Chemotaxis Signaling Pathway Research Articles

Potassium-mediated bacterial chemotactic response.

Bacteria in biofilms secrete potassium ions to attract free swimming cells. However, the basis of chemotaxis to potassium remains poorly understood. Here, using a microfluidic device, we found that Escherichia coli can rapidly accumulate in regions of high potassium concentration on the order of millimoles. Using a bead assay, we measured the dynamic response of individual flagellar motors to stepwise changes in potassium concentration, finding that the response resulted from the chemotaxis signaling pathway. To characterize the chemotactic response to potassium, we measured the dose-response curve and adaptation kinetics via an Förster resonance energy transfer (FRET) assay, finding that the chemotaxis pathway exhibited a sensitive response and fast adaptation to potassium. We further found that the two major chemoreceptors Tar and Tsr respond differently to potassium. Tar receptors exhibit a biphasic response, whereas Tsr receptors respond to potassium as an attractant. These different responses were consistent with the responses of the two receptors to intracellular pH changes. The sensitive response and fast adaptation allow bacteria to sense and localize small changes in potassium concentration. The differential responses of Tar and Tsr receptors to potassium suggest that cells at different growth stages respond differently to potassium and may have different requirements for potassium.

Potassium-mediated bacterial chemotactic response

Bacteria in biofilms secrete potassium ions to attract free swimming cells. However, the basis of chemotaxis to potassium remains poorly understood. Here, using a microfluidic device, we found that Escherichia coli can rapidly accumulate in regions of high potassium concentration on the order of millimoles. Using a bead assay, we measured the dynamic response of individual flagellar motors to stepwise changes in potassium concentration, finding that the response resulted from the chemotaxis signaling pathway. To characterize the chemotactic response to potassium, we measured the dose–response curve and adaptation kinetics via an Förster resonance energy transfer (FRET) assay, finding that the chemotaxis pathway exhibited a sensitive response and fast adaptation to potassium. We further found that the two major chemoreceptors Tar and Tsr respond differently to potassium. Tar receptors exhibit a biphasic response, whereas Tsr receptors respond to potassium as an attractant. These different responses were consistent with the responses of the two receptors to intracellular pH changes. The sensitive response and fast adaptation allow bacteria to sense and localize small changes in potassium concentration. The differential responses of Tar and Tsr receptors to potassium suggest that cells at different growth stages respond differently to potassium and may have different requirements for potassium.

Cronkhite‒Canada syndrome as inflammatory hamartomatous polyposis: new evidence from whole transcriptome sequencing of colonic polyps

BackgroundCronkhite-Canada syndrome (CCS) is a rare, nonhereditary disease characterized by diffuse gastrointestinal polyposis and ectodermal abnormalities. Although it has been proposed to be a chronic inflammatory condition, direct evidence of its pathogenesis is lacking. This study aims to investigate the pathophysiology of CCS by analyzing transcriptomic changes in the colonic microenvironment.MethodsNext-generation sequencing-based genome-wide transcriptional profiling was performed on colonic hamartomatous polyps from four CCS patients and normal colonic mucosa from four healthy volunteers. Analyses of differential expression and multiple enrichment analyses were conducted from the molecular level to the cellular level. Quantitative real-time PCR (qRT-PCR) was carried out to validate the sequencing accuracy in samples from six CCS patients and six healthy volunteers.ResultsA total of 543 differentially expressed genes were identified, including an abundance of CC- and CXC-chemokines. Innate immune response-related pathways and processes, such as leukocyte chemotaxis, cytokine production, IL-17, TNF, IL-1 and NF-kB signaling pathways, were prominently enhanced in CCS colonic polyps. Upregulation of wound healing, epithelial-mesenchymal transition, Wnt, and PI3K-Akt signaling pathways were also observed. Enrichment analyses at different levels identified extracellular structure disorganization, dysfunction of the gut mucosal barrier, and increased angiogenesis. Validation by qRT-PCR confirmed increased expression of the LCN2, IL1B, CXCL1, and CXCL3 genes in CCS colonic polyps.ConclusionsThis case-control whole transcriptome analysis of active CCS colonic hamartomatous polyps revealed intricate molecular pathways, emphasizing the role of the innate immune response, extracellular matrix disorganization, inflammatory cell infiltration, increased angiogenesis, and potential epithelial to mesenchymal transition. These findings supports CCS as a chronic inflammatory condition and sheds light on potential therapeutic targets, paving the way for more effective and personalized management of CCS in the future.

