H-NS controls pap and daa fimbrial transcription in Escherichia coli in response to multiple environmental cues

Mechanisms and implications of phenotypic switching in bacterial pathogens

Bacteria encounter various stressful conditions within a variety of dynamic environments, which they must overcome for survival. One way they achieve this is by developing phenotypic heterogeneity to introduce diversity within their population. Such distinct subpopulations can arise through endogenous fluctuations in regulatory components, wherein bacteria can express diverse phenotypes and switch between them, sometimes in a heritable and reversible manner. This switching may also lead to antigenic variation, enabling pathogenic bacteria to evade the host immune response. Therefore, phenotypic heterogeneity plays a significant role in microbial pathogenesis, immune evasion, antibiotic resistance, host niche tissue establishment, and environmental persistence. This heterogeneity can result from stochastic and responsive switches, as well as various genetic and epigenetic mechanisms. The development of phenotypic heterogeneity may create clonal populations that differ in their level of virulence, contribute to the formation of biofilms, and allow for antibiotic persistence within select morphological variants. This review delves into the current understanding of the molecular switching mechanisms underlying phenotypic heterogeneity, highlighting their roles in establishing infections caused by select bacterial pathogens.

T3SS protein EsrC binds to the lacI-like operator of type 1 fimbrial operon to suppress adhesion of Edwardsiella piscicida

Type 1 fimbria, the short hair-like appendage assembled on the bacterial surface, plays a pivotal role in adhesion and invasion in Edwardsiella piscicida. The type III secretion system (T3SS), another bacterial surface appendage, facilitates E. piscicida's replication in vivo by delivering effectors into host cells. Our previous research demonstrated that E. piscicida T3SS protein EseJ inhibits adhesion and invasion of E. piscicida by suppressing type 1 fimbria. However, how EseJ suppresses type 1 fimbria remains elusive. In this study, a lacI-like operator (nt -245 to -1 of fimA) upstream of type 1 fimbrial operon in E. piscicida was identified, and EseJ inhibits type 1 fimbria through the lacI-like operator. Moreover, through DNA pull-down and electrophoretic mobility shift assay, an AraC-type T3SS regulator, EsrC, was screened and verified to bind to nt -145 to -126 and nt -50 to -1 of fimA, suppressing type 1 fimbria. EseJ is almost abolished upon the depletion of EsrC. EsrC and EseJ impede type 1 fimbria expression. Intriguingly, nutrition and microbiota-derived indole activate type 1 fimbria through downregulating T3SS, alleviating EsrC or EseJ's inhibitory effect on lacI-like operator of type 1 fimbrial operon. By this study, it is revealed that upon entering the gastrointestinal tract, rich nutrients and indole downregulate T3SS and thereof upregulate type 1 fimbria, stimulating efficient adhesion and invasion; upon being internalized into epithelium, the limit in indole and nutrition switches on T3SS and thereof switches off type 1 fimbria, facilitating effector delivery to guarantee E. piscicida's survival/replication in vivo.IMPORTANCEIn this work, we identified the lacI-like operator of type 1 fimbrial operon in E. piscicida, which was suppressed by the repressors-T3SS protein EseJ and EsrC. We unveiled that E. piscicida upregulates type 1 fimbria upon sensing rich nutrition and the microbiota-derived indole, thereof promoting the adhesion of E. piscicida. The increase of indole and nutrition promotes type 1 fimbria by downregulating T3SS. The decrease in EseJ and EsrC alleviates their suppression on type 1 fimbria, and vice versa.

Type 1 fimbria and P pili: regulatory mechanisms of the prototypical members of the chaperone-usher fimbrial family

Adherence to both cellular and abiotic surfaces is a crucial step in the interaction of bacterial pathogens and commensals with their hosts. Bacterial surface structures known as fimbriae or pili play a fundamental role in the early colonization stages by providing specificity or tropism. Among the various fimbrial families, the chaperone-usher family has been extensively studied due to its ubiquity, diversity, and abundance. This family is named after the components that facilitate their biogenesis. Type 1 fimbria and P pilus, two chaperone-usher fimbriae associated with urinary tract infections, have been thoroughly investigated and serve as prototypes that have laid the foundations for understanding the biogenesis of this fimbrial family. Additionally, the study of the mechanisms regulating their expression has also been a subject of great interest, revealing that the regulation of the expression of the genes encoding these structures is a complex and diverse process, involving both common global regulators and those specific to each operon.

Diversity in Genetic Regulation of Bacterial Fimbriae Assembled by the Chaperone Usher Pathway

Bacteria express different types of hair-like proteinaceous appendages on their cell surface known as pili or fimbriae. These filamentous structures are primarily involved in the adherence of bacteria to both abiotic and biotic surfaces for biofilm formation and/or virulence of non-pathogenic and pathogenic bacteria. In pathogenic bacteria, especially Gram-negative bacteria, fimbriae play a key role in bacteria-host interactions which are critical for bacterial invasion and infection. Fimbriae assembled by the Chaperone Usher pathway (CUP) are widespread within the Enterobacteriaceae, and their expression is tightly regulated by specific environmental stimuli. Genes essential for expression of CUP fimbriae are organised in small blocks/clusters, which are often located in proximity to other virulence genes on a pathogenicity island. Since these surface appendages play a crucial role in bacterial virulence, they have potential to be harnessed in vaccine development. This review covers the regulation of expression of CUP-assembled fimbriae in Gram-negative bacteria and uses selected examples to demonstrate both dedicated and global regulatory mechanisms.

Differential Afa/Dr Fimbriae Expression in the Multidrug-Resistant Escherichia coli ST131 Clone

Many antibiotic resistant uropathogenic Escherichia coli (UPEC) strains belong to clones defined by their multilocus sequence type (ST), with ST131 being the most dominant. Although we have a good understanding of resistance development to fluoroquinolones and third-generation cephalosporins by ST131, our understanding of the virulence repertoire that has contributed to its global dissemination is limited. Here we show that the genes encoding Afa/Dr fimbriae, a group of adhesins strongly associated with UPEC that cause gestational pyelonephritis and recurrent cystitis, are found in approximately one third of all ST131 strains. Sequence comparison of the AfaE adhesin protein revealed a unique allelic variant carried by 82.9% of afa-positive ST131 strains. We identify the afa regulatory region as a hotspot for the integration of insertion sequence (IS) elements, all but one of which alter afa transcription. Close investigation demonstrated that the integration of an IS1 element in the afa regulatory region leads to increased expression of Afa/Dr fimbriae, promoting enhanced adhesion to kidney epithelial cells and suggesting a mechanism for altered virulence. Finally, we provide evidence for a more widespread impact of IS1 on ST131 genome evolution, suggesting that IS dynamics contribute to strain level microevolution that impacts ST131 fitness. IMPORTANCE E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. Here, we utilized a large collection of ST131 isolates to investigate the prevalence, regulation, and function of Afa/Dr fimbriae, a well-characterized UPEC colonization and virulence factor. We show that the afa genes are found frequently in ST131 and demonstrate how the integration of IS elements in the afa regulatory region modulates Afa expression, presenting an example of altered virulence capacity. We also exploit a curated set of ST131 genomes to map the integration of the antibiotic resistance-associated IS1 element in the ST131 pangenome, providing evidence for its widespread impact on ST131 genome evolution.

