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Deg-U-P Represses Expression of the Motility fla-che Operon in Bacillus subtilis.
No full textBacillus subtilis implements several adaptive strategies to cope with nutrient limitation experienced at the end of exponential growth. The DegS-DegU two-component system is part of the network involved in the regulation of postexponential responses, such as competence development, the production of exoenzymes, and motility. The degU32(Hy) mutation extends the half-life of the phosphorylated form of DegU (DegU-P); this in turn increases the production of alkaline protease, levan-sucrase, and other exoenzymes and inhibits motility and the production of flagella. The expression of the flagellum-specific sigma factor SigD, of the flagellin gene hag, and of the fla-che operon is strongly reduced in a degU32(Hy) genetic background. To investigate the mechanism of action of DegU-P on motility, we isolated mutants of degU32(Hy) that completely suppressed the motility deficiency. The mutations were genetically mapped and characterized by PCR and sequencing. Most of the mutations were found to delete a transcriptional termination signal upstream of the main flagellar operon, fla-che, thus allowing transcriptional readthrough from the cod operon. Two additional mutations improved the {sigma}A-dependent promoter sequence of the fla-che operon. Using an electrophoretic mobility shift assay, we have demonstrated that purified DegU binds specifically to the PA promoter region of the fla-che operon. The data suggest that DegU represses transcription of the fla-che operon, and they indicate a central role of the operon in regulating the synthesis and assembly of flagella
An Auto-Regulatory Loop Governing Motility in Bacillus subtilis
No full textWe will show that transcription of swrAA, the gene required for swarming migration in B. subtilis, is driven by two promoters: a sigD-dependent promoter, active during liquid growth, and a putative sigA-regulated promoter, active in the presence of the phosphorylated form of the response regulator DegU, and in swarming. Since sigD transcription is enhanced by SwrAA (Kearns and Losick, 2005), the finding that swrAA is, in turn, sigD-dependent, delineates the existence of a positive feed-back loop, one possible mechanism to set up bistability.
We will also demonstrate that the positive action played by SwrAA is prevented in strains carrying a deletion of the two component system degS-degU, and this effect is independent from swrAA transcription. As seen by other authors (Verhamme et al., 2007; Kobayashi, 2007), degU is necessary for swarming; however, we will show that also the positive effect of SwrAA on swimming motility is lost in delta-degU strains.
The epistatic effect of degU on swrAA points to a cooperation of the two gene products in the pathway leading to Bacillus motility. This effect might not be unique, as also the activation of the pgs operon, driving the synthesis of gamma-poly-glutamic acid, depends on the concerted action of DegU-P and SwrAA
Transcriptional regulation of swrAA, a gene involved in motility and in the synthesis of gamma-poly-glutamic acid in Bacillus subtilis
No full textWe demonstrate that transcription of the gene swrAA, required for swarming migration in B. subtilis, is driven by two promoters:
a sigD-dependent promoter, active during growth in liquid LB medium, and a putative sigA-dependent promoter,
active in the presence of the phosphorylated form of the response regulator DegU and in swarming conditions. The
existence of a positive feed-back loop, with SwrAA enhancing sigD expression and being in turn SigD-dependent, is confirmed
by the level of the swrA operon transcription in swrAA+ and swrAA- strains. Furthermore, our data indicate that
DegU is necessary for swimming as well as for swarming and this requirement is independent from swrAA transcription,
since SwrAA over-expression does not restore motility in strains carrying a deletion of the two component system degSdegU.
Besides motility, we show that SwrAA and DegU, the latter in the constitutively active form degU32(Hy), are both
necessary for the activation of the pgs operon, driving the synthesis of gamma-poly-glutamic acid (PGA)
The swrAA gene, regulating swarming behaviour in Bacillus subtilis, is sigD-dependent but displays additional regulative features
No full textIn Bacillus subtilis, a wild-type copy of swrAA gene is necessary for swarming and stimulates swimming motility. The biological function of its product is presently unknown. SwrAA shows no homology to any entry in Protein databases, and no particular feature can be found by in silico analysis. We therefore concentrated our efforts on the expression profile of this gene, in order to gain some insight on the role it plays in the activation of the swarming behavior.
Accurate inspection of swrAA upstream sequence, suggested the presence of sequences (TTGCCT-N17-TACAAT and TAAA-N12-CCCGATAT) for the binding of Sigma A and Sigma D respectively, the latter being almost identical to the consensus. In in vitro transcription assay, we confirmed the promoter dependence on the presence of SigD but no transcription could be detected with E(sigA). In vivo, site-directed mutagenesis of the SigD consensus sequence completely abolishes transcription of a PswrAA-lacZ transcriptional fusion.
swrAA expression is extremely low in conditions where other sigD-dependent genes are normally well expressed but displays additional regulative features which do not affect other sigD-dependent promoters.
We explored the expression profile of PswrAA in the presence of mutations which are known to impair motility. In swimming assays, the positive role of SwrAA is lost in the absence of the DegS/DegU two component system.
Taken together our results (see also the work presented by Amati et al.) point to a central role of SwrAA in the decision process B. subtilis cells face at the end of the exponential growth, possibly finely tuning the responses regulated by DegS/DegU
SwrAA activates poly-gamma-glutamate synthesis inaddition to swarming in Bacillus subtilis
No full textPoly-gamma-glutamic acid (γ-PGA) is an extracellular polymer produced by various strains of Bacillus. Ιt was first described as the component of the capsule in B. anthracis, where it plays a relevant role in virulence. γ-PGA is also a distinctive component of “natto”, a Japanese traditional food consisting of soybean fermented by B. subtilis (natto). Domesticated B. subtilis strains do not synthesize γ-PGA although they possess the functional biosynthetic pgs operon. In the present work we explore the correlation between the genetic determinants, swrAA and degU, which allow a derivative of the domestic strain JH642 to display a mucoid colony morphology on LB agar plates due to the production of γ-PGA. Full activation of the pgs operon requires the co-presence of SwrAA and the phosphorylated form of DegU (DegU~P). The presence of either DegU~P or SwrAA alone has only marginal effects on pgs operon transcription and γ-PGA production.
Although SwrAA was identified as necessary for swarming and full swimming motility together with DegU, we show that motility is not involved in γ-PGA production. Activation of γ-PGA synthesis is therefore a motility-independent phenotype in which SwrAA and DegU~P display a cooperative effect
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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