Modified Bushen Yiqi Formula mitigates pulmonary inflammation and airway remodeling by inhibiting neutrophils chemotaxis and IL17 signaling pathway in rats with COPD

Ethnopharmacological relevanceChronic obstructive pulmonary disease (COPD) is a major global health concern characterized by pulmonary inflammation and airway remodeling. Traditional Chinese medicine, such as Modified Jiawei Bushen Yiqi Formula (MBYF), has been used as a complementary therapy for COPD in China. Aim of the studyTo investigate the therapeutic potential of MBYF in a rat model of COPD induced by cigarette smoke (CS) exposure and explore the underlying mechanism. Materials and methodsThe COPD rat model was established through 24 weeks of CS exposure, with MBYF administration starting in the 9th week. Pulmonary function, histological analysis, inflammatory cell count and molecular assays were employed to assess the effects of MBYF on airway remodeling, pulmonary inflammation, neutrophils chemotaxis and the IL17 signaling pathway. ResultsMBYF treatment effectively delayed airway remodeling, as evidenced by improved pulmonary function parameters. Histological examination and bronchoalveolar lavage fluid analysis revealed that MBYF mitigated CS-induced pulmonary inflammation by reducing inflammatory cell infiltration. Pharmacological network analysis suggested that MBYF may act through the IL17 signaling pathway to regulate inflammatory responses. RNA-sequencing and molecular assays indicated that MBYF inhibited neutrophils chemotaxis through downregulating the CXCL1/CXCL5/CXCL8-CXCR2 axis, and suppressed IL17A, IL17F and its downstream cytokines, including IL6, TNFα, IL1β, and COX2. Furthermore, MBYF inhibited the activation of NF-κB and MAPKs in the IL17 signaling pathway. ConclusionMBYF exhibits potential as an adjunct or alternative treatment for COPD, effectively mitigating CS-induced pulmonary inflammation and airway remodeling through the inhibition of neutrophil chemotaxis and IL17 signaling pathway.

A nonequilibrium allosteric model for receptor-kinase complexes: The role of energy dissipation in chemotaxis signaling

The Escherichia coli chemotaxis signaling pathway has served as a model system for the adaptive sensing of environmental signals by large protein complexes. The chemoreceptors control the kinase activity of CheA in response to the extracellular ligand concentration and adapt across a wide concentration range by undergoing methylation and demethylation. Methylation shifts the kinase response curve by orders of magnitude in ligand concentration while incurring a much smaller change in the ligand binding curve. Here, we show that the disproportionate shift in binding and kinase response is inconsistent with equilibrium allosteric models. To resolve this inconsistency, we present a nonequilibrium allosteric model that explicitly includes the dissipative reaction cycles driven by adenosine triphosphate (ATP) hydrolysis. The model successfully explains all existing joint measurements of ligand binding, receptor conformation, and kinase activity for both aspartate and serine receptors. Our results suggest that the receptor complex acts as an enzyme: Receptor methylation modulates the ON-state kinetics of the kinase (e.g., phosphorylation rate), while ligand binding controls the equilibrium balance between kinase ON/OFF states. Furthermore, sufficient energy dissipation is responsible for maintaining and enhancing the sensitivity range and amplitude of the kinase response. We demonstrate that the nonequilibrium allosteric model is broadly applicable to other sensor-kinase systems by successfully fitting previously unexplained data from the DosP bacterial oxygen-sensing system. Overall, this work provides a nonequilibrium physics perspective on cooperative sensing by large protein complexes and opens up research directions for understanding their microscopic mechanisms through simultaneous measurements and modeling of ligand binding and downstream responses.