A Shift to Human Body Temperature (37°C) Rapidly Reprograms Multiple Adaptive Responses in Escherichia coli That Would Facilitate Niche Survival and Colonization

One of the first environmental cues sensed by a microbe as it enters a human host is an upshift in temperature to 37°C. In this dynamic time point analysis, we demonstrate that this environmental transition rapidly signals a multitude of gene expression changes in Escherichia coli. Bacteria grown at 23°C under aerobic conditions were shifted to 37°C, and mRNA expression was measured at time points after the shift to 37°C (t = 0.5, 1, and 4 h). The first hour is characterized by a transient shift to anaerobic respiration strategies and stress responses, particularly acid resistance, indicating that temperature serves as a sentinel cue to predict and prepare for various niches within the host. The temperature effects on a subset of stress response genes were shown to be mediated by RpoS and directly correlated with RpoS, DsrA, and RprA levels, and increased acid resistance was observed that was dependent on 23°C growth and RpoS. By 4 h, gene expression shifted to aerobic respiration pathways and decreased stress responses, coupled with increases in genes associated with biosynthesis (amino acid and nucleotides), iron uptake, and host defense. ompT, a gene that confers resistance to antimicrobial peptides, was highly thermoregulated, with a pattern conserved in enteropathogenic and uropathogenic E. coli strains. An immediate decrease in curli gene expression concomitant with an increase in flagellar gene expression implicates temperature in this developmental decision. Together, our studies demonstrate that temperature signals a reprogramming of gene expression immediately upon an upshift that may predict, prepare, and benefit the survival of the bacterium within the host.

IMPORTANCE As one of the first cues sensed by the microbe upon entry into a human host, understanding how bacteria like E. coli modulate gene expression in response to temperature improves our understanding of how bacteria immediately initiate responses beneficial for survival and colonization. For pathogens, understanding the various pathways of thermal regulation could yield valuable targets for anti-infective chemotherapeutic drugs or disinfection measures. In addition, our data provide a dynamic examination of the RpoS stress response, providing genome-wide support for how temperature impacts RpoS through changes in RpoS stability and modulation by small regulatory RNAs.

A Thermosensitive, Phase-Variable Epigenetic Switch: pap Revisited

It has been more than a decade since the last comprehensive review of the phase-variable uropathogen-associated pyelonephritis-associated pilus (pap) genetic switch. Since then, important data have come to light, including additional factors that regulate pap expression, better characterization of H-NS regulation, the structure of the Lrp octamer in complex with pap regulatory DNA, the temperature-insensitive phenotype of a mutant lacking the acetyltransferase RimJ, evidence that key components of the regulatory machinery are acetylated, and new insights into the role of DNA binding by key regulators in shaping both the physical structure and regulatory state of the papI and papBA promoters. This review revisits pap, integrating these newer observations with older ones to produce a new model for the concerted behavior of this virulence-regulatory region.

Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome-wide data analysis

Fis (Factor for inversion stimulation) and H-NS (Histone-like nucleoid-structuring protein) are two well-known nucleoid-associated proteins (NAPs) in proteobacteria, which play crucial roles in genome organization and transcriptional regulation. We performed RNA-sequencing to identify genes regulated by these NAPs. Study reveals that Fis and H-NS affect expression of 462 and 88 genes respectively in Escherichia coli at mid-exponential growth phase. By integrating available ChIP-seq data, we identified direct and indirect regulons of Fis and H-NS proteins. Functional analysis reveals that Fis controls expression of genes involved in translation, oxidative phosphorylation, sugar metabolism and transport, amino acid metabolism, bacteriocin transport, cell division, two-component system, biofilm formation, pilus organization and lipopolysaccharide biosynthesis pathways. However, H-NS represses expression of genes in cell adhesion, recombination, biofilm formation and lipopolysaccharide biosynthesis pathways under mid-exponential growth condition. The current regulatory networks thus provide a global glimpse of coordinated regulatory roles for these two important NAPs.

The Coli Surface Antigen CS3 of Enterotoxigenic Escherichia coli Is Differentially Regulated by H-NS, CRP, and CpxRA Global Regulators

Enterotoxigenic Escherichia coli produces a myriad of adhesive structures collectively named colonization factors (CFs). CS3 is a CF, which is assembled into fine wiry fibrillae encoded by the cstA-H gene cluster. In this work we evaluated the influence of environmental cues such as temperature, osmolarity, pH, and carbon source on the expression of CS3 genes. The transcription of cstH major pilin gene was stimulated by growth of the bacteria in colonization factor broth at 37°C; the presence of glycerol enhanced cstH transcription, while glucose at high concentration, high osmolarity, and the depletion of divalent cations such as calcium and magnesium repressed cstH expression. In addition, we studied the role of H-NS, CpxRA, and CRP global regulators in CS3 gene expression. H-NS and CpxRA acted as repressors and CRP as an activator of cstH expression. Under high osmolarity, H-NS, and CpxRA were required for cstH repression. CS3 was required for both, bacterial adherence to epithelial cells and biofilm formation. Our data strengthens the existence of a multi-factorial regulatory network that controls transcription of CS3 genes in which global regulators, under the influence of environmental signals, control the production of this important intestinal colonization factor.

Differential Regulation of Escherichia coli fim Genes following Binding to Mannose Receptors

Regulation of the uropathogenic Escherichia coli (UPEC) fimB and fimE genes was examined following type 1 pili binding to mannose-coated Sepharose beads. Within 25 min after mannose attachment, fimE expression dropped eightfold, whereas fimB transcription increased about two- to fourfold. Because both fim genes encode site-specific recombinases that affect the position of the fimS element containing the fimA promoter, the positioning of fimS was also examined. The fimS element changed to slightly more Phase-OFF in bacteria mixed with plain beads, whereas UPEC cells interacting with mannose-coated beads had significantly less Phase-OFF orientation of fimS under pH 7 conditions. On the other hand, Phase-OFF oriented fimS increased fourfold when UPEC cells were mixed with plain beads in a pH 5.5 environment. Positioning of fimS was also affected by fimH mutations, demonstrating that the FimH ligand binding to its receptor facilitates the changes. Moreover, enzyme immunoassays showed that UPEC cells had greater type 1 pili expression when mixed with mannose-coated beads versus plain beads. These results indicate that, after type 1 pilus binding to tethered mannose receptors, the physiology of the E. coli cells changes to maintain the expression of type 1 pili even when awash in an acidic environment.

