Biofilm Formation and Dispersal under the Influence of the Global Regulator CsrA of Escherichia coli

The predominant mode of growth of bacteria in the environment is within sessile, matrix-enclosed communities known as biofilms. Biofilms often complicate chronic and difficult-to-treat infections by protecting bacteria from the immune system, decreasing antibiotic efficacy, and dispersing planktonic cells to distant body sites. While the biology of bacterial biofilms has become a major focus of microbial research, the regulatory mechanisms of biofilm development remain poorly defined and those of dispersal are unknown. Here we establish that the RNA binding global regulatory protein CsrA (carbon storage regulator) of Escherichia coli K-12 serves as both a repressor of biofilm formation and an activator of biofilm dispersal under a variety of culture conditions. Ectopic expression of the E. coli K-12 csrA gene repressed biofilm formation by related bacterial pathogens. A csrA knockout mutation enhanced biofilm formation in E. coli strains that were defective for extracellular, surface, or regulatory factors previously implicated in biofilm formation. In contrast, this csrA mutation did not affect biofilm formation by a glgA (glycogen synthase) knockout mutant. Complementation studies with glg genes provided further genetic evidence that the effects of CsrA on biofilm formation are mediated largely through the regulation of intracellular glycogen biosynthesis and catabolism. Finally, the expression of a chromosomally encoded csrA'-'lacZ translational fusion was dynamically regulated during biofilm formation in a pattern consistent with its role as a repressor. We propose that global regulation of central carbon flux by CsrA is an extremely important feature of E. coli biofilm development.     

Identification of UvrY as the cognate response regulator for the BarA sensor kinase in Escherichia coli

BarA is a membrane-associated protein that belongs to a subclass of tripartite sensors of the two-component signal transduction system family. In this study, we report that UvrY is the cognate response regulator for BarA of Escherichia coli. This conclusion is based upon homologies with analogous two-component systems and demonstrated by both biochemical and genetic means. We show that the purified BarA protein is able to autophosphorylate when incubated with [gamma-(32)P]ATP but not with [alpha-(32)P]ATP or [gamma-(32)P]GTP. Phosphorylated BarA, in turn, acts as an efficient phosphoryl group donor to UvrY but not to the non-cognate response regulators ArcA, PhoB, or CpxR. The specificity of the transphosphorylation reaction is further supported by the fact that UvrY can receive the phosphoryl group from BarA-P but not from the non-cognate tripartite sensor ArcB-P or ATP. In addition, genetic evidence that BarA and UvrY mediate the same signal transduction pathway is provided by the finding that both uvrY and barA mutant strains exhibit the same hydrogen peroxide hypersensitive phenotype. These results provide the first biochemical evidence as well as genetic support for a link between BarA and UvrY, suggesting that the two proteins constitute a new two-component system for gene regulation in Escherichia coli.     

Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System

Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli’s natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or “coliroids,” rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by β-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein’s local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system’s performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling.     

The Staphylococcus aureus ArlRS Two-Component System Is a Novel Regulator of Agglutination and Pathogenesis

Staphylococcus aureus is a prominent bacterial pathogen that is known to agglutinate in the presence of human plasma to form stable clumps. There is increasing evidence that agglutination aids S. aureus pathogenesis, but the mechanisms of this process remain to be fully elucidated. To better define this process, we developed both tube based and flow cytometry methods to monitor clumping in the presence of extracellular matrix proteins. We discovered that the ArlRS two-component system regulates the agglutination mechanism during exposure to human plasma or fibrinogen. Using divergent S. aureus strains, we demonstrated that arlRS mutants are unable to agglutinate, and this phenotype can be complemented. We found that the ebh gene, encoding the Giant Staphylococcal Surface Protein (GSSP), was up-regulated in an arlRS mutant. By introducing an ebh complete deletion into an arlRS mutant, agglutination was restored. To assess whether GSSP is the primary effector, a constitutive promoter was inserted upstream of the ebh gene on the chromosome in a wildtype strain, which prevented clump formation and demonstrated that GSSP has a negative impact on the agglutination mechanism. Due to the parallels of agglutination with infective endocarditis development, we assessed the phenotype of an arlRS mutant in a rabbit combined model of sepsis and endocarditis. In this model the arlRS mutant displayed a large defect in vegetation formation and pathogenesis, and this phenotype was partially restored by removing GSSP. Altogether, we have discovered that the ArlRS system controls a novel mechanism through which S. aureus regulates agglutination and pathogenesis.     