Abstract PR016: Systemic T cell metabolic and effector function changes following treatment with PD1 and CTLA4 in patients with kidney cancer

Abstract Background: We have previously shown that dysfunctional renal cell carcinoma (RCC) tumor infiltrating lymphocytes (TIL) have glycolytic insufficiencies, and effector function can be rescued by bypassing glycolysis and modulating mitochondrial fitness (Beckermann et al., 2020). We have also shown that RCC TIL biology may be captured in a subset of the peripheral blood T cells, providing an opportunity to assess the tumor immune landscape in noninvasive liquid biopsy from peripheral blood samples (Siska et al., 2018). Methods: We evaluated the peripheral blood of twenty patients with RCC undergoing systemic therapy with PD1 and CTLA4, ten of whom had primary progressive disease and ten who had clinical benefit (SD, PR, CR for 6 months or greater), studying samples before and after three weeks on treatment. Single Cell mRNA gene expression and TCR clonal analysis was assessed in a subset of patients as well as ArcherDx V(D)J sequencing on matched tumor tissue. To assess the impact of mitochondrial membrane potential on T cell responses in patients with ccRCC we flow sorted viable, CD3+ PBMCs with high or low mitochondrial potential. The peripheral blood was analyzed for protein changes using a 44-plex labeled CyTOF antibody panel focused on T cells surface markers, as well as effector and metabolic function. Results: From peripheral blood of patients with ccRCC we find that CD3+ T cells are predominantly composed of subgroups with mitochondrial high membrane potential and expand in number after αPD1+αCTLA4 therapy. Peripheral T cells with low mitochondrial membrane potential are enriched for gene expression pathways associated with cytotoxicity. T cells with mitochondrial low potential also tended to have oligoclonal TCR expansion that were frequently shared between tumor and blood compared to that of mitochondrial high potential T cells. Mitochondrial low T cells were enriched for genes associated with cytotoxicity including CTSW, CD8, KLRK1, and KLRD. The tumor T cell repertoire demonstrated the greatest similarity with peripheral T cells that had low mitochondrial membrane potential. Shared T cells between the tumor and periphery are enriched for chemotaxis, antigen binding, and cytotoxicity signaling pathways. At the protein level, patients with response have lower metabolic activity and greater CD4+ effector T cells, consistent with the scRNA-seq data, while patients with progressive disease have more metabolically active profiles. Conclusions: Single cell gene expression and mass cytometry analysis shows that systemic changes occur in patients with kidney cancer undergoing αPD1 and αCTLA4 treatment. Shared TCR from TIL exist in oligoclonally expanded T cells in the peripheral blood. These shared T cells are enriched in subsets with low mitochondrial membrane potential and express markers of effector function and upregulate cytotoxic T cell pathways. Citation Format: Dalton Greenwood, Paul Lindau, Caroline Roe, Madelyn Landis, Rachel Hongo, Brian Rini, Jonathan Irish, W. Kimryn Rathmell, Jeffrey Rathmell, Kathryn Beckermann. Systemic T cell metabolic and effector function changes following treatment with PD1 and CTLA4 in patients with kidney cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR016.

Timescale separation in the coordinated switching of bacterial flagellar motors

The output of the bacterial chemotaxis signaling pathway, the level of the intracellular regulator CheY-P, modulates the rotation direction of the flagellar motor, thereby regulating bacterial run-and-tumble behavior. The multiple flagellar motors on an E. coli cell are controlled by a common cytoplasmic pool of CheY-P. Fluctuation of the CheY-P level was thought to be able to coordinate the switching of multiple motors. Here, we measured the correlation of rotation directions between two motors on a cell, finding that it surprisingly exhibits two well separated timescales. We found that the slow timescale (∼6 s) can be explained by the slow fluctuation of the CheY-P level due to stochastic activity of the chemotactic adaptation enzymes, whereas the fast timescale (∼0.3 s) can be explained by the random pulse-like fluctuation of the CheY-P level, due probably to the activity of the chemoreceptor clusters. We extracted information on the properties of the fast CheY-P pulses based on the correlation measurements. The two well-separated timescales in the fluctuation of CheY-P level help to coordinate multiple motors on a cell and to enhance bacterial chemotactic performance.