TosR-Mediated Regulation of Adhesins and Biofilm Formation in Uropathogenic Escherichia coli

Uropathogenic Escherichia coli strains utilize a variety of adherence factors that assist in colonization of the host urinary tract. TosA (type one secretion A) is a nonfimbrial adhesin that is predominately expressed during murine urinary tract infection (UTI), binds to kidney epithelial cells, and promotes survival during invasive infections. The tosRCBDAEF operon encodes the secretory machinery necessary for TosA localization to the E. coli cell surface, as well as the transcriptional regulator TosR. TosR binds upstream of the tos operon and in a concentration-dependent manner either induces or represses tosA expression. TosR is a member of the PapB family of fimbrial regulators that can participate in cross talk between fimbrial operons. TosR also binds upstream of the pap operon and suppresses PapA production. However, the scope of TosR-mediated cross talk is understudied and may be underestimated. To quantify the global effects of TosR-mediated regulation on the E. coli CFT073 genome, we induced expression of tosR, collected mRNA, and performed high-throughput RNA sequencing (RNA-Seq). These findings show that production of TosR affected the expression of genes involved with adhesins, including P, F1C, and Auf fimbriae, nitrate-nitrite transport, microcin secretion, and biofilm formation.IMPORTANCE Uropathogenic E. coli strains cause the majority of UTIs, which are the second most common bacterial infection in humans. During a UTI, bacteria adhere to cells within the urinary tract, using a number of different fimbrial and nonfimbrial adhesins. Biofilms can also develop on the surfaces of catheters, resulting in complications such as blockage. In this work, we further characterized the regulator TosR, which links both adhesin production and biofilm formation and likely plays a crucial function during UTI and disseminated infection.

Functional analysis of Escherichia coli Yad fimbriae reveals their potential role in environmental persistence

Initial adhesion of bacterial cells to surfaces or host tissues is a key step in colonisation and biofilm formation processes, and is mediated by cell surface appendages. It was previously demonstrated that Escherichia coli K-12 possesses an arsenal of silenced chaperone-usher fimbriae that were functional when constitutively expressed. Among them, production of prevalent Yad fimbriae induces adhesion to abiotic surfaces. Functional characterisation of Yad fimbriae were undertook, and YadN was identified as the most abundant and potential major pilin, and YadC as the potential tip-protein of Yad fimbriae. It was showed that Yad production participates to binding of E. coli K-12 to human eukaryotic cells (Caco-2) and inhibits macrophage phagocytosis, but also enhances E. coli K-12 binding to xylose, a major component of the plant cell wall, through its tip-lectin YadC. Consistently, it was demonstrated that Yad production provides E. coli with a competitive advantage in colonising corn seed rhizospheres. The latter phenotype is correlated with induction of Yad expression at temperatures below 37°C, and under anaerobic conditions, through a complex regulatory network. Taken together, these results suggest that Yad fimbriae are versatile adhesins that beyond potential capacities to modulate host-pathogen interactions might contribute to E. coli environmental persistence.

Animal Enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) is the most common cause of E. coli diarrhea in farm animals. ETEC are characterized by the ability to produce two types of virulence factors: adhesins that promote binding to specific enterocyte receptors for intestinal colonization and enterotoxins responsible for fluid secretion. The best-characterized adhesins are expressed in the context of fimbriae, such as the F4 (also designated K88), F5 (K99), F6 (987P), F17, and F18 fimbriae. Once established in the animal small intestine, ETEC produce enterotoxin(s) that lead to diarrhea. The enterotoxins belong to two major classes: heat-labile toxins that consist of one active and five binding subunits (LT), and heat-stable toxins that are small polypeptides (STa, STb, and EAST1). This review describes the disease and pathogenesis of animal ETEC, the corresponding virulence genes and protein products of these bacteria, their regulation and targets in animal hosts, as well as mechanisms of action. Furthermore, vaccines, inhibitors, probiotics, and the identification of potential new targets by genomics are presented in the context of animal ETEC.

CRP-Cyclic AMP Regulates the Expression of Type 3 Fimbriae via Cyclic di-GMP in Klebsiella pneumoniae

Klebsiella pneumoniae is the predominant pathogen isolated from liver abscesses of diabetic patients in Asian countries. However, the effects of elevated blood glucose levels on the virulence of this pathogen remain largely unknown. Type 3 fimbriae, encoded by the mrkABCDF genes, are important virulence factors in K. pneumoniae pathogenesis. In this study, the effects of exogenous glucose and the intracellular cyclic AMP (cAMP) signaling pathway on type 3 fimbriae expression regulation were investigated. The production of MrkA, the major subunit of type 3 fimbriae, was increased in glucose-rich medium, whereas cAMP supplementation reversed the effect. MrkA production was markedly increased by cyaA or crp deletion, but slightly decreased by cpdA deletion. In addition, the mRNA levels of mrkABCDF genes and the activity of P_mrkA were increased in Δcrp strain, as well as the mRNA levels of mrkHIJ genes that encode cyclic di-GMP (c-di-GMP)-related regulatory proteins that influence type 3 fimbriae expression. Moreover, the activities of P_mrkHI and P_mrkJ were decreased in ΔlacZΔcrp strain. These results indicate that CRP-cAMP down-regulates mrkABCDF and mrkHIJ at the transcriptional level. Further deletion of mrkH or mrkI in Δcrp strain diminished the production of MrkA, indicating that MrkH and MrkI are required for the CRP regulation of type 3 fimbriae expression. Furthermore, the high activity of P_mrkHI in the ΔlacZΔcrp strain was diminished in ΔlacZΔcrpΔmrkHI, but increased in the ΔlacZΔcrpΔmrkJ strain. Deletion of crp increased the intracellular c-di-GMP concentration and reduced the phosphodiesterase activity. Moreover, we found that the mRNA levels of multiple genes related to c-di-GMP metabolism were altered in Δcrp strain. These indicate that CRP regulates type 3 fimbriae expression indirectly via the c-di-GMP signaling pathway. In conclusion, we found evidence of a coordinated regulation of type 3 fimbriae expression by the CRP-cAMP and c-di-GMP signaling pathways in K. pneumoniae.

The Histone-Like Nucleoid Structuring Protein (H-NS) Is a Negative Regulator of the Lateral Flagellar System in the Deep-Sea Bacterium Shewanella piezotolerans WP3

Although the histone-like nucleoid structuring protein (H-NS) is well known for its involvement in the adaptation of mesophilic bacteria, such as Escherichia coli, to cold environments and high-pressure stress, an understanding of the role of H-NS in the cold-adapted benthic microorganisms that live in the deep-sea ecosystem, which covers approximately 60% of the earth's surface, is still lacking. In this study, we characterized the function of H-NS in Shewanella piezotolerans WP3, which was isolated from West Pacific sediment at a depth of 1,914 m. Anhns gene deletion mutant (WP3Δhns) was constructed, and comparative whole-genome microarray analysis was performed. H-NS had a significant influence (fold change, >2) on the expression of a variety of WP3 genes (274 and 280 genes were upregulated and downregulated, respectively), particularly genes related to energy production and conversion. Notably, WP3Δhnsexhibited higher expression levels of lateral flagellar genes than WP3 and showed enhanced swarming motility and lateral flagellar production compared to those of WP3. The DNA gel mobility shift experiment showed that H-NS bound specifically to the promoter of lateral flagellar genes. Moreover, the high-affinity binding sequences of H-NS were identified by DNase I protection footprinting, and the results support the "binding and spreading" model for H-NS functioning. To our knowledge, this is the first attempt to characterize the function of the universal regulator H-NS in a deep-sea bacterium. Our data revealed that H-NS has a novel function as a repressor of the expression of genes related to the energy-consuming secondary flagellar system and to swarming motility.

