Complete Genome Sequence of the Gordonia Bacteriophage BiggityBass.

Here, we characterized the complete genome of the Siphoviridae BiggityBass, a lytic subcluster DR bacteriophage infecting Gordonia terrae CAG3. Its 63.2-kb genome contains 84 protein-coding genes, of which 40 could be assigned a putative function. BiggityBass is related most closely to AnClar and Yago84 with 90.61% and 90.52% nucleotide identity, respectively.

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.

Genome Sequences of Four Subcluster L2 Mycobacterium Phages, Finemlucis, Miley16, Wilder, and Zakai.

Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect Mycobacterium smegmatis mc2155 were isolated. The four phages are closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative protein-coding genes, including tyrosine integrases, cro, immunity repressors, and excise genes involved in the establishment of lysogeny.

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

The 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.

Genetic analysis of an important oxidative stress locus in the anaerobe Bacteroides fragilis.

The obligate anaerobe, Bacteroides fragilis, is a highly aerotolerant intestinal tract organism that has evolved a complex oxidative stress response (OSR). The redox regulator OxyR controls several OSR genes (katB, dps, and ahpC), but there is little else known about other genes it regulates. To identify additional genes in the OxyR regulon, two-dimensional gel electrophoresis was used to isolate proteins from a mutant that constitutively expresses genes in the regulon. The 28,500 Da protein thioredoxin peroxidase (Tpx) was identified. Two additional genes induced during oxidative stress were identified adjacent to tpx, a putative RNA-binding protein (rbpA) and a cytochrome-c peroxidase (ccp). Transcriptional analyses showed that tpx and rbpA were transcribed as monocistronic mRNA species or as a bicistronic operon. Transcription of tpx was induced by exposure to air or H(2)O(2) from an OxyR-dependent promoter and to a lesser extent from a second OxyR-independent promoter. Expression of the rbpA gene during oxidative stress was regulated by the OxyR-dependent tpx promoter resulting in the bicistronic tpx/rbp mRNA. The ccp gene was expressed only as a monocistronic message and induction was only observed after exposure to H(2)O(2) in an OxyR-independent manner. Disruption of the tpx operon or ccp resulted in sensitivity to the organic peroxides cumene hydroperoxide (CHP) and t-butyl hydroperoxide (TBHP) but not to H(2)O(2). This work brings the total of oxyR-controlled genes in B. fragilis to five and suggests the existence of a second peroxide response regulator that controls ccp expression.

LuxS contributes to virulence in avian pathogenic Escherichia coli O78:K80:H9.

Avian pathogenic Escherichia coli (APEC) cause avian colibacillosis, a poultry disease characterized by multiple organ infections resulting in significant economic loss in the poultry industry. Several virulence factors are important for disease manifestation in APEC of which, role of quorum sensing has not been investigated. Quorum sensing is a population dependent cell-cell signaling system which modulates numerous physiological processes such as biofilm formation and virulence in multiple species. LuxS, a well-known controller in the QS, plays a role in regulating virulence in various bacterial species. Here we investigated the role of LuxS in regulating virulence in APEC O78:K80:H9. Mutation of luxS resulted in a significant reduction of virulence in APEC O78:K80:H9, evidenced by both in vivo and in vitro assays such as decreased invasion of internal organs in chicken embryo, reduced lethality in chicken embryo lethality assay, and altered lipopolysaccharide (LPS) profile. In addition, the abilities of the knockout strain to survive in chicken macrophage cell lines and to invade in chicken embryo fibroblast cells were significantly diminished. Further, structure and expression level of the LPS profile was significantly altered in the knockout strain, which may be one of the contributing factors for the persistence and virulence of APEC. Complementation of luxS gene in trans restored the virulence of the knockout strain to the level of wild-type bacteria. Taken together, these results show that LuxS contributes to the virulence in APEC O78:K80:H9 strain and partly explain the role played by LuxS in the pathogenesis of APEC strains.

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.

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.

The BarA-UvrY two-component system regulates virulence in avian pathogenic Escherichia coli O78:K80:H9.

The BarA-UvrY two-component system (TCS) in Escherichia coli is known to regulate a number of phenotypic traits. Both in vitro and in vivo assays, including the chicken embryo lethality assay, showed that this TCS regulates virulence in avian pathogenic E. coli (APEC) serotype O78:K80:H9. A number of virulence determinants, such as the abilities to adhere, invade, persist within tissues, survive within macrophages, and resist bactericidal effects of serum complement, were compromised in mutants lacking either the barA or uvrY gene. The reduced virulence was attributed to down regulation of type 1 and Pap fimbriae, reduced exopolysaccharide production, and increased susceptibility to oxidative stress. Our results indicate that BarA-UvrY regulates virulence properties in APEC and that the chicken embryo lethality assay can be used as a surrogate model to determine virulence determinants and their regulation in APEC strains.

The complex oxidative stress response of Bacteroides fragilis: the role of OxyR in control of gene expression.

Gram-negative anaerobes in the genus Bacteroides are the predominant members of the GI-tract microflora where they play an important role in normal intestinal physiology. Bacteroides spp. also are significant opportunistic pathogens responsible for an array of intra-abdominal and other infections. Bacteroides fragilis is the most common anaerobic pathogen and it possesses virulence factors such as a capsule and neuraminidase that contribute to its success as a pathogen. Infection occurs when organisms escape from the anaerobic colon to aerobic sites such as the peritoneum where O(2) concentrations average 6%. Thus in addition to the classic virulence factors, resistance to oxidative stress is essential and may be involved in the initiation and persistence of infection. In fact, B. fragilis is highly O(2) tolerant, surviving extended periods (>24h) of O(2) exposure without a significant affect on viability. For protection against this oxidative stress B. fragilis mounts a complex physiological response that includes induction of >28 proteins involved in detoxification of oxygen radicals, protection of macromolecules, and adaptive physiology. One experimental strategy used to characterize this oxidative stress response is the direct detection of genes and proteins induced during exposure to O(2) or H(2)O(2). The methods employed have included RNA differential display to capture unique mRNA transcripts produced during oxidative stress, and native or 2D-gel electrophoresis to isolate and identify newly formed stress-induced proteins. Using these and other approaches a wide array of genes induced by oxidative stress have been discovered. These include genes for catalase, superoxide dismutase, thioredoxin-peroxidase, p20-peroxidase, cytochrome c peroxidase, Dps, alkyl hydroperoxidase, aerobic ribonucleotide reductase, ruberythrin, starch utilization, aspartate decarboxylase, and an RNA binding protein. The genes encoding these activities fall into three regulatory classes: (1) induced by O(2) only, (2) induced by H(2)O(2) only, and (3) induced by either O(2) or H(2)O(2). Such a complex regulatory response will likely involve multiple regulators. Thus far one regulator has been identified, OxyR, which controls a subset of the class 3 genes that are induced by either O(2) or H(2)O(2). OxyR responds rapidly to oxidative stress and transcriptional analyses have shown that OxyR-controlled genes are activated by as little as 0.5% O(2) or 10 microM H(2)O(2). Maximal expression of most OxyR regulon genes was reached at 50 microM H(2)O(2) and 2% O(2). These oxidant concentrations are similar to environmental levels that would be experienced by the organisms in tissues outside of the colon suggesting that the OxyR regulon would be induced during the course of an infection.