Precise Measurement of the Stoichiometry of the Adaptive Bacterial Flagellar Switch.

The cytoplasmic ring (C-ring) of the bacterial flagellar motor controls the motor rotation direction, thereby controlling bacterial run-and-tumble behavior. The C-ring has been shown to undergo adaptive remodeling in response to changes in motor directional bias. However, the stoichiometry and arrangement of the C-ring is still unclear due to contradiction between the results from fluorescence studies and cryo-electron microscopy (cryo-EM) structural analysis. Here, by using the copy number of FliG molecules (34) in the C-ring as a reference, we precisely measured the copy numbers of FliM molecules in motors rotating exclusively counterclockwise (CCW) and clockwise (CW). We surprisingly found that there are on average 45 and 58 FliM molecules in CW and CCW rotating motors, respectively, which are much higher than previous estimates. Our results suggested a new mechanism of C-ring adaptation, that is, extra FliM molecules could be bound to the primary C-ring with probability depending on the motor rotational direction. We further confirmed that all of the FliM molecules in the C-ring function in chemotaxis signaling transduction because all of them could be bound by the chemotactic response regulator CheY-P. Our measurements provided new insights into the structure and arrangement of the flagellar switch. IMPORTANCE The bacterial flagellar switch can undergo adaptive remodeling in response to changes in motor rotation direction, thereby shifting its operating point to match the output of the chemotaxis signaling pathway. However, it remains unclear how the flagellar switch accomplishes this adaptive remodeling. Here, via precise fluorescence studies, we measured the absolute copy numbers of the critical component in the switch for motors rotating counterclockwise and clockwise, obtaining much larger numbers than previous relative estimates. Our results suggested a new mechanism of adaptive remodeling of the flagellar switch and provided new insights for updating the conformation spread model of the switch.

Constraint-induced movement therapy alleviates motor impairment by inhibiting the accumulation of neutrophil extracellular traps in ischemic cortex

Stroke is a major cause of mortality and morbidity and most acute strokes are ischemic. Evidence-based medicine has demonstrated the effectiveness of constraint-induced movement therapy (CIMT) in the recovery of motor function in patients after ischemic stroke, but the specific treatment mechanism remains unclear. Herein, our integrated transcriptomics and multiple enrichment analysis studies, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) studies show that CIMT conduction broadly curtails immune response, neutrophil chemotaxis, and chemokine-mediated signaling pathway, CCR chemokine receptor binding. Those suggest the potential effect of CIMT on neutrophils in ischemic mice brain parenchyma. Recent studies have found that accumulating granulocytes release extracellular web-like structures composed of DNA and proteins called neutrophil extracellular traps (NETs), which destruct neurological function primarily by disrupting the blood–brain barrier and promoting thrombosis. However, the temporal and spatial distribution of neutrophils and their released NETs in parenchyma and their damaging effects on nerve cells remain unclear. Thus, utilizing immunofluorescence and flow cytometry, our analyses uncovered that NETs erode multiple regions such as primary motor cortex (M1), striatum (Str), nucleus of the vertical limb of the diagonal band (VDB), nucleus of the horizontal limb of the diagonal band (HDB) and medial septal nucleus (MS), and persist in the brain parenchyma for at least 14 days, while CIMT can reduce the content of NETs and chemokines CCL2 and CCL5 in M1. Intriguingly, CIMT failed to further reduce neurological deficits after inhibiting the NET formation by pharmacologic inhibition of peptidylarginine deiminase 4 (PAD4). Collectively, these results demonstrate that CIMT could alleviate cerebral ischemic injury induced locomotor deficits by modulating the activation of neutrophils. These data are expected to provide direct evidence for the expression of NETs in ischemic brain parenchyma and novel insights into the mechanisms of CIMT protecting against ischemic brain injury.