Regulation and production of Tcf, a cable-like fimbriae from Salmonella enterica serovar Typhi

tcf (Typhi colonization factor) is one of the 12 putative chaperone/usher fimbrial clusters present in the Salmonella enterica serovar Typhi genome. We investigated the production, expression and regulation of tcf as well as its role during interaction with human cells. The tcf gene cluster was cloned and induced in Escherichia coli and S. Typhi, and the production of intertwined fibres similar to the Cbl (cable) pili of Burkholderia cepacia was observed on the bacterial surface by electron microscopy. In S. Typhi, tcf was expressed more after growth in M63 minimal medium than in standard Luria-Bertani medium. Analysis of the promoter region identified putative binding sites for the global regulators RcsB, ArgR and Fur. The expression of tcf was measured in isogenic strains lacking these global regulators. Under the conditions tested, the results showed that tcf expression was higher in the fur mutant and was regulated by iron concentration. Fur may regulate these fimbriae indirectly via the small RNAs RyhB1 and RyhB2. An isogenic mutant harbouring a deletion of the tcf cluster did not demonstrate any defect in adhesion or invasion of human epithelial cells, or in phagocytosis or survival in macrophages, when compared to the WT serovar Typhi strain. However, the tcf cluster contributed to adherence to human epithelial cells when introduced into E. coli. Thus, tcf genes encode functional fimbriae that can act as an adhesin and may contribute to colonization during typhoid fever.

Regulation of Expression of Uropathogenic Escherichia coli Nonfimbrial Adhesin TosA by PapB Homolog TosR in Conjunction with H-NS and Lrp

Urinary tract infections (UTIs) are a major burden to human health. The overwhelming majority of UTIs are caused by uropathogenic Escherichia coli (UPEC) strains. Unlike some pathogens, UPEC strains do not have a fixed core set of virulence and fitness factors but do have a variety of adhesins and regulatory pathways. One such UPEC adhesin is the nonfimbrial adhesin TosA, which mediates adherence to the epithelium of the upper urinary tract. The tos operon is AT rich, resides on pathogenicity island aspV, and is not expressed under laboratory conditions. Because of this, we hypothesized that tosA expression is silenced by H-NS. Lrp, based on its prominent function in the regulation of other adhesins, is also hypothesized to contribute to tos operon regulation. Using a variety of in vitro techniques, we mapped both the tos operon promoter and TosR binding sites. We have now identified TosR as a dual regulator of the tos operon, which could control the tos operon in association with H-NS and Lrp. H-NS is a negative regulator of the tos operon, and Lrp positively regulates the tos operon. Exogenous leucine also inhibits Lrp-mediated tos operon positive regulation. In addition, TosR binds to the pap operon, which encodes another important UPEC adhesin, P fimbria. Induction of TosR synthesis reduces production of P fimbria. These studies advance our knowledge of regulation of adhesin expression associated with uropathogen colonization of a host.

Adhesins of Enterotoxigenic Escherichia coli Strains That Infect Animals

The first described adhesive antigen of Escherichia coli strains isolated from animals was the K88 antigen, expressed by strains from diarrheic pigs. The K88 antigen was visible by electron microscopy as a surface-exposed filament that was thin and flexible and had hemagglutinating properties. Many different fimbriae have been identified in animal enterotoxigenic E. coli (ETEC) and have been discussed in this article. The role of these fimbriae in the pathogenesis of ETEC has been best studied with K88, K99, 987P, and F41. Each fimbrial type carries at least one adhesive moiety that is specific for a certain host receptor, determining host species, age, and tissue specificities. ETEC are the most frequently diagnosed pathogens among neonatal and post-weaning piglets that die of diarrhea. Immune electron microscopy of animal ETEC fimbriae usually shows that the minor subunits are located at the fimbrial tips and at discrete sites along the fimbrial threads. Since fimbriae most frequently act like lectins by binding to the carbohydrate moieties of glycoproteins or glycolipids, fimbrial receptors have frequently been studied with red blood cells of various animal species. Identification and characterization of the binding moieties of ETEC fimbrial adhesins should be useful for the design of new prophylactic or therapeutic strategies. Some studies describing potential receptor or adhesin analogues that interfere with fimbria-mediated colonization have been described in the article.

Pathogenesis of human diffusely adhering Escherichia coli expressing Afa/Dr adhesins (Afa/Dr DAEC): current insights and future challenges

The pathogenicity and clinical pertinence of diffusely adhering Escherichia coli expressing the Afa/Dr adhesins (Afa/Dr DAEC) in urinary tract infections (UTIs) and pregnancy complications are well established. In contrast, the implication of intestinal Afa/Dr DAEC in diarrhea is still under debate. These strains are age dependently involved in diarrhea in children, are apparently not involved in diarrhea in adults, and can also be asymptomatic intestinal microbiota strains in children and adult. This comprehensive review analyzes the epidemiology and diagnosis and highlights recent progress which has improved the understanding of Afa/Dr DAEC pathogenesis. Here, I summarize the roles of Afa/Dr DAEC virulence factors, including Afa/Dr adhesins, flagella, Sat toxin, and pks island products, in the development of specific mechanisms of pathogenicity. In intestinal epithelial polarized cells, the Afa/Dr adhesins trigger cell membrane receptor clustering and activation of the linked cell signaling pathways, promote structural and functional cell lesions and injuries in intestinal barrier, induce proinflammatory responses, create angiogenesis, instigate epithelial-mesenchymal transition-like events, and lead to pks-dependent DNA damage. UTI-associated Afa/Dr DAEC strains, following adhesin-membrane receptor cell interactions and activation of associated lipid raft-dependent cell signaling pathways, internalize in a microtubule-dependent manner within urinary tract epithelial cells, develop a particular intracellular lifestyle, and trigger a toxin-dependent cell detachment. In response to Afa/Dr DAEC infection, the host epithelial cells generate antibacterial defense responses. Finally, I discuss a hypothetical role of intestinal Afa/Dr DAEC strains that can act as "silent pathogens" with the capacity to emerge as "pathobionts" for the development of inflammatory bowel disease and intestinal carcinogenesis.

Expression of the Escherichia coli ompW colicin S4 receptor gene is regulated by temperature and modulated by the H-NS and StpA nucleoid-associated proteins

The OmpW family consists of a ubiquitous group of small outer membrane (OM) β-barrel proteins of Gram-negative bacteria with proposed roles in environmental adaptation but poorly understood mechanisms of expression. We report here that Escherichia coli K-12 OmpW contents are drastically modified by temperature changes compatible with the leap from the environment to warm-blooded hosts and/or vice versa. Thus, while OmpW is present in the OM of bacteria grown at 37 °C, it sharply disappears at 23 °C with the concomitant acquisition of colicin S4 resistance by the cells. ompW::lacZY fusions indicated that temperature regulation operates at the level of transcription, being ompW expression almost abolished at 23 °C as compared to 37 °C. Moreover, E. coli Δhns mutants lacking H-NS showed reductions in ompW transcription and OmpW contents at 37 °C, indicating positive modulatory roles for this nucleoid-structuring protein in ompW expression. Also, ΔhnsΔstpA double mutants simultaneously lacking H-NS and its paralog StpA showed more severe reductions in ompW expression at 37 °C, resulting in the complete loss of OmpW. The overall results indicate that OmpW contents in E. coli are regulated by both temperature and H-NS and reinforce OmpW functions in bacterial adaptation to warm-blooded hosts.