细胞因子信号的部分负调控因子

免疫和造血细胞的生长、分化及其他功能受到细胞因子网络的控制。由于大多数细胞因子受体缺乏胞浆段的激酶结构域 ,配体依赖的酪氨酸磷酸化由非受体酪氨酸激酶来中介。细胞因子刺激后早期激活的主要酪氨酸激酶是Ｊａｎｕｓｋｉｎａｓｅ(ＪＡＫ)家族。事实上 ,ＪＡＫ ＳＴＡＴ途径是许多细胞因子激活基因转录最重要机制之一。当细胞因子结合到细胞表面的受体 ,引起受体的二聚化 ,进而活化ＪＡＫ激酶 ,活化的ＪＡＫ激酶反过来磷酸化细胞因子受体 ,导致其他的信号分子如ＳＴＡＴ家族蛋白的介入并被激活 ,活化的ＳＴＡＴ转入细胞核 ,激活大量细…     

Mcs4, a Two-Component System Response Regulator Homologue, Regulates the Schizosaccharomyces Pombe Cell Cycle Control

The Schizosaccharomyces pombe cdc2-3w wee1-50 double mutant displays a temperature-sensitive lethal phenotype termed mitotic catastrophe. Six mitotic catastrophe suppressor (mcs1-6) genes were identified in a genetic screen designed to identify regulators of cdc2. Mutations in mcs1-6 suppress the cdc2-3w wee1-50 temperature-sensitive growth defect. Here, the cloning of mcs4 is described. The mcs4 gene product displays significant sequence homology to members of the two-component system response regulator protein family. Strains carrying the mcs4 and cdc25 mutations display a synthetic osmotic lethal phenotype along with an inability to grow on minimal synthetic medium. These phenotypes are suppressed by a mutation in wee1. In addition, the wis1 gene, encoding a stress-activated mitogen-activated protein kinase kinase, was identified as a dosage suppressor in this screen. These findings link the two-component signal transduction system to stress response and cell cycle control in S. pombe.     

Construction of a Global Pain Systems Network Highlights Phospholipid Signaling as a Regulator of Heat Nociception

The ability to perceive noxious stimuli is critical for an animal''s survival in the face of environmental danger, and thus pain perception is likely to be under stringent evolutionary pressure. Using a neuronal-specific RNAi knock-down strategy in adult Drosophila, we recently completed a genome-wide functional annotation of heat nociception that allowed us to identify α2δ3 as a novel pain gene. Here we report construction of an evolutionary-conserved, system-level, global molecular pain network map. Our systems map is markedly enriched for multiple genes associated with human pain and predicts a plethora of novel candidate pain pathways. One central node of this pain network is phospholipid signaling, which has been implicated before in pain processing. To further investigate the role of phospholipid signaling in mammalian heat pain perception, we analysed the phenotype of PIP5Kα and PI3Kγ mutant mice. Intriguingly, both of these mice exhibit pronounced hypersensitivity to noxious heat and capsaicin-induced pain, which directly mapped through PI3Kγ kinase-dead knock-in mice to PI3Kγ lipid kinase activity. Using single primary sensory neuron recording, PI3Kγ function was mechanistically linked to a negative regulation of TRPV1 channel transduction. Our data provide a systems map for heat nociception and reinforces the extraordinary conservation of molecular mechanisms of nociception across different species.     

Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics

Aberrant signaling causes many diseases, and manipulating signaling pathways with kinase inhibitors has emerged as a promising area of drug research. Most kinase inhibitors target the conserved ATP-binding pocket; therefore specificity is a major concern. Proteomics has previously been used to identify the direct targets of kinase inhibitors upon affinity purification from cellular extracts. Here we introduce a complementary approach to evaluate the effects of kinase inhibitors on the entire cell signaling network. We used triple labeling SILAC (stable isotope labeling by amino acids in cell culture) to compare cellular phosphorylation levels for control, epidermal growth factor stimulus, and growth factor combined with kinase inhibitors. Of thousands of phosphopeptides, less than 10% had a response pattern indicative of targets of U0126 and SB202190, two widely used MAPK inhibitors. Interestingly, 83% of the growth factor-induced phosphorylation events were affected by either or both inhibitors, showing quantitatively that early signaling processes are predominantly transmitted through the MAPK cascades. In contrast to MAPK inhibitors, dasatinib, a clinical drug directed against BCR-ABL, which is the cause of chronic myelogenous leukemia, affected nearly 1,000 phosphopeptides. In addition to the proximal effects on ABL and its immediate targets, dasatinib broadly affected the downstream MAPK pathways. Pathway mapping of regulated sites implicated a variety of cellular functions, such as chromosome remodeling, RNA splicing, and cytoskeletal organization, some of which have been described in the literature before. Our assay is streamlined and generic and could become a useful tool in kinase drug development.The advent of Gleevec® (imatinib) less than 10 years ago was a landmark for utilizing small molecule compounds as kinase inhibitor drugs (1–3). This type of drug is usually directed against one specific kinase whose malfunctioning plays a key role in the given disease. Generally these drugs are thought to be selective, easy to modify, and effective. As the molecular principles of various diseases are better understood, kinase inhibitors are being developed in various fields with cancer remaining the predominant one (4). Kinase inhibitor compounds constitute about 30% of all drug development programs in the pharmaceutical industry (5).Kinase inhibitor drugs are typically developed with a targeted and “rational” strategy, often focusing on a kinase known to be involved in the etiology of a disease. Large libraries of chemical compounds, for example ATP analogs, are screened in vitro against the activity of this kinase, and their effects on a panel of manually selected kinases with similar sequences or structures are evaluated to assess specificity (6, 7). A few promising leads are then selected for further improvement. In recent years, high throughput technologies have been introduced to speed up these enzyme assays. Innovations include the phage display assay (8, 9), yeast three-hybrid assay (10), and chemical proteomics assay (11, 12). These methods achieve better coverage of the kinome and thus provide less biased results.Although these in vitro assays are very informative, they have several limitations. First, chemical or genetic modifications are often required, such as generating fusion proteins or adding chemical linkers to the inhibitor, which may change the binding properties of the kinases and the inhibitor compounds. Second, these methods investigate the direct binding targets of the inhibitor compounds but do not determine their influence on the entire cellular signaling network. As more and more kinases are proven to function in multiple signaling pathways, inhibitor compounds may influence cellular functions that are not easily predicted. Third, cancer cells are notoriously known to evolve point mutations or to activate alternative signaling proteins to escape drug inhibition (13, 14). Therefore, the concept of utilizing multiple kinase inhibitors is increasingly established in the clinic (15, 16). This has complicated drug evaluation as different inhibitor compounds can generate synergistic or counteracting effects. Certainly a whole cell-based approach, which allows a systems-wide elucidation of inhibitor function, should improve the target evaluation process and help to monitor drug effects in vivo.Increasingly powerful imaging methods can, in principle, provide a comprehensive assessment of signaling pathways. Multiplexed fluorescence provides direct visualization of localization and activities of the selected pathway molecules in vivo after kinase inhibition (17–20). However, imaging methods require hundreds or thousands of experiments to cover all molecules of interest. In contrast, quantitative mass spectrometry is able to measure protein expression and modification events in single experiments at a global level and in a simultaneous manner. Stable isotope labeling by amino acids in cell culture (SILAC)1 generates completely labeled cell populations that are otherwise equal to non-labeled cells (21, 22). This system enables a direct and large-scale comparison of several cell populations with different biological or chemical treatments (23–25). When SILAC was used to study the effect of the HER2 kinase inhibitor PD168393, changes of the tyrosine phosphorylated proteins could be quantified (26). In recent years, studies of phosphorylation at a site-specific level have been greatly enhanced by progress in MS instrumentation and algorithms. Combined with key advances in phosphopeptide enrichment methods, such as immobilized metal ion affinity chromatography (IMAC) and titanium dioxide (TiO₂) chromatography, this has enabled detection and quantitation of thousands of phosphorylation sites, completely changing the capabilities of the phosphoproteomics field (27–34).Chronic myelogenous leukemia (CML) is one of the diseases caused by constitutively active signaling and is characterized by overproliferation of myeloid cells. The fundamental principle of its etiology is the fusion of chromosomes 9 and 22 to produce the so-called Philadelphia chromosome and the constitutively activated tyrosine kinase BCR-ABL fusion protein (35). Treatment of CML has been greatly advanced by small inhibitor compounds that selectively inhibit the kinase activity of BCR-ABL. The striking success of the first BCR-ABL inhibitor drug Gleevec, or imatinib, proved the concept of using small kinase inhibitor compounds as drugs (36). Later, a second generation of drugs was developed to inhibit Gleevec-resistant, point-mutated versions of BCR-ABL. Among these is dasatinib, a highly potent, orally active inhibitor for both inactive and active BCR-ABL that inhibits most BCR-ABL variants found in CML patients (37, 38).Dasatinib binds to the kinase domain of ABL kinase. It has similar potency toward SRC family kinases and the platelet-derived growth factor receptor family (39). Research into the mechanism of action of dasatinib focuses on two major themes: the direct binding targets and more downstream signaling molecules. Mass spectrometry has played an important role in these investigations. Recently Goss et al. (40) analyzed immunoprecipitated proteins by tandem MS and derived a common phosphotyrosine signature for BCR-ABL in six different CML cell lines. Hantschel et al. (41) and Bantscheff et al. (12) combined affinity purification techniques with quantitative MS to screen for binding targets of dasatinib. In the study of Bantscheff et al. (12) several broad band kinase inhibitors were combined and immobilized on one affinity resin (kinobeads). Different kinase inhibitor compounds were then used to compete with the unspecific interaction used in immobilization. The kinase beads covered 65% of the phylogenetic human kinome tree.We reasoned that the combination of SILAC and state of the art phosphoproteomics techniques should provide an excellent tool to explore the effects of kinase inhibitors on individual phosphorylation sites and on the entire cellular network of signal transduction. We first examined two inhibitor compounds widely used in signal transduction laboratories: U0126 inhibits MEK1/2, and SB202190 inhibits p38α/β MAPK. We then applied the same technique to determine the effects of dasatinib, a clinical drug for inhibition of mutated BCR-ABL in CML, on the phosphoproteome.     