The Only Chemoreceptor Encoded by che Operon Affects the Chemotactic Response of Agrobacterium to Various Chemoeffectors.

Chemoreceptor (also called methyl-accepting chemotaxis protein, MCP) is the leading signal protein in the chemotaxis signaling pathway. MCP senses and binds chemoeffectors, specifically, and transmits the sensed signal to downstream proteins of the chemotaxis signaling system. The genome of Agrobacterium fabrum (previously, tumefaciens) C58 predicts that a total of 20 genes can encode MCP, but only the MCP-encoding gene atu0514 is located inside the che operon. Hence, the identification of the exact function of atu0514-encoding chemoreceptor (here, named as MCP514) will be very important for us to understand more deeply the chemotaxis signal transduction mechanism of A. fabrum. The deletion of atu0514 significantly decreased the chemotactic migration of A. fabrum in a swim plate. The test of atu0514-deletion mutant (Δ514) chemotaxis toward single chemicals showed that the deficiency of MCP514 significantly weakened the chemotactic response of A. fabrum to four various chemicals, sucrose, valine, citric acid and acetosyringone (AS), but did not completely abolish the chemotactic response. MCP514 was localized at cell poles although it lacks a transmembrane (TM) region and is predicted to be a cytoplasmic chemoreceptor. The replacement of residue Phe328 showed that the helical structure in the hairpin subdomain of MCP514 is a direct determinant for the cellular localization of MCP514. Single respective replacements of key residues indicated that residues Asn336 and Val353 play a key role in maintaining the chemotactic function of MCP514.

Establishment of GC–MS method for the determination of Pseudomonas aeruginosa biofilm and its application in metabolite enrichment analysis

PA forms a biofilm resistant to antibiotics, hindering antibiotics efficacy and preventing the eradication of PA, has attracted much attention for its biofilm. In this study, we first established and validated an efficient and sensitive gas chromatography-mass spectrometry (GC–MS) method for the quantification of metabolites in biofilm. Decanoic acid was used as the internal standard. The separation of Palmitic acid, stearic acid and Decanoic acid was conducted on an Elite-5 MS column (30 m × 0.25 mm, 0.25 μm) using gradient elution condition at a flow rate of 1 mL/min. Palmitic acid, stearic acid and Decanoic acid were determined under the positive ionization mode, respectively. The calibration curve of Palmitic acid and stearic acid were established in the range of 4 to 128 μg/mL (r2 = 0.999). The recovery of palmitic acid and stearic acid were between 98.76% and 113.91%, RSD ＜ 5%. The well validated method was used to detect the metabolites of Pseudomonas aeruginosa biofilm. 54 metabolites were isolated and identified from biofilm samples, and 7 important signal pathways were identified by KEGG enrichment analysis. ABC transporters and bacterial chemotaxis signaling pathways have an important impact on the growth of PA biofilm among these metabolic pathways. This study provides valuable references for the further study of PA biofilm, especially the change of metabolite content and the search for biomarkers.

Direct Mapping from Intracellular Chemotaxis Signaling to Single-Cell Swimming Behavior

Bacterial chemotaxis allows bacteria to sense the chemical environment and modulate their swimming behavior accordingly. Although the intracellular chemotaxis signaling pathway has been studied extensively, experimental studies are still lacking that could provide direct link from the pathway output (the intracellular concentration of the phosphorylated form of the response regulator phosphorylated CheY (CheY-P)) to single-cell swimming behavior. Here, we measured the swimming behavior of individual Escherichia coli cells while simultaneously detecting the intracellular CheY-P concentration, thereby providing a direct relationship between the intracellular CheY-P concentration and the single-cell run-and-tumble behavior. The measured relationship is consistent with the ultrasensitivity of the motor switch and a “veto model” that describes the interaction among individual flagella, although contribution from the voting mechanism could not be ruled out.