Thermosensing to adjust bacterial virulence in a fluctuating environment

The lifecycle of most microbial pathogens can be divided into two states: existence outside and inside their hosts. The sudden temperature upshift experienced upon entry from environmental or vector reservoirs into a warm-blooded host is one of the most crucial signals informing the pathogens to adjust virulence gene expression and their host-stress survival program. This article reviews the plethora of sophisticated strategies that bacteria have evolved to sense temperature, and outlines the molecular signal transduction mechanisms used to modulate synthesis of crucial virulence determinants. The molecular details of thermal control through conformational changes of DNA, RNA and proteins are summarized, complex and diverse thermosensing principles are introduced and their potential as drug targets or synthetic tools are discussed.

Programmed heterogeneity: epigenetic mechanisms in bacteria

Contrary to the traditional view that bacterial populations are clonal, single-cell analysis reveals that phenotypic heterogeneity is common in bacteria. Formation of distinct bacterial lineages appears to be frequent during adaptation to harsh environments, including the colonization of animals by bacterial pathogens. Formation of bacterial subpopulations is often controlled by epigenetic mechanisms that generate inheritable phenotypic diversity without altering the DNA sequence. Such mechanisms are diverse, ranging from relatively simple feedback loops to complex self-perpetuating DNA methylation patterns.

Regulatory control of the Escherichia coli O157:H7 lpf1 operon by H-NS and Ler

Long polar fimbriae 1 (Lpf1) of Escherichia coli O157:H7 is a tightly regulated adhesin, with H-NS silencing the transcriptional expression of the lpf1 operon while Ler (locus of enterocyte effacement-encoded regulator) acts as an antisilencer. We mapped the minimal regulatory region of lpf1 required for H-NS- and Ler-mediated regulation and found that it is 79% AT rich. Three putative sites for H-NS binding were identified. Two of them, named silencer regulatory sequence 1 (SRS1) and SRS2, are located on a region that covers both of the lpf1 promoters (P1 and P2). The third putative H-NS binding site is located within the lpfA1 gene in a region extending from +258 bp to +545 bp downstream of ATG; however, this site does not seem to play a role in lpfA1 regulation under the conditions tested in this work. Ler was also found to interact with Ler binding sites (LBSs). Ler binding site 1 (LBS1) and LBS2 are located upstream of the two promoters. LBS1 overlaps SRS1, while LBS3 overlaps the P1 promoter and SRS2. Based on the experimental data, we propose that H-NS silences lpf1 expression by binding to both of the SRSs on the promoter region, forming an SRS-H-NS complex that prevents RNA polymerase-mediated transcription. A model of the regulation of the lpfA1 operon of E. coli O157:H7 by H-NS and Ler is discussed.

Norepinephrine-dependently released Dr fimbriae of diffusely adhering Escherichia coli strain IH11128 promotes a mitogen-activated protein kinase ERK1/2-dependent production of pro-inflammatory cytokine, IL-8 in human intestinal Caco-2/TC7 cells

The diffusely adhering Escherichia coli (Afa/Dr DAEC) are associated with recurrent urinary tract infections in adults as well as with diarrheal disease in infants. We previously demonstrated that in wild-type strain IH11128, the Dr fimbriae is released in the extracellular medium in response to multiple environmental signals such as temperature, low aeration and rich medium. A number of molecules of eukaryotic origin, such as catecholamines, have been reported to stimulate bacterial growth and virulence factor production. We show that norepinephrine affects the production and release of Dr fimbriae in Afa/Dr DAEC WT-IH11128 bacteria. The regulatory mechanism involved with norepinephrine-induced Dr fimbriae liberation was apparently due to a differential induction of genes draC, encoding the usher, and draE, encoding the major fimbrial subunit. In addition, we show that the released Dr fimbriae induces the phosphorylation of the mitogen-activated protein kinase, extracellular signal-regulated kinase 1/2 (ERK1/2) and the production of the pro-inflammatory cytokine, IL-8 in fully differentiated cultured human intestinal Caco-2/TC7 cells.

Seasonal influence on heat-resistant proteolytic capacity of Pseudomonas lundensis and Pseudomonas fragi, predominant milk spoilers isolated from Belgian raw milk samples

Psychrotolerant bacteria and their heat-resistant proteases play a major role in the spoilage of UHT-processed dairy products. Summer and winter raw milk samples were screened for the presence of such bacteria. One hundred and three proteolytic psychrotolerant bacteria were isolated, characterized by API tests, rep-PCR fingerprint analysis and evaluated for heat-resistant protease production. Twenty-nine strains (representing 79% of the complete collection) were further identified by 16S rRNA gene sequencing, rpoB gene sequencing and DNA-DNA hybridizations. A seasonal inter- and intra-species influence on milk spoilage capacity (e.g. growth rate and/or protease production) was demonstrated. Moreover, this polyphasic approach led to the identification of Pseudomonas fragi and Pseudomonas lundensis (representing 53% of all isolates) as predominant producers of heat-resistant proteases in raw milk. The role of Pseudomonas fluorescens, historically reported as important milk spoiler, could not unequivocally be established. The use of more reliable identification techniques and further revision of the taxonomy of P. fluorescens will probably result in a different perspective on its role in the milk spoilage issue.

Genome-wide identification of H-NS-controlled, temperature-regulated genes in Escherichia coli K-12

DNA microarrays demonstrate that H-NS controls 69% of the temperature regulated genes in Escherichia coli K-12. H-NS is shown to be a common regulator of multiple iron and other nutrient acquisition systems preferentially expressed at 37 degrees C and of general stress response, biofilm formation, and cold shock genes highly expressed at 23 degrees C.

Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12

Using DNA microarrays, we identified 126 genes in Escherichia coli K-12 whose expression is increased at human body temperature (37 degrees C) compared to growth at 23 degrees C. Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. Using quantitative real-time PCR, we investigated the thermoregulatory response for representative genes in each of these three categories (hisJ, cysP, srlE, garP, fes, and cirA), along with the fimbrial gene papB. Increased expression at 37 degrees C compared to 23 degrees C was retained in both exponential and stationary phases for all of the genes and in most of the various media tested, supporting the relative importance of this cue in adapting to changing environments. Because iron acquisition is important for both growth and virulence, we analyzed the regulation of the iron utilization genes cirA and fes and found that growth in iron-depleted medium abrogated the thermoregulatory effect, with high-level expression at both temperatures, contrasting with papB thermoregulation, which was not greatly altered by limiting iron levels. A positive role for the environmental regulator H-NS was found for fes, cirA, hisJ, and srlE transcription, whereas it had a primarily negative effect on cysP and garP expression. Together, these studies indicate that temperature is a broadly used cue for regulating gene expression in E. coli and that H-NS regulates iron, carbohydrate, and amino acid utilization gene expression.