A Novel Two-Component Signaling System Facilitates Uropathogenic Escherichia coli's Ability to Exploit Abundant Host Metabolites

Two-component signaling systems (TCSs) are major mechanisms by which bacteria adapt to environmental conditions. It follows then that TCSs would play important roles in the adaptation of pathogenic bacteria to host environments. However, no pathogen-associated TCS has been identified in uropathogenic Escherichia coli (UPEC). Here, we identified a novel TCS, which we termed KguS/KguR (KguS: α-ketoglutarate utilization sensor; KguR: α-ketoglutarate utilization regulator) in UPEC CFT073, a strain isolated from human pyelonephritis. kguS/kguR was strongly associated with UPEC but was found only rarely among other E. coli including commensal and intestinal pathogenic strains. An in vivo competition assay in a mouse UTI model showed that deletion of kguS/kguR in UPEC CFT073 resulted in a significant reduction in its colonization of the bladders and kidneys of mice, suggesting that KguS/KguR contributed to UPEC fitness in vivo. Comparative proteomics identified the target gene products of KguS/KguR, and sequence analysis showed that TCS KguS/KguR and its targeted-genes, c5032 to c5039, are encoded on a genomic island, which is not present in intestinal pathogenic E. coli. Expression of the target genes was induced by α-ketoglutarate (α-KG). These genes were further shown to be involved in utilization of α-KG as a sole carbon source under anaerobic conditions. KguS/KguR contributed to the regulation of the target genes with the direct regulation by KguR verified using an electrophoretic mobility shift assay. In addition, oxygen deficiency positively modulated expression of kguS/kguR and its target genes. Taken altogether, this study describes the first UPEC-associated TCS that functions in controlling the utilization of α-ketoglutarate in vivo thereby facilitating UPEC adaptation to life inside the urinary tract.