Differences in biomarkers of inflammation and immune responses in chronic smokers and moist snuff users

BackgroundCigarette smoking is a major risk factor for cancer and other diseases. While smoking induces chronic inflammation and aberrant immune responses, the effects of smokeless tobacco products (STPs) on immune responses is less clear. Here we evaluated markers related to immune regulation in smokers (SMK), moist snuff consumers (MSC) and non-tobacco consumers (NTC) to better understand the effects of chronic tobacco use. Materials and methodsSeveral markers associated with immune regulation were measured in peripheral blood mononuclear cells (PBMCs) from SMK (n = 40), MSC (n = 40), and NTC (n = 40) by flow cytometry. ResultsRelative to NTC, seven markers were significantly suppressed in SMK, whereas in MSC, only one marker was significantly suppressed. In a logistic regression model, markers including granzyme B+ lymphocytes, perforin+ lymphocytes, granzyme B+ CD8+T cells, and KLRB1+ CD8+ T cells remained as statistically significant predictors for classifying the three cohorts. Further, cell-surface receptor signaling pathways and cell–cell signaling processes were downregulated in SMK relative to MSC; chemotaxis and LPS-mediated signaling pathways, were upregulated in SMK compared to MSC. A network of the tested markers was constructed to visualize the immunosuppression in SMK relative to MSC. ConclusionMoist snuff consumption is associated with significantly fewer perturbations in inflammation and immune function biomarkers relative to smoking. ImpactThis work identifies several key immunological biomarkers that differentiate the effects of chronic smoking from the use of moist snuff. Additionally, a molecular basis for aberrant immune responses that could render smokers more susceptible for infections and cancer is provided.

A novel risk score system of immune genes associated with prognosis in endometrial cancer

BackgroundEndometrial cancer was the commonest gynecological malignancy in developed countries. Despite striking advances in multimodality management, however, for patients in advanced stage, targeted therapy still remained a challenge. Our study aimed to investigate new biomarkers for endometrial cancer and establish a novel risk score system of immune genes in endometrial cancer.MethodsThe clinicopathological characteristics and gene expression data were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) of immune genes between tumors and normal tissues were identified. Protein–protein interaction (PPI) network of immune genes and transcriptional factors was integrated and visualized in Cytoscape. Univariate and multivariate analysis were employed for key genes to establish a new risk score system. Receiver operating characteristic (ROC) curve and survival analysis were performed to investigate the prognostic value of the model. Association between clinical characteristics and the model was analyzed by logistic regression. For validation, we identified 34 patients with endometrial cancer from Fudan University Shanghai Cancer Center (FUSCC). We detected 14-genes mRNA expression and calculated the risk scores of each patients and we performed survival analysis between the high-risk group and the low-risk group.Results23 normal tissues and 552 tumor tissues were obtained from TCGA database. 410 immune-related DEGs was identified by difference analysis and correlation analysis. KEGG and GO analysis revealed these DEGs were enriched in cell adhesion, chemotaxis, MAPK pathways and PI3K-Akt signaling pathway, which might regulate tumor progression and migration. All genes were screened for risk model construction and 14 hub immune-related genes (HTR3E, CBLC, TNF, PSMC4, TRAV30, PDIA3, FGF8, PDGFRA, ESRRA, SBDS, CRHR1, LTA, NR2F1, TNFRSF18) were prognostic in endometrial cancer. The area under the curve (AUC) was 0.787 and the high-risk group estimated by the model possessed worse outcome (P < 0.001). Multivariate analysis suggested that the model was indeed an independent prognostic factor (high-risk vs. low-risk, HR = 1.14, P < 0.001). Meanwhile, the high-risk group was prone to have higher grade (P = 0.002) and advanced clinical stage (P = 0.018). In FUSCC validation set, the high-risk group had worse survival than the low-risk group (P < 0.001).ConclusionsIn conclusion, the novel risk model of immune genes had some merits in predicting the prognosis of endometrial cancer and had strong correlation with clinical outcomes. Furthermore, it might provide new biomarkers for targeted therapy in endometrial cancer.