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.

Epigenetic gene regulation in the bacterial world

Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.

The role of phenotypic variation in rhizosphere Pseudomonas bacteria

Colony phase variation is a regulatory mechanism at the DNA level which usually results in high frequency, reversible switches between colonies with a different phenotype. A number of molecular mechanisms underlying phase variation are known: slipped-strand mispairing, genomic rearrangements, spontaneous mutations and epigenetic mechanisms such as differential methylation. Most examples of phenotypic variation or phase variation have been described in the context of host-pathogen interactions as mechanisms allowing pathogens to evade host immune responses. Recent reports indicate that phase variation is also relevant in competitive root colonization and biological control of phytopathogens. Many rhizospere Pseudomonas species show phenotypic variation, based on spontaneous mutation of the gacA and gacS genes. These morphological variants do not express secondary metabolites and have improved growth characteristics. The latter could contribute to efficient root colonization and success in competition, especially since (as shown for one strain) these variants were observed to revert to their wild-type form. The observation that these variants are present in rhizosphere-competent Pseudomonas bacteria suggests the existence of a conserved strategy to increase their success in the rhizosphere.

Environmental signals implicated in Dr fimbriae release by pathogenic Escherichia coli

Afa/Dr diffusely adhering Escherichia coli have been shown to cause urinary tract infections and enteric infections. Virulence of Dr-positive IH11128 bacteria is associated with the presence of Dr fimbriae. In this report, we show for the first time that the Dr fimbriae are released in the extracellular medium in response to multiple environmental signals. Production and secretion of Dr fimbriae are clearly thermoregulated. A comparison of the amounts of secreted fimbriae showed that the secretion is drastically increased during anaerobic growth in minimal medium. The effect of anaerobiosis on secretion seemed to depend on both the growth phase and the culture medium. The secretion was maximal during the logarithmic-phase growth and corresponded to 27 and 57% of total Dr fimbriae produced by bacteria grown in mineral medium+glucose and LB broth, respectively. Thus, the anaerobic environment of the colon would favour the secretion of Dr fimbriae during bacterial multiplication. The controlled release of the Dr fimbriae, which is carried out in the absence of cellular lysis, appears independent of the action of proteases or a process of maturation. The mechanism employed in the liberation of Dr fimbriae thus seems different from that described for the adhesins FHA and Hap of Bordetella pertussis and Haemophilus influenzae.

The thin pili of Acinetobacter sp. strain BD413 mediate adhesion to biotic and abiotic surfaces

Two structurally different appendages, thin and thick pili, are found in members of the genus Acinetobacter. The presence of pilus structures correlates with different phenotypes, such as adherence to surfaces, a trait not only observed in pathogenic Acinetobacter species, as well as motility. However, their distinct individual roles were unknown. To characterize the role of different pili in the physiology of Acinetobacter, we isolated the thin pili from the cell surface of Acinetobacter sp. strain BD413 (recently recognized as representative of Acinetobacter baylyi), a soil bacterium that rapidly takes up naked DNA from its environment. Electron microscopy revealed that the pilus has an external diameter of 2 to 3 nm for single filaments. The filaments are packed into right-handed bundles. The major protein constituting the pilus was purified, and the encoding gene, acuA, was cloned. AcuA was found to be weakly related to the structural subunit of F17 pili of Escherichia coli. Analyses of the acuA flanking DNA region led to the identification of three closely associated genes, acuD, acuC, and acuG, whose deduced proteins are similar to chaperone, usher, and adhesin of F17-related pili, respectively. Transcriptional analyses revealed that acuA expression is maximal in the late-stationary-growth phase. Mutation of acuA led to a loss of thin pili and concomitantly loss of adhesion to polystyrene and erythrocytes but not loss of competence. Therefore, thin pili of Acinetobacter sp. strain BD413 are suggested to be assembled by the chaperone/usher pathway and are involved in adherence to biotic and abiotic surfaces.

Identification of Actinobacillus suis genes essential for the colonization of the upper respiratory tract of swine

Actinobacillus suis has emerged as an important opportunistic pathogen of high-health-status swine. A colonization challenge method was developed, and using PCR-based signature-tagged transposon mutagenesis, 13 genes belonging to 9 different functional classes were identified that were necessary for A. suis colonization of the upper respiratory tract of swine.

Adhesins of Diffusely Adherent and Enteroaggregative Escherichia coli

Epidemiological studies have implicated enteroaggregative Escherichia coli (EAEC) strains in acute and persistent diarrhea in children, in food-borne diarrhea outbreaks, and in traveler's diarrhea, and this group is recognized as an emerging pathotype of enteric disease. Diffusely adherent E. coli (DAEC) have been implicated as a cause of diarrhea, especially in children more than 2 years old, in both developing and developed countries. Although EAEC and DAEC strains appear to have different molecular equipment for attachment to host cell surfaces, identification and characterization of the gene clusters encoding adherence evidenced close relatedness between those determinants most frequently detected in isolates belonging to these two pathotypes of diarrheagenic E. coli. DAEC strains are a heterogeneous group of E. coli isolates, many of which express the related so-called Dr adhesins. The single designation is based on the identification of one similar cellular receptor for all these proteins. Although structurally different, they all recognize the Dr human blood group antigen on the decay-accelerating factor (DAF or CD55). These adhesins are encoded by a family of closely related operons, the first characterized and sequenced being the afa operon. Consequently, it has been suggested that this group of DAEC strains producing such adhesins be named the Afa/Dr DAEC family. Three distinct but closely related gene clusters coding for phenotypically and morphologically distinct aggregative adherence fimbriae (AAF) have been characterized. In each case, electron microscopy revealed that bacterial surfaces were surrounded by long, relatively flexible fimbrial structures.

LRP and H-NS - cooperative partners for transcription regulation atEscherichia colirRNA promoters

The synthesis of ribosomal RNAs in bacteria is tightly coupled to changes in the environment. This rapid adaptation is the result of several intertwined regulatory networks. The two proteins FIS and H-NS have previously been described to act as antagonistic transcription factors for rRNA synthesis. Here we provide evidence for another player, the regulatory protein LRP, which binds with high specificity to all seven Escherichia coli rRNA P1 promoter upstream regions (UAS). Comparison of the binding properties of LRP and H-NS, and characterization of the stabilities of the various complexes formed with the rRNA UAS regions revealed different binding modes. Binding studies with LRP and H-NS in combination demonstrated that the two proteins interacted with obvious synergism. The efficiency of LRP binding to the rRNA regulatory region is modified by the presence of the effector amino acid leucine, as has been shown for several other operons regulated by this transcription factor. The effect of LRP on the binding of RNA polymerase to the rrnB P1 promoter and in vitro transcription experiments indicated that LRP acts as a transcriptional repressor, thus resembling the activity of H-NS described previously. The results show for the first time that LRP binds to the regulatory region of bacterial rRNA promoters, and very likely contributes in combination with H-NS to the control of rRNA synthesis. From the known properties of LRP a mechanism can be inferred that couples rRNA synthesis to changes in nutritional quality.

