formation by environmental isolates. The "threshold" for mucin-mediated biofilm formation appeared to be lower than that for SIgA-mediated biofilm formation, perhaps reflecting disparate roles of mucin and SIgA in mediating biofilm formation in the gut. These studies also provide the first procedures for the growth of bacterial biofilms on live epithelial cells in vitro, an important development that may facilitate future studies on the effects of bacterial biofilms on epithelial cells.

Secretion of curli fibre subunits is mediated by the outer membrane-localized CsgG protein

Produced by many Enterobacteriaceae spp., curli are biologically important amyloid fibres that have been associated with biofilm formation, host cell adhesion and invasion, and immune system activation. CsgA is the major fibre subunit and CsgE, CsgF and CsgG are non-structural proteins involved in curli biogenesis. We have characterized the role of CsgG in curli subunit secretion across the outer membrane. Directed mutagenesis of CsgG confirmed that its activity is dependent on localization to the outer membrane. Rotary Shadow electron microscopy of purified CsgG suggested that this protein assembles into an oligomeric complex with an apparent central pore. Oligomeric CsgG complexes were confirmed using co-purification experiments. Antibiotic sensitivity assays demonstrated that overexpression of CsgG rendered Escherichia coli susceptible to the antibiotic erythromycin. A 22-amino-acid sequence at the N-terminus of CsgA was sufficient to direct heterologous proteins to the CsgG secretion apparatus. Finally, we determined that CsgG participates in an outer membrane complex with two other curli assembly proteins, CsgE and CsgF.

The Cpx system of Escherichia coli, a strategic signaling pathway for confronting adverse conditions and for settling biofilm communities?

Amongst the thirty or so two-component systems known in Escherichia coli, the Cpx system has been described as being a stress response system the main function of which is to respond to damage to the cell envelope via activation of proteases and folding catalysts. Nevertheless, the size of the Cpx regulon (several dozens of target genes) and the diversity of the physiological functions associated with it (resistance to hostile conditions, mobility, adherence factors, metabolism, etc.) indicate that the role of Cpx in cell physiology is undoubtedly more complex. The range of cellular functions affected by activation of the Cpx pathway corresponds quite closely to the description of the physiological state of cells grown in biofilms. We suggest that Cpx is a strategic signaling pathway for facing adverse conditions and for settling biofilm communities. Current knowledge of the regulatory mechanisms of the CpxR response (transcriptional and post-transcriptional) and the interactions between CpxR and the other bacterial regulatory systems are presented.

The Rcs phosphorelay: a complex signal transduction system

RcsC, RcsB, and RcsA were first identified as a sensor kinase, a response regulator, and an auxiliary regulatory protein, respectively, regulating the genes of capsular polysaccharide synthesis. Recent advances have demonstrated that these proteins are part of a complex phosphorelay, in which phosphate travels from the histidine kinase domain in RcsC to a response regulator domain in the same protein; from there to a phosphotransfer protein, RcsD; and from there to RcsB. In addition to capsule synthesis, which requires the unstable regulatory protein RcsA, RcsB also stimulates transcription of a small RNA, RprA; the cell division gene ftsZ; and genes encoding membrane and periplasmic proteins, including the osmotically inducible genes osmB and osmC. The Rcs system appears to play an important role in the later stages of biofilm development; induction of Rcs signaling by surfaces is consistent with this role.

Salmonella enterica virulence genes are required for bacterial attachment to plant tissue

Numerous Salmonella enterica food-borne illness outbreaks have been associated with contaminated vegetables, in particular sprouted seeds, and the incidence of reported contamination has steadily risen. In order to understand the physiology of S. enterica serovar Newport on plants, a screen was developed to identify transposon mutants that were defective in attachment to alfalfa sprouts. Twenty independent mutants from a pool of 6,000 were selected for reduced adherence to alfalfa sprouts. Sixty-five percentage of these mutants had insertions in uncharacterized genes. Among the characterized genes were strains with insertions in the intergenic region between agfB, the surface-exposed aggregative fimbria (curli) nucleator, and agfD, a transcriptional regulator of the LuxR superfamily, and rpoS, the stationary-phase sigma factor. Both AgfD and RpoS have been reported to regulate curli and cellulose production and RpoS regulates other adhesins such as pili. The intergenic and rpoS mutants were reduced in initial attachment to alfalfa sprouts by 1 log unit compared to the wild type. Mutations of agfA, curli subunit, and agfB in S. enterica serovar Enteritidis differentially affected attachment to plant tissue. The agfA mutation was not reduced in ability to attach to or colonize alfalfa sprouts, whereas the agfB mutation was reduced. Thus, agfB alone can play a role in attachment of S. enterica to plant tissue. These results reveal that S. enterica genes important for virulence in animal systems are also required for colonization of plants, a secondary host that can serve as a vector of S. enterica from animal to animal.

The Escherichia coli CpxA-CpxR envelope stress response system regulates expression of the porins ompF and ompC

We performed transposon mutagenesis of a two-color fluorescent reporter strain to identify new regulators of the porin genes ompF and ompC in Escherichia coli. Screening of colonies by fluorescence microscopy revealed numerous mutants that exhibited interesting patterns of porin expression. One mutant harbored an insertion in the gene encoding the histidine kinase CpxA, the sensor for a two-component signaling system that responds to envelope stress. The cpxA mutant exhibited increased transcription of ompC and a very strong decrease in transcription of ompF under conditions in which acetyl phosphate levels were high. Subsequent genetic analysis revealed that this phenotype is dependent on phosphorylation of the response regulator CpxR and that activation of CpxA in wild-type cells results in similar regulation of porin expression. Using DNase I footprinting, we demonstrated that CpxR binds upstream of both the ompF and ompC promoters. It thus appears that two distinct two-component systems, CpxA-CpxR and EnvZ-OmpR, converge at the porin promoters. Within the context of envelope stress, outer membrane beta-barrel proteins have generally been associated with the sigma E pathway. However, at least for the classical porins OmpF and OmpC, our results show that the Cpx envelope stress response system plays a role in regulating their expression.

CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli

The RNA-binding protein CsrA represses biofilm formation, while the non-coding RNAs CsrB and CsrC activate this process by sequestering CsrA. We now provide evidence that the pgaABCD transcript, required for the synthesis of the polysaccharide adhesin PGA (poly-beta-1,6-N-acetyl-d-glucosamine) of Escherichia coli, is the key target of biofilm regulation by CsrA. csrA disruption causes an approximately threefold increase in PGA production and an approximately sevenfold increase in expression of a pgaA'-'lacZ translational fusion. A DeltacsrBDeltacsrC mutant exhibits a modest decrease in pgaA'-'lacZ expression, while the response regulator UvrY, a transcriptional activator of csrB and csrC, stimulates this expression. Biofilm formation is not regulated by csrA, csrB or uvrY in a DeltapgaC mutant, which cannot synthesize PGA. Gel mobility shift and toeprint analyses demonstrate that CsrA binds cooperatively to pgaA mRNA and competes with 30S ribosome subunit for binding. CsrA destabilizes the pgaA transcript in vivo. RNA footprinting and boundary analyses identify six apparent CsrA binding sites in the pgaA mRNA leader, the most extensive arrangement of such sites in any mRNA examined to date. Substitution mutations in CsrA binding sites overlapping the Shine-Dalgarno sequence and initiation codon partially relieve repression by CsrA. These studies define the crucial mechanisms, though not the only means, by which the Csr system influences biofilm formation.