Whole Transcriptome Analysis Reveals That Filifactor alocis Modulates TNFα-Stimulated MAPK Activation in Human Neutrophils.

Periodontitis is an irreversible, bacteria-induced, chronic inflammatory disease that compromises the integrity of tooth-supporting tissues and adversely affects systemic health. As the immune system's first line of defense against bacteria, neutrophils use their microbicidal functions in the oral cavity to protect the host against periodontal disease. However, periodontal pathogens have adapted to resist neutrophil microbicidal mechanisms while still propagating inflammation, which provides essential nutrients for the bacteria to proliferate and cause disease. Advances in sequencing technologies have recognized several newly appreciated bacteria associated with periodontal lesions such as the Gram-positive anaerobic rod, Filifactor alocis. With the discovery of these oral bacterial species, there is also a growing need to assess their pathogenic potential and determine their contribution to disease progression. Currently, few studies have addressed the pathogenic mechanisms used by oral bacteria to manipulate the neutrophil functional responses at the level of the transcriptome. Thus, this study aims to characterize the global changes at the gene expression level in human neutrophils during infection with F. alocis. Our results indicate that the challenge of human neutrophils with F. alocis results in the differential expression of genes involved in multiple neutrophil effector functions such as chemotaxis, cytokine and chemokine signaling pathways, and apoptosis. Moreover, F. alocis challenges affected the expression of components from the TNF and MAPK kinase signaling pathways. This resulted in transient, dampened p38 MAPK activation by secondary stimuli TNFα but not by fMLF. Functionally, the F. alocis-mediated inhibition of p38 activation by TNFα resulted in decreased cytokine production but had no effect on the priming of the respiratory burst response or the delay of apoptosis by TNFα. Since the modulatory effect was characteristic of viable F. alocis only, we propose this as one of F. alocis' mechanisms to control neutrophils and their functional responses.

Long noncoding RNA MIR22HG is down-regulated in prostate cancer.

Prostate cancer (PCa) is one of the most common cancer in males. Previous studies indicated that MIR22HG was a tumor suppressor in various cancers. However, the expression pattern and functional roles of MIR22HG in PCa remained to be further investigated. In this study, we for the first time showed MIR22HG was down-regulated in PCa. Furthermore, we observed the lower expression levels of MIR22HG were significantly related to higher Gleason score and T stage. Of note, we found that higher MIR22HG expression was associated with better disease-free survival and overall survival time in PCa. Moreover, we constructed a MIR22HG mediated co-expression network. Bioinformatics analysis showed MIR22HG was associated with regulating inflammatory response, regulation of transcription, cellular response to tumor necrosis factor, neutrophil chemotaxis, cell-cell signaling, and TNF signaling pathway. These results showed that MIR22HG could serve as a novel biomarker for prostate cancer.

Chemotaxis and cyclic‐di‐GMP signalling control surface attachment of Escherichia coli

Attachment to surfaces is an important early step during bacterial infection and during formation of submerged biofilms. Although flagella-mediated motility is known to be important for attachment of Escherichia coli and other bacteria, implications of motility regulation by cellular signalling remain to be understood. Here, we show that motility largely promotes attachment of E. coli, including that mediated by type 1 fimbriae, by allowing cells to reach, get hydrodynamically trapped at and explore the surface. Inactivation or inhibition of the chemotaxis signalling pathway improves attachment by suppressing cell reorientations and thereby increasing surface residence times. The attachment is further enhanced by deletion of genes encoding the cyclic diguanosine monophosphate (c-di-GMP)-dependent flagellar brake YcgR or the diguanylate cyclase DgcE. Such increased attachment in absence of c-di-GMP signalling is in contrast to its commonly accepted function as a positive regulator of the sessile state. It is apparently due to the increased swimming speed of E. coli in absence of YcgR-mediated motor control, which strengthens adhesion mediated by the type 1 fimbriae. Thus, both signalling networks that regulate motility of E. coli also control its engagement with both biotic and abiotic surfaces, which has likely implications for infection and biofilm formation.