Stochastic modeling of the phase-variable pap operon regulation in uropathogenic Escherichia coli

Regulation of the pap operon in uropathogenic Escherichia coli is phase variable. This phase variation arises from competition between regulatory proteins at two sites within the regulatory region, GATC(dist) and GATC(prox). We have used the available literature data to design a stochastic model of the molecular interactions of pap regulation and expression during growth in a non-glucose environment at 37 degrees C. The resulting wild-type model is consistent with reported data. The wild-type model served as a basis for two "in silico" mutant models for investigating the role of key regulatory components, the GATC(dist) binding site and the PapI interaction with Lrp at the GATC(prox) site. Our results show that competition at GATC(dist) is required for phase variation, as previously reported. However, our results suggest that removal of competition at GATC(dist) does not affect initial state dependence. Additionally, the PapI involvement in Lrp translocation from GATC(prox) to GATC(dist) is required for the initial state dependence but not for phase variation. Our results also predict that pap expression is maximized at low growth rates and minimized at high growth rates. These predictions provide a basis for further experimental investigation.

Markov Chain modeling of pyelonephritis-associated pili expression in uropathogenic Escherichia coli

Pyelonephritis-associated pili (Pap) expression in uropathogenic Escherichia coli is regulated by a complex phase variation mechanism involving the competition between leucine-responsive regulatory protein (Lrp) and DNA adenine methylase (Dam). Population dynamics of pap gene expression has been studied extensively and the detailed molecular mechanism has been largely elucidated, providing sufficient information for mathematical modeling. Although the Gillespie algorithm is suited for modeling of stochastic systems such as the pap operon, it becomes computationally expensive when detailed molecular steps are explicitly modeled in a population. Here we developed a Markov Chain model to simplify the computation. Our model is analytically derived from the molecular mechanism. The model presented here is able to reproduce results presented using the Gillespie method, but since the regulatory information is incorporated before simulation, our model runs more efficiently and allows investigation of additional regulatory features. The model predictions are consistent with experimental data obtained in this work and in the literature. The results show that pap expression in uropathogenic E. coli is initial-state-dependent, as previously reported. However, without environment stimuli, the pap-expressing fraction in a population will reach an equilibrium level after approximately 50-100 generations. The transient time before reaching equilibrium is determined by PapI stability and Lrp and Dam copy numbers per cell. This work demonstrates that the Markov Chain model captures the essence of the complex molecular mechanism and greatly simplifies the computation.

Regulation of the pap epigenetic switch by CpxAR: phosphorylated CpxR inhibits transition to the phase ON state by competition with Lrp

Pap pili gene expression is controlled by a reversible OFF/ON phase switch that is orchestrated by binding of Lrp to pap pilin promoter proximal sites 1, 2, and 3 (OFF) or pap promoter distal sites 4, 5, and 6 (ON). Movement of Lrp between proximal and distal sites controls pap pilin transcription and is modulated by PapI and DNA adenine methylase. Here we show that activation of the environmentally responsive CpxAR two-component regulatory system inhibits Pap phase variation by generation of phosphorylated CpxR (CpxR-P). CpxR-P competes with Lrp for binding to both promoter proximal and distal pap DNA binding sites, inhibiting pap transcription in vitro and pili expression in vivo. In contrast to Lrp, CpxR-P is methylation insensitive and does not form DNA methylation patterns in vivo. CpxAR-dependent repression of pap transcription is also observed in response to alkaline growth conditions. These results provide insight into a mechanism for environmental control of epigenetically regulated gene expression.

F4 fimbriae expressed by porcine enterotoxigenic Escherichia coli, an example of an eccentric fimbrial system?

An overwhelming number of infectious diseases in both humans and animals are initiated by bacterial adhesion to carbohydrate structures on a mucosal surface. Most bacterial pathogens mediate this adhesion by fimbriae or pili which contain an adhesive lectin subunit. The importance of fimbriae as virulence factors led to research elucidating the regulation of fimbrial expression and their molecular assembly process. This review provides an overview of the current knowledge of induction, expression and assembly of F4 (K88) fimbriae and discusses its unique as well as its identical characteristics compared to other intensively studied fimbriae or pili expressed by Escherichia coli.

The intricate workings of a bacterial epigenetic switch

Bacteria have developed epigenetic mechanisms to control the reversible Off-to-On switching of cell surface structures such as pyelonephritis-associated pili (PAP). The pap pili switch is primarily controlled by the global regulator leucine-responsive regulatory protein (Lrp), the local regulator PapI, and DNA adenine methylase (Dam). There are two sets of binding sites for Lrp in the pap regulatory region: promoter proximal sites 1,2,3 and promoter distal sites 4,5,6. The pilin promoter proximal (GATCprox) and distal (GATCdist) targets for Dam are located within Lrp binding sites 2 and 5, respectively. In the Off state, Lrp binds cooperatively to sites 1,2,3 overlapping the papBA pilin promoter, shutting off pilin transcription, and blocking methylation of GATCprox. Binding of Lrp at sites 1,2,3, together with methylation of GATCdist, reduces the affinity of Lrp for sites 4,5,6, preventing simultaneous binding of Lrp at sites 4,5,6 upstream. Switching to the phase. On state requires the environmentally regulated PapI co-regulator, which increases the affinity of Lrp for sites 5 and 2. PapI binds specifically to Lrp-pap DNA complexes via binding with Lrp as well as contact with DNA sequences within pap sites 5 and 2. Directionality in switching from Off to On appears to be due to methylation of GATCprox, which prevents formation of the PapI-Lrp-pap site 2 ternary complex. A switch model is presented in which DNA replication is proposed to play a critical role by generating a hemimethylated GATCdist site and displacing Lrp from sites 1,2,3. This facilitates methylation of GATCprox and binding of PapI-Lrp to sites 4,5,6, with subsequent activation of pap transcription. The first gene product of the pap operon, PapB, positively regulates papI transcription, resulting in a positive feedback loop that helps maintain the On state. The pap switch is environmentally regulated by a number of factors including the CpxAR two-component regulatory system, the Histone-like nucleoid structuring protein H-NS, and cAMP-Catabolite Gene Activator Protein (CAP), which all involve binding of regulatory binding proteins to pap DNA sequences with subsequent alteration of PapI and Lrp binding. The Pap switch mechanism, with interesting variations, is conserved among a number of enteric bacteria, controlling expression of many unrelated pili-adhesin complexes.

Phase and antigenic variation in bacteria

Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. This form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. This review provides an overview of the many bacterial proteins and structures that are under the control of phase or antigenic variation. The context is mainly within the role of the proteins and variation for pathogenesis, which reflects the main body of literature. The occurrence of phase variation in expression of genes not readily recognizable as virulence factors is highlighted as well, to illustrate that our current knowledge is incomplete. From recent genome sequence analysis, it has become clear that phase variation may be more widespread than is currently recognized, and a brief discussion is included to show how genome sequence analysis can provide novel information, as well as its limitations. The current state of knowledge of the molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the way in which these mechanisms form part of the general regulatory network of the cell is addressed. Arguments both for and against a role of phase and antigenic variation in immune evasion are presented and put into new perspective by distinguishing between a role in bacterial persistence in a host and a role in facilitating evasion of cross-immunity. Finally, examples are presented to illustrate that phase-variable gene expression should be taken into account in the development of diagnostic assays and in the interpretation of experimental results and epidemiological studies.

