Integration of AI-2 Based Cell-Cell Signaling with Metabolic Cues in Escherichia coli

Citation: Mitra, A., Herren, C. D., Patel, I. R., Coleman, A., & Mukhopadhyay, S. (2016). Integration of AI-2 Based Cell-Cell Signaling with Metabolic Cues in Escherichia coli. Plos One, 11(6), 19. doi:10.1371/journal.pone.0157532The quorum sensing molecule Autoinducer-2 (AI-2) is generated as a byproduct of activated methyl cycle by the action of LuxS in Escherichia coli. AI-2 is synthesized, released and later internalized in a cell-density dependent manner. Here, by mutational analysis of the genes, uvrY and csrA, we describe a regulatory circuit of accumulation and uptake of AI-2. We constructed a single-copy chromosomal luxS-lacZ fusion in a luxS (+) merodiploid strain and evaluated its relative expression in uvrY and csrA mutants. At the entry of stationary phase, the expression of the fusion and AI-2 accumulation was positively regulated by uvrY and negatively regulated by csrA respectively. A deletion of csrA altered message stability of the luxS transcript and CsrA protein exhibited weak binding to 5' luxS regulatory region. DNA protein interaction and chromatin immunoprecipitation analysis confirmed direct interaction of UvrY with the luxS promoter. Additionally, reduced expression of the fusion in hfq deletion mutant suggested involvement of small RNA interactions in luxS regulation. In contrast, the expression of lsrA operon involved in AI-2 uptake, is negatively regulated by uvrY and positively by csrA in a cell-density dependent manner. The dual role of csrA in AI-2 synthesis and uptake suggested a regulatory crosstalk of cell signaling with carbon regulation in Escherichia coli. We found that the cAMP-CRP mediated catabolite repression of luxS expression was uvrY dependent. This study suggests that luxS expression is complex and regulated at the level of transcription and translation. The multifactorial regulation supports the notion that cell-cell communication requires interaction and integration of multiple metabolic signals

A Functional Proteomic Method for Biomarker Discovery

The sequencing of the human genome holds out the hope for personalized medicine, but it is clear that analysis of DNA or RNA content alone is not sufficient to understand most disease processes. Proteomic strategies that allow unbiased identification of proteins and their post-transcriptional and -translation modifications are an essential complement to genomic strategies. However, the enormity of the proteome and limitations in proteomic methods make it difficult to determine the targets that are particularly relevant to human disease. Methods are therefore needed that allow rational identification of targets based on function and relevance to disease. Screening methodologies such as phage display, SELEX, and small-molecule combinatorial chemistry have been widely used to discover specific ligands for cells or tissues of interest, such as tumors. Those ligands can be used in turn as affinity probes to identify their cognate molecular targets when they are not known in advance. Here we report an easy, robust and generally applicable approach in which phage particles bearing cell- or tissue-specific peptides serve directly as the affinity probes for their molecular targets. For proof of principle, the method successfully identified molecular binding partners, three of them novel, for 15 peptides specific for pancreatic cancer

BarA-UvrY Two-Component System Regulates Virulence of Uropathogenic E. coli CFT073

Uropathogenic Escherichia coli (UPEC), a member of extraintestinal pathogenic E. coli, cause ∼80% of community-acquired urinary tract infections (UTI) in humans. UPEC initiates its colonization in epithelial cells lining the urinary tract with a complicated life cycle, replicating and persisting in intracellular and extracellular niches. Consequently, UPEC causes cystitis and more severe form of pyelonephritis. To further understand the virulence characteristics of UPEC, we investigated the roles of BarA-UvrY two-component system (TCS) in regulating UPEC virulence. Our results showed that mutation of BarA-UvrY TCS significantly decreased the virulence of UPEC CFT073, as assessed by mouse urinary tract infection, chicken embryo killing assay, and cytotoxicity assay on human kidney and uroepithelial cell lines. Furthermore, mutation of either barA or uvrY gene reduced the production of hemolysin, lipopolysaccharide (LPS), proinflammatory cytokines (TNF-α and IL-6) and chemokine (IL-8). The virulence phenotype was restored similar to that of wild-type by complementation of either barA or uvrY gene in trans. In addition, we discussed a possible link between the BarA-UvrY TCS and CsrA in positively and negatively controlling virulence in UPEC. Overall, this study provides the evidences for BarA-UvrY TCS regulates the virulence of UPEC CFT073 and may point to mechanisms by which virulence regulations are observed in different ways may control the long-term survival of UPEC in the urinary tract