Bioinformatics Analysis of Key Genes and Pathways in Colorectal Cancer.

Colorectal cancer (CRC) is the third most prevalent cancer in the world. Although great progress has been made, the specific molecular mechanism remains unclear. This study aimed to explore the differentially expressed genes (DEGs) and underlying mechanisms of CRC using bioinformatics analysis. In this study, we identified a total of 1353 DEGs in the database of GSE113513, including 715 up- and 638 downregulated genes. Gene ontology analysis results showed that upregulated DEGs were significantly enriched in cell division, cell proliferation, and DNA replication. The downregulated DEGs were enriched in immune response, relation of cell growth and inflammatory response. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that upregulated DEGs were enriched in cell cycle and p53 signaling pathway, whereas the downregulated DEGs were enriched in drug metabolism, metabolism of xenobiotics by cytochrome P450, and nitrogen metabolism. A total of 124 up-key genes and 35 down-key genes were identified from the protein-protein interaction networks. Furthermore, we identified five up-modules (up-A, up-B, up-C, up-D, and up-E) and three down-modules (d-A, d-B, and d-C) by module analysis. The module up-A was enriched in sister chromatid cohesion, cell division, and mitotic nuclear division. Pathways associated with cell cycle, progesterone-mediated oocyte maturation, oocyte meiosis, and p53 signaling pathway. Whereas the d-A was mainly enriched in G-protein coupled receptor signaling pathway, cell chemotaxis, and chemokine-mediated signaling pathway. The pathways enriched in chemokine signaling pathway, cytokine-cytokine receptor interaction, and alcoholism. These key genes and pathways might be used as molecular targets and diagnostic biomarkers for the treatment of CRC.

Propagation of regulatory fluctuations induces coordinated switching of flagellar motors in chemotaxis signaling pathway of single bacteria

The random motion of E. coli is driven by multiple flagella motors. When all motors rotate in the counter clockwise direction, the bacteria swims smoothly. A recent experimental report by Terasawa et al. [Biophys J,100,2193,(2011)] demonstrated that a coordination of the motors can occur through signaling pathways, and perturbation of a regulatory molecule disrupted the coordination. Here, we develop a mathematical model to show that a large temporal fluctuation in the regulator concentration can induce a correlated switching of the multiple motors. Such a large fluctuation is generated by a chemotaxis receptor cluster in unilateral cell pole, which then exhibits a spatial propagation through the cytoplasm from the receptor position to the motor around cell periphery. Our numerical simulation successfully reproduces synchronized switching and the lag time in the motions of two distant motors, which has been observed experimentally. We further show that the large fluctuation in the regulator concentration at the motor positions can expand the dynamic range that the motor can respond, which confers robustness to the signaling system.

A Chemotaxis-Like Pathway of Azorhizobium caulinodans Controls Flagella-Driven Motility, Which Regulates Biofilm Formation, Exopolysaccharide Biosynthesis, and Competitive Nodulation.

The genome of the Azorhizobium caulinodans ORS571 contains a unique chemotaxis gene cluster (che) including five chemotaxis genes: cheA, cheW, cheY1, cheB, and cheR. Analysis of the role of the chemotaxis cluster of A. caulinodans using deletion mutant strains revealed that CheA or the Che signaling pathway controls chemotaxis behavior and flagella-driven motility and plays important roles in formation of biofilms and production of extracellular polysaccharides (EPS). Furthermore, the deletion mutants (ΔcheA and ΔcheA-R) were defective in competitive adsorption and colonization on the root surface of host plants. In addition, a functional CheA or Che pathway promoted competitive nodulation on roots and stems. Interestingly, a nonflagellated mutant, ΔfliM, displayed a phenotype highly similar to that of the ΔcheA or ΔcheA-R mutant strains. These findings suggest that through controlling flagella-driven motility behavior, the chemotaxis signaling pathway in A. caulinodans coordinates biofilm formation, EPS, and competitive colonization and nodulation.