Transcriptional and posttranscriptional control of cable pilus gene expression in Burkholderia cenocepacia

Burkholderia cenocepacia is an important member of the Burkholderia cepacia complex, a group of closely related bacteria that inhabits a wide variety of environmental niches in nature and that also colonizes the lungs of compromised humans. Certain strains of B. cenocepacia express peritrichous adherence organelles known as cable pili, thought to be important in the colonization of the lower respiratory tract. The genetic locus required for cable pilus biogenesis is comprised of at least five genes, designated cblB, cblA, cblC, cblD, and cblS. In this study a transcriptional analysis of cbl gene expression was undertaken. The principal promoter, located upstream of the cbl locus, was identified and characterized. By using lacZ transcriptional fusions, the effects of multiple environmental cues on cbl gene expression were examined. High osmolarity, temperature of 37 degrees C, acidic pH, and low iron bioavailability were found to induce cbl gene expression. Northern hybridization analysis of the cbl locus identified a single, stable transcript corresponding to cblA, encoding the major pilin subunit. Transcriptional fusion studies combined with reverse transcription-PCR analysis indicated that the stable cblA transcript is the product of an mRNA processing event. This event may ensure high levels of expression of the major pilin, relative to other components of the assembly pathway. Our findings lend further insight into the control of cable pilus biogenesis in B. cenocepacia and provide evidence for regulation of cbl gene expression on both the transcriptional and posttranscriptional levels.

Self-perpetuating epigenetic pili switches in bacteria

Bacteria have developed an epigenetic phase variation mechanism to control cell surface pili-adhesin complexes between heritable expression (phase ON) and nonexpression (phase OFF) states. In the pyelonephritis-associated pili (pap) system, global regulators [catabolite gene activator protein (CAP), leucine-responsive regulatory protein (Lrp), DNA adenine methylase (Dam)] and local regulators (PapI and PapB) control phase switching. Lrp binds cooperatively to three pap DNA binding sites, sites 1-3, proximal to the papBA pilin promoter in phase OFF cells, whereas Lrp is bound to sites 4-6 distal to papBA in phase ON cells. Two Dam methylation targets, GATC(prox) and GATC(dist), are located in Lrp binding sites 2 and 5, respectively. In phase OFF cells, binding of Lrp at sites 1-3 inhibits methylation of GATC(prox), forming the phase OFF DNA methylation pattern (GATC(dist) methylated, GATC(prox) nonmethylated). Binding of Lrp at sites 1-3 blocks pap pili transcription and reduces the affinity of Lrp for sites 4-6. Together with methylation of GATC(dist), which inhibits Lrp binding at sites 4-6, the phase OFF state is maintained. We hypothesize that transition to the phase ON state requires DNA replication to dissociate Lrp and generate a hemimethyated GATC(dist) site. PapI and methylation of GATC(prox) act together to increase the affinity of Lrp for sites 4-6. Binding of Lrp at the distal sites protects GATC(dist) from methylation, forming the phase ON methylation pattern (GATC(dist) nonmethyated, GATC(prox) methylated). Lrp binding at sites 4-6 together with cAMP-CAP binding 215.5 bp upstream of the papBA transcription start, is required for activation of pilin transcription. The first gene product of the papBA transcript, PapB, helps maintain the switch in the ON state by activating papI transcription, which in turn maintains Lrp binding at sites 4-6.

The N-acetyltransferase RimJ responds to environmental stimuli to repress pap fimbrial transcription in Escherichia coli

In uropathogenic Escherichia coli, P pili (Pap) facilitate binding to host epithelial cells and subsequent colonization. Whereas P pili can be produced at 37 degrees C, the expression of these fimbriae is suppressed at 23 degrees C. Previously, insertion mutations in rimJ, a gene encoding the N-terminal acetyltransferase of ribosomal protein S5, were shown to disrupt this thermoregulatory response, allowing papBA transcription at low temperature. In this study, we created an in-frame deletion of rimJ. This deletion relieved the repressive effects not only of low temperature but also of rich (Luria-Bertani [LB]) medium and glucose on papBA transcription, indicating that RimJ modulates papBA transcription in response to multiple environmental stimuli. papI transcription was also shown to be regulated by RimJ. papBA transcription is also controlled by a phase variation mechanism. We demonstrated that the regulators necessary to establish a phase ON state--PapI, PapB, Dam, Lrp, and cyclic AMP-CAP-are still required for papBA transcription in a rimJ mutant strain. rimJ mutations increase the rate at which bacteria transition into the phase ON state, indicating that RimJ inhibits the phase OFF-->ON transition. A DeltarimJ hns651 mutant is viable on LB medium but not on minimal medium. This synthetic lethality, along with transcriptional analyses, indicates that RimJ and H-NS work through separate pathways to control papBA transcription. Mutations in rimJ do not greatly influence the transcription of the fan, daa, or fim operon, suggesting that RimJ may be a pap-specific regulator. Overexpression of rimJ under conditions repressive for papBA transcription complements the DeltarimJ mutation but has little effect on transcription under activating conditions, indicating that the ability of RimJ to regulate transcription is environmentally controlled.

The N-acetyltransferase RimJ responds to environmental stimuli to repress pap fimbrial transcription in Escherichia coli

In uropathogenic Escherichia coli, P pili (Pap) facilitate binding to host epithelial cells and subsequent colonization. Whereas P pili can be produced at 37 degrees C, the expression of these fimbriae is suppressed at 23 degrees C. Previously, insertion mutations in rimJ, a gene encoding the N-terminal acetyltransferase of ribosomal protein S5, were shown to disrupt this thermoregulatory response, allowing papBA transcription at low temperature. In this study, we created an in-frame deletion of rimJ. This deletion relieved the repressive effects not only of low temperature but also of rich (Luria-Bertani [LB]) medium and glucose on papBA transcription, indicating that RimJ modulates papBA transcription in response to multiple environmental stimuli. papI transcription was also shown to be regulated by RimJ. papBA transcription is also controlled by a phase variation mechanism. We demonstrated that the regulators necessary to establish a phase ON state--PapI, PapB, Dam, Lrp, and cyclic AMP-CAP-are still required for papBA transcription in a rimJ mutant strain. rimJ mutations increase the rate at which bacteria transition into the phase ON state, indicating that RimJ inhibits the phase OFF-->ON transition. A DeltarimJ hns651 mutant is viable on LB medium but not on minimal medium. This synthetic lethality, along with transcriptional analyses, indicates that RimJ and H-NS work through separate pathways to control papBA transcription. Mutations in rimJ do not greatly influence the transcription of the fan, daa, or fim operon, suggesting that RimJ may be a pap-specific regulator. Overexpression of rimJ under conditions repressive for papBA transcription complements the DeltarimJ mutation but has little effect on transcription under activating conditions, indicating that the ability of RimJ to regulate transcription is environmentally controlled.