Modular Approach to Therapy for Anxiety, Depression, Trauma, or Conduct Problems in outpatient child and adolescent mental health services in New Zealand: study protocol for a randomized controlled trial

Background: Mental health disorders are common and disabling for young people because of the potential to disrupt key developmental tasks. Implementation of evidence-based psychosocial therapies in New Zealand is limited, owing to the inaccessibility, length, and cost of training in these therapies. Furthermore, most therapies address one problem area at a time, although comorbidity and changing clinical needs commonly occur in practice. A more flexible approach is needed. The Modular Approach to Therapy for Children with Anxiety, Depression, Trauma, or Conduct Problems (MATCH-ADTC) is designed to overcome these challenges; it provides a range of treatment modules addressing different problems, within a single training program. A clinical trial of MATCH-ADTC in the USA showed that MATCH-ADTC outperformed usual care and standard evidence-based treatment on several clinical measures. We aim to replicate these findings and evaluate the impact of providing training and supervision in MATCH-ADTC to: (1) improve clinical outcomes for youth attending mental health services; (2) increase the amount of evidence-based therapy content; (3) increase the efficiency of service delivery. Methods: This is an assessor-blinded multi-site effectiveness randomized controlled trial. Randomization occurs at two levels: (1) clinicians (≥60) are randomized to intervention or usual care; (2) youth participants (7–14 years old) accepted for treatment in child and adolescent mental health services (with a primary disorder that includes anxiety, depression, trauma-related symptoms, or disruptive behavior) are randomly allocated to receive MATCH-ADTC or usual care. Youth participants are recruited from ‘mainstream’, Māori-specific, and Pacific-specific child and adolescent mental health services. We originally planned to recruit 400 youth participants, but this has been revised to 200 participants. Centralized computer randomization ensures allocation concealment. The primary outcome measures are: (i) the difference in trajectory of change of clinical severity between groups (using the parent-rated Brief Problem Monitor); (ii) clinicians’ use of evidence-based treatment procedures during therapy sessions; (iii) total time spent by clinicians delivering therapy. Discussion: If MATCH-ADTC demonstrates effectiveness it could offer a practical efficient method to increase access to evidence-based therapies, and improve outcomes for youth attending secondary care services

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching

Pleiotropic roles of uvrY on biofilm formation, motility and virulence in uropathogenic Escherichia coli CFT073.

Urinary tract infections primarily caused by uropathogenic strains of Escherichia coli (E. coli) remain a significant public health problem in both developed and developing countries. An important virulence determinant in uropathogenesis is biofilm formation which requires expression of fimbriae, flagella, and other surface components such as lipopolysaccharides. In this study, we explored the regulation of uvrY and csrA genes in biofilm formation, motility and virulence determinants in uropathogenic E. coli. We found that mutation in uvrY suppressed biofilm formation on abiotic surfaces such as polyvinyl chloride, polystyrene and glass, and complementation of uvrY in the mutant restored the biofilm phenotype. We further evaluated the role of uvrY gene in expression of type 1 fimbriae, an important adhesin that facilitates adhesion to various abiotic surfaces. We found that phase variation of type 1 fimbriae between fimbriated and afimbriated mode was modulated by uvrY at its transcriptional level. Deletion mutant of uvrY lowered expression of fimbrial recombinase genes, such as fimB, fimE, and fimA, a gene encoding major fimbrial subunit. Furthermore, transcription of virulence specific genes such as papA, hlyB and galU was also reduced in the deletion mutant. Swarming motility and expression of flhD and flhC was also diminished in the mutant. Taken together, our findings unravel a possible mechanism in which uvrY facilitates biofilm formation, persistence and virulence of uropathogenic E. coli

Effect of <i>uvrY</i> and <i>csrA</i> on <i>fimB</i>, <i>fimE</i> and <i>fimA</i> transcription in UPEC strain CFT073.

<p><b>A</b>. Transcript levels of <i>fimB</i>, <i>fimE</i> and <i>fimA</i> were evaluated by quantitative RT-PCR. The <i>rrnA</i> was used as an internal control. <b>B</b>. Relative expression levels of various transcripts were calculated by normalization of the actual intensity of bands with <i>rrnA</i> control and expressed as fold change relative to the wild-type. The wild-type was set at one. Bars represent mean ± S.E.M of three